eaogorg.files.wordpress.com · Web viewGEOCHEMISTRY ARTICLES – March 2018. Analytical Chemistry. Atapattu, S.N., Rosenfeld, J.M., 2019. Micro scale analytical derivatizations on

GEOCHEMISTRY ARTICLES – March 2018

Analytical Chemistry

Atapattu, S.N., Rosenfeld, J.M., 2019. Micro scale analytical derivatizations on solid phase. TrAC Trends in Analytical Chemistry 113, 351-356.

Drouin, N., Kubáň, P., Rudaz, S., Pedersen-Bjergaard, S., Schappler, J., 2019. Electromembrane extraction: Overview of the last decade. TrAC Trends in Analytical Chemistry 113, 357-363.

Dutta, S.B., Shrivastava, R., Krishna, H., Khan, K.M., Gupta, S., Majumder, S.K., 2019. Nanotrap-enhanced Raman spectroscopy: An efficient technique for trace detection of bioanalytes. Analytical Chemistry 91, 3555–3560.

Gascon, G., Negrin, J., Garcia-Montoto, V., Acevedo, S., Lienemann, C.-P., Bouyssiere, B., 2019. Simplification of heavy matrices by liquid–liquid extraction: Part I—How to separate LMW, MMW, and HMW compounds in maltene fractions of V, Ni, and S compounds. Energy & Fuels 33, 1922-1927.

Hu, S., Chen, X., Wang, R.-q., Yang, L., Bai, X.-h., 2019. Natural product applications of liquid-phase microextraction. TrAC Trends in Analytical Chemistry 113, 340-350.

Long, J., Wang, K., Yang, M., Zhong, W., 2019. Rapid crude oil analysis using near-infrared reflectance spectroscopy. Petroleum Science and Technology 37, 354-360.

Lorenzo-Parodi, N., Kaziur, W., Stojanović, N., Jochmann, M.A., Schmidt, T.C., 2019. Solventless microextraction techniques for water analysis. TrAC Trends in Analytical Chemistry 113, 321-331.

Psillakis, E., 2019. Vortex-assisted liquid-liquid microextraction revisited. TrAC Trends in Analytical Chemistry 113, 332-339.

Walder, B.J., Berk, C., Liao, W.-C., Rossini, A.J., Schwarzwälder, M., Pradere, U., Hall, J., Lesage, A., Copéret, C., Emsley, L., 2019. One- and two-dimensional high-resolution NMR from flat surfaces. ACS Central Science 5, 515=523.

GAS CHROMATOGRAPHY/GC×GC/GC-MS

Alexandrino, G.L., Malmborg, J., Augusto, F., Christensen, J.H., 2019. Investigating weathering in light diesel oils using comprehensive two-dimensional gas chromatography–High resolution mass spectrometry and pixel-based analysis: Possibilities and limitations. Journal of Chromatography A 1591, 155-161.

Andersen, S.L., Briggs, F.B.S., Winnike, J.H., Natanzon, Y., Maichle, S., Knagge, K.J., Newby, L.K., Gregory, S.G., 2019. Metabolome-based signature of disease pathology in MS. Multiple Sclerosis and Related Disorders 31, 12-21.

Bahaghighat, H.D., Freye, C.E., Synovec, R.E., 2019. Recent advances in modulator technology for comprehensive two dimensional gas chromatography. TrAC Trends in Analytical Chemistry 113, 379-391.

Biedermann, M., Grob, K., 2019. Advantages of comprehensive two-dimensional gas chromatography for comprehensive analysis of potential migrants from food contact materials. Analytica Chimica Acta 1057, 11-17.

Chibwe, L., Manzano, C.A., Muir, D., Atkinson, B., Kirk, J.L., Marvin, C.H., Wang, X., Teixeira, C., Shang, D., Harner, T., De Silva, A.O., 2019. Deposition and source identification of nitrogen heterocyclic polycyclic aromatic compounds in snow, sediment, and air samples from the Athabasca oil sands region. Environmental Science & Technology 53, 2981-2989.

Cho, E., Park, M., Hur, M., Kang, G., Kim, Y.H., Kim, S., 2019. Molecular-level investigation of soils contaminated by oil spilled during the Gulf War. Journal of Hazardous Materials 373, 271-277.

Cordero, C., Kiefl, J., Reichenbach, S.E., Bicchi, C., 2019. Characterization of odorant patterns by comprehensive two-dimensional gas chromatography: A challenge in omic studies. TrAC Trends in Analytical Chemistry 113, 364-378.

García-Cicourel, A.R., Janssen, H.-G., 2019. Direct analysis of aromatic hydrocarbons in purified mineral oils for foods and cosmetics applications using gas chromatography with vacuum ultraviolet detection. Journal of Chromatography A 1590, 113-120.

Guo, Q., Yu, J., Zhao, Y., Liu, T., Su, M., Jia, Z., Zhao, Y., Mu, Z., Yang, M., 2019. Identification of fishy odor causing compounds produced by Ochromonas sp. and Cryptomonas ovate with gas chromatography-olfactometry and comprehensive two-dimensional gas chromatography. Science of The Total Environment 671, 149-156.

Hernandez-Baez, D.M., Reid, A., Chapoy, A., Tohidi, B., 2019. Determination of distribution factors for heavy n-alkanes (nC12-nC98) in high temperature gas chromatography. Journal of Chromatography A 1591, 138-146.

Hernandez-Baez, D.M., Reid, A., Chapoy, A., Tohidi, B., Bounaceur, R., 2019. Establishing the maximum carbon number for reliable quantitative gas chromatographic analysis of heavy ends hydrocarbons. Part 3. Coupled pyrolysis-GC modeling. Energy & Fuels 33, 2045-2056.

Jeleń, H.H., Majcher, M., Szwengiel, A., 2019. Key odorants in peated malt whisky and its differentiation from other whisky types using profiling of flavor and volatile compounds. LWT Food Science and Technology 107, 56-63.

Jiang, M., 2019. Facile approach for calculation of second dimensional retention indices in comprehensive two dimensional gas chromatography with single injection. Analytical Chemistry 91, 4085-4091.

Kang, S., Yan, H., Zhu, Y., Liu, X., Lv, H.-P., Zhang, Y., Dai, W.-D., Guo, L., Tan, J.-F., Peng, Q.-H., Lin, Z., 2019. Identification and quantification of key odorants in the World’s four most famous black teas. Food Research International 121, 73-83.

Potgieter, H., de Coning, P., Bekker, R., Rohwer, E., Amirav, A., 2019. The pre-separation of oxygen containing compounds in oxidised heavy paraffinic fractions and their identification by GC-MS with supersonic molecular beams. Journal of Mass Spectrometry 54, 328-341.

Rathsack, P., Wollmerstaedt, H., Kuchling, T., Kureti, S., 2019. Analysis of hydrogenation products of biocrude obtained from hydrothermally liquefied algal biomass by comprehensive gas chromatography mass spectrometry (GC×GC-MS). Fuel 248, 178-188.

Shashkov, M.V., Sidelnikov, V.N., 2019. Orthogonality and quality of GC × GC separations for complex samples with ionic liquid stationary phases in first dimension. Chromatographia 82, 615-624.

Tranchida, P.Q., Aloisi, I., Giocastro, B., Zoccali, M., Mondello, L., 2019. Comprehensive two-dimensional gas chromatography-mass spectrometry using milder electron ionization conditions: A preliminary evaluation. Journal of Chromatography A 1589, 134-140.

Vendruscolo, R.G., Fagundes, M.B., Jacob-Lopes, E., Wagner, R., 2019. Analytical strategies for using gas chromatography to control and optimize microalgae bioprocessing. Current Opinion in Food Science 21, 73-81.

Vozka, P., Kilaz, G., 2019. How to obtain a detailed chemical composition for middle distillates via GC × GC-FID without the need of GC × GC-TOF/MS. Fuel 247, 368-377.

Wang, G., Naeher, S., Li, J., Shi, S., Chang, R., 2019. 1H-pyrrole-2,5-diones (maleimides): the novel biomarkers in petroleum geochemistry Acta Petrolei Sinica 40, 176-181.

Wu, Y., Liu, Y., Wang, Y., Xia, Y., Wang, Y., 2019. Advances on separation diastereomers of acyclic isoprenoid alkanes by gas chromatography and its geochemical significance. Petroleum Science and Technology 37, 268-274.

Xia, D., Gao, L., Zheng, M., Sun, Y., Qiao, L., Huang, H., Zhang, H., Fu, J., Wu, Y., Li, J., Zhang, L., 2019. Identification and evaluation of chlorinated nonane paraffins in the environment: A persistent organic pollutant candidate for the Stockholm Convention? Journal of Hazardous Materials 371, 449-455.

Zajickova, Z., Špánik, I., 2019. Applications of monolithic columns in gas chromatography and supercritical fluid chromatography. Journal of Separation Science 42, 999-1011.

Zushi, Y., Yamatori, Y., Nagata, J., Nabi, D., 2019. Comprehensive two-dimensional gas-chromatography-based property estimation to assess the fate and behavior of complex mixtures: A case study of vehicle engine oil. Science of The Total Environment 669, 739-745.

IMAGING: AFM

Lee, J.K., Lee, G.-D., Lee, S., Yoon, E., Anderson, H.L., Briggs, G.A.D., Warner, J.H., 2019. Atomic scale imaging of reversible ring cyclization in graphene nanoconstrictions. ACS Nano 13, 2379-2388.

IMAGING: SEM, TEM, HIM

Akinmosin, A., Bankole, S.I., Eyogwe, S.O., 2019. Reservoir geology and effects on exploitation of natural bitumen deposits (Nigerian deposits as a case study). Journal of Petroleum Exploration and Production Technology 9, 191-205.

Bai, Y.-N., Wang, X.-N., Lu, Y.-Z., Fu, L., Zhang, F., Lau, T.-C., Zeng, R.J., 2019. Microbial selenite reduction coupled to anaerobic oxidation of methane. Science of The Total Environment 669, 168-174.

Cavelan, A., Boussafir, M., Rozenbaum, O., Laggoun-Défarge, F., 2019. Organic petrography and pore structure characterization of low-mature and gas-mature marine organic-rich mudstones: Insights into porosity controls in gas shale systems. Marine and Petroleum Geology 103, 331-350.

Hui, D., Pan, Y., Luo, P., Zhang, Y., Sun, L., Lin, C., 2019. Effect of supercritical CO2 exposure on the high-pressure CO2 adsorption performance of shales. Fuel 247, 57-66.

Kumar, S., Mendhe, V.A., Kamble, A.D., Varma, A.K., Mishra, D.K., Bannerjee, M., Buragohain, J., Prasad, A.K., 2019. Geochemical attributes, pore structures and fractal characteristics of Barakar shale deposits of Mand-Raigarh Basin, India. Marine and Petroleum Geology 103, 377-396.

Langenhorst, F., Campione, M., 2019. Ideal and real structures of different forms of carbon, with some remarks on their geological significance. Journal of the Geological Society 176, 337-347.

Liang, C., Xiao, L., Zhou, C., Wang, H., Hu, F., Liao, G., Jia, Z., Liu, H., 2019. Wettability characterization of low-permeability reservoirs using nuclear magnetic resonance: An experimental study. Journal of Petroleum Science and Engineering 178, 121-132.

Liu, A.G., McMahon, S., Matthews, J.J., Brasier, A.T., Still, J.W., 2019. Petrological evidence supports the death mask model for the preservation of Ediacaran soft-bodied organisms in South Australia. Geology 47, 215-218.

Liu, X.-x., Hu, X., Cao, Y., Pang, W.-j., Huang, J.-y., Guo, P., Huang, L., 2019. Biodegradation of phenanthrene and heavy metal removal by acid-tolerant Burkholderia fungorum FM-2. Frontiers in Microbiology 10, 408. doi: 410.3389/fmicb.2019.00408.

Luo, M., Chen, Z.-Q., Shi, G.R., Feng, X., Yang, H., Fang, Y., Li, Y., 2019. Microbially induced sedimentary structures (MISSs) from the Lower Triassic Kockatea Formation, northern Perth Basin, Western Australia: Palaeoenvironmental implications. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 236-247.

Misch, D., Gross, D., Hawranek, G., Horsfield, B., Klaver, J., Mendez-Martin, F., Urai, J.L., Vranjes-Wessely, S., Sachsenhofer, R.F., Schmatz, J., Li, J., Zou, C., 2019. Solid bitumen in shales: Petrographic characteristics and implications for reservoir characterization. International Journal of Coal Geology 205, 14-31.

Mohammadi, M., Safari, M., Ghasemi, M., Daryasafar, A., Sedighi, M., 2019. Asphaltene adsorption using green nanocomposites: Experimental study and adaptive neuro-fuzzy interference system modeling. Journal of Petroleum Science and Engineering 177, 1103-1113.

Peng, N., He, S., Hu, Q., Zhang, B., He, X., Zhai, G., He, C., Yang, R., 2019. Organic nanopore structure and fractal characteristics of Wufeng and lower member of Longmaxi shales in southeastern Sichuan, China. Marine and Petroleum Geology 103, 456-472.

Saricicek, Y.E., Gurbanov, R., Pekcan, O., Gozen, A.G., 2019. Comparison of microbially induced calcium carbonate precipitation eligibility using Sporosarcina pasteurii and Bacillus licheniformis on two different sands. Geomicrobiology Journal 36, 42-52.

Xin, F., Xu, H., Tang, D., Yang, J., Chen, Y., Cao, L., Qu, H., 2019. Pore structure evolution of low-rank coal in China. International Journal of Coal Geology 205, 126-139.

Yamazaki, T., Suzuki, Y., Kouduka, M., Kawamura, N., 2019. Dependence of bacterial magnetosome morphology on chemical conditions in deep-sea sediments. Earth and Planetary Science Letters 513, 135-143.

Zhang, J., Li, X., Xiaoyan, Z., Zhao, G., Zhou, B., Li, J., Xie, Z., Wang, F., 2019. Characterization of the full-sized pore structure of coal-bearing shales and its effect on shale gas content. Energy & Fuels 33, 1969-1982.

IMAGING: XRAY CT

Akai, T., Alhammadi, A.M., Blunt, M.J., Bijeljic, B., 2019. Modeling oil recovery in mixed-wet rocks: Pore-scale comparison between experiment and simulation. Transport in Porous Media 127, 393-414.

Bergen, K.J., Johnson, P.A., de Hoop, M.V., Beroza, G.C., 2019. Machine learning for data-driven discovery in solid Earth geoscience. Science 363, Article eaau0323.

Dong, H., Sun, J., Zhu, J., Liu, L., Lin, Z., Golsanami, N., Cui, L., Yan, W., 2019. Developing a new hydrate saturation calculation model for hydrate-bearing sediments. Fuel 248, 27-37.

El Albani, A., Mangano, M.G., Buatois, L.A., Bengtson, S., Riboulleau, A., Bekker, A., Konhauser, K., Lyons, T., Rollion-Bard, C., Bankole, O., Lekele Baghekema, S.G., Meunier, A., Trentesaux, A., Mazurier, A., Aubineau, J., Laforest, C., Fontaine, C., Recourt, P., Chi Fru, E., Macchiarelli, R., Reynaud, J.Y., Gauthier-Lafaye, F., Canfield, D.E., 2019. Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago. Proceedings of the National Academy of Sciences 116, 3431-3436.

Gil, S.-M., Shin, H.-J., Lim, J.-S., Lee, J., 2019. Numerical analysis of dissociation behavior at critical gas hydrate saturation using depressurization method. Journal of Geophysical Research: Solid Earth 124, 1222-1235.

Imai, M., Mikami, K., Suganuma, T., Tsuchiya, Y., Nakagawa, K., Takahashi, S., 2019. Determination of binary diffusion coefficients between hot liquid solvents and bitumen with X-ray CT. Journal of Petroleum Science and Engineering 177, 496-507.

Rezaei, F., Izadi, H., Memarian, H., Baniassadi, M., 2019. The effectiveness of different thresholding techniques in segmenting micro CT images of porous carbonates to estimate porosity. Journal of Petroleum Science and Engineering 177, 518-527.

Schlüter, S., Zawallich, J., Vogel, H.J., Dörsch, P., 2019. Physical constraints for respiration in microbial hotspots in soil and their importance for denitrification. Biogeosciences Discussions 2019, 1-31.

Tsuji, T., Ikeda, T., Jiang, F., 2019. Evolution of hydraulic and elastic properties of reservoir rocks due to mineral precipitation in CO2 geological storage. Computers & Geosciences 126, 84-95.

Wang, Y., Zhang, D., Hu, Y.Z., 2019. X-ray computed tomography characterization of soil and rock mixture under cyclic triaxial testing: the effects of confining pressure on meso-structural changes. Environmental Earth Sciences 78, 185.

LIQUID CHROMATOGRAPHY/LC-MS/SFC

Brezinski, K., Gorczyca, B., 2019. Multi-spectral characterization of natural organic matter (NOM) from Manitoba surface waters using high performance size exclusion chromatography (HPSEC). Chemosphere 225, 53-64.

Lübeck, J.S., Malmquist, L.M.V., Christensen, J.H., 2019. Supercritical fluid chromatography for the analysis of oxygenated polycyclic aromatic compounds in unconventional oils. Journal of Chromatography A 1589, 162-172.

Martín-Ortiz, A., Ruiz-Matute, A.I., Sanz, M.L., Moreno, F.J., Herrero, M., 2019. Separation of di- and trisaccharide mixtures by comprehensive two-dimensional liquid chromatography. Application to prebiotic oligosaccharides. Analytica Chimica Acta 1060, 125-132.

Moldovan, R.-C., Bodoki, E., Servais, A.-C., Crommen, J., Oprean, R., Fillet, M., 2019. Selectivity evaluation of phenyl based stationary phases for the analysis of amino acid diastereomers by liquid chromatography coupled with mass spectrometry. Journal of Chromatography A 1590, 80-87.

Termopoli, V., Famiglini, G., Palma, P., Piergiovanni, M., Rocio-Bautista, P., Ottaviani, M.F., Cappiello, A., Saeed, M., Perry, S., 2019. Evaluation of a liquid electron ionization liquid chromatography–mass spectrometry interface. Journal of Chromatography A 1591, 120-130.

Wang, C., Huang, Z., Xing, Z., Chen, Y., Yu, J., Liu, F., Yuan, M., 2019. Direct determination of ultra-trace polycyclic aromatic hydrocarbons in water by liquid chromatography coupled with online solid phase extraction. Chinese Journal of Chromatography 37, 239-245.

Wang, Z., Fu, R., Ji, J., Chen, B., 2019. Simultaneous determination of chlorogenic acid and cynaroside contents in Lonicerae Japonica Flos by high resolution sampling two-dimensional liquid chromatography. Chinese Journal of Chromatography 37, 201-206.

Wang, Z., Xie, T.-T., Yan, X., Xue, S., Chen, J.-W., Wu, Z., Qiu, Y.-K., 2019. Gradual gradient two-dimensional preparative liquid chromatography system for preparative separation of complex natural products. Chromatographia 82, 543-552.


MASS SPECTROSCOPY/ICR-FTMS/ORBITRAP

Bauer, A.E., Frank, R.A., Headley, J.V., Milestone, C.B., Batchelor, S., Peru, K.M., Rudy, M.D., Barrett, S.E., Vanderveen, R., Dixon, D.G., Hewitt, L.M., 2019. A preparative method for the isolation and fractionation of dissolved organic acids from bitumen-influenced waters. Science of The Total Environment 671, 587-597.

Bauer, A.E., Hewitt, L.M., Parrott, J.L., Bartlett, A.J., Gillis, P.L., Deeth, L.E., Rudy, M.D., Vanderveen, R., Brown, L., Campbell, S.D., Rodrigues, M.R., Farwell, A.J., Dixon, D.G., Frank, R.A., 2019. The toxicity of organic fractions from aged oil sands process-affected water to aquatic species. Science of The Total Environment 669, 702-710.

Chen, L., Huang, J., Liu, S., Huang, B., 2019. Molecular composition of in-situ combustion and steam assisted gravity drainage crude oils. Petroleum Science and Technology 37, 589-594.



Dong, X., Zhang, Y., Milton, J., Yerabolu, R., Easterling, L., Kenttämaa, H.I., 2019. Investigation of the relative abundances of single-core and multicore compounds in asphaltenes by using high-resolution in-source collision-activated dissociation and medium-energy collision-activated dissociation mass spectrometry with statistical considerations. Fuel 246, 126-132.

Farré, M.J., Jaén-Gil, A., Hawkes, J., Petrovic, M., Catalán, N., 2019. Orbitrap molecular fingerprint of dissolved organic matter in natural waters and its relationship with NDMA formation potential. Science of The Total Environment 670, 1019-1027.

Gonsior, M., Powers, L.C., Williams, E., Place, A., Chen, F., Ruf, A., Hertkorn, N., Schmitt-Kopplin, P., 2019. The chemodiversity of algal dissolved organic matter from lysed Microcystis aeruginosa cells and its ability to form disinfection by-products during chlorination. Water Research 155, 300-309.

Huang, X.-M., Wu, Y., Cui, J.-T., Wang, F.-H., Wang, X., Li, Y.-F., Wu, W.-Y., 2019. Applications of high-resolution mass spectrometry in determination of chlorinated paraffins. Chinese Journal of Analytical Chemistry 47, 323-334.

Huang, Z., Lv, J., Cao, D., Zhang, S., 2019. Iron plays an important role in molecular fractionation of dissolved organic matter at soil-water interface. Science of The Total Environment 670, 300-307.

Léon, A., Cariou, R., Hutinet, S., Hurel, J., Guitton, Y., Tixier, C., Munschy, C., Antignac, J.-P., Dervilly-Pinel, G., Le Bizec, B., 2019. HaloSeeker 1.0: A user-friendly software to highlight halogenated chemicals in nontargeted high-resolution mass spectrometry data sets. Analytical Chemistry 91, 3500–3507.

Li, P., Tao, J., Lin, J., He, C., Shi, Q., Li, X., Zhang, C., 2019. Stratification of dissolved organic matter in the upper 2000 m water column at the Mariana Trench. Science of The Total Environment 668, 1222-1231.

Roveretto, M., Li, M., Hayeck, N., Brüggemann, M., Emmelin, C., Perrier, S., George, C., 2019. Real-time detection of gas-phase organohalogens from aqueous photochemistry using Orbitrap mass spectrometry. ACS Earth and Space Chemistry 3, 329-334.

Spivey, E.C., McMillen, J.C., Ryan, D.J., Spraggins, J.M., Caprioli, R.M., 2019. Combining MALDI-2 and transmission geometry laser optics to achieve high sensitivity for ultra-high spatial resolution surface analysis. Journal of Mass Spectrometry 54, 366-370.

Wu, C., Yang, J., Fu, Q., Zhu, B., Ruan, T., Jiang, G., 2019. Molecular characterization of water-soluble organic compounds in PM2.5 using ultrahigh resolution mass spectrometry. Science of The Total Environment 668, 917-924.

Zacs, D., Perkons, I., Bartkevics, V., 2019. Evaluation of analytical performance of gas chromatography coupled with atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry (GC-APCI-FT-ICR-MS) in the target and non-targeted analysis of brominated and chlorinated flame retardants in food. Chemosphere 225, 368-377.

MASS SPECTROSCOPY/OTHER

Li, H., Chen, X., Wu, J., Zhang, Y., Liu, X., Shi, Q., Zhao, S., Xu, C., Hsu, C.S., 2019. Selective methylation of sulfides in petroleum for electrospray ionization mass spectrometry analysis. Energy & Fuels 33, 1797-1802.

METABOLOMICS/LIPIDOMICS


Bale, N.J., Sorokin, D.Y., Hopmans, E.C., Koenen, M., Rijpstra, W.I.C., Villanueva, L., Wienk, H., Sinninghe Damsté, J.S., 2019. New insights into the polar lipid composition of extremely halo(alkali)philic Euryarchaea from hypersaline lakes. Frontiers in Microbiology 10, 377. doi: 310.3389/fmicb.2019.00377.

Caesar, L.K., Kellogg, J.J., Kvalheim, O.M., Cech, N.B., 2019. Opportunities and limitations for untargeted mass spectrometry metabolomics to identify biologically active constituents in complex natural product mixtures. Journal of Natural Products 82, 469-484.

Deng, K., Zhang, F., Tan, Q., Huang, Y., Song, W., Rong, Z., Zhu, Z.-J., Li, Z., Li, K., 2019. WaveICA: a novel algorithm to remove batch effects for large-scale untargeted metabolomics data based on wavelet analysis. Analytica Chimica Acta 1061, 60-69.

Domingo-Almenara, X., Montenegro-Burke, J.R., Guijas, C., Majumder, E.L.W., Benton, H.P., Siuzdak, G., 2019. Autonomous METLIN-guided in-source fragment annotation for untargeted metabolomics. Analytical Chemistry 91, 3246–3253.

Fan, S., Kind, T., Cajka, T., Hazen, S.L., Tang, W.H.W., Kaddurah-Daouk, R., Irvin, M.R., Arnett, D.K., Barupal, D.K., Fiehn, O., 2019. Systematic error removal using random forest for normalizing large-scale untargeted lipidomics data. Analytical Chemistry 91, 3590–3596.

Hill, R.A., Hunt, J., Sanders, E., Tran, M., Burk, G.A., Mlsna, T.E., Fitzkee, N.C., 2019. Effect of biochar on microbial growth: A metabolomics and bacteriological investigation in E. coli. Environmental Science & Technology 53, 2635–2646.

Hoffmann, N., Rein, J., Sachsenberg, T., Hartler, J., Haug, K., Mayer, G., Alka, O., Dayalan, S., Pearce, J.T.M., Rocca-Serra, P., Qi, D., Eisenacher, M., Perez-Riverol, Y., Vizcaíno, J.A., Salek, R.M., Neumann, S., Jones, A.R., 2019. mzTab-M: A data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry 91, 3302–3310.

Jan, S., Ahmad, P., 2019. Ecometabolomics. Metabolic Fluxes versus Environmental Stoichiometry. Academic Press, 401 pp.

Korte, A.R., Morris, N.J., Vertes, A., 2019. High throughput complementary analysis and quantitation of metabolites by MALDI- and silicon nanopost array-laser desorption/ionization-mass spectrometry. Analytical Chemistry 91, 3951-3958.

Liu, C., Gu, C., Huang, W., Sheng, X., Du, J., Li, Y., 2019. Targeted UPLC-MS/MS high-throughput metabolomics approach to assess the purine and pyrimidine metabolism. Journal of Chromatography B 1113, 98-106.

Peris-Díaz, M.D., Rodak, O., Sweeney, S.R., Krężel, A., Sentandreu, E., 2019. Chemometrics-assisted optimization of liquid chromatography-quadrupole-time-of-flight mass spectrometry analysis for targeted metabolomics. Talanta 199, 380-387.

Smirnov, K.S., Forcisi, S., Moritz, F., Lucio, M., Schmitt-Kopplin, P., 2019. Mass difference maps and their application for the recalibration of mass spectrometric data in nontargeted metabolomics. Analytical Chemistry 91, 3350–3358.

Wang, J., Wang, C., Han, X., 2019. Tutorial on lipidomics. Analytica Chimica Acta 1061, 28-41.

Yu, X., Chen, K., Li, S., Wang, Y., Shen, Q., 2019. Lipidomics differentiation of soft-shelled turtle strains using hydrophilic interaction liquid chromatography and mass spectrometry. Journal of Chromatography B 1112, 11-15.

Zhang, Q., Xu, H., Liu, R., Gao, P., Yang, X., Jin, W., Zhang, Y., Bi, K., Li, Q., 2019. A novel strategy for targeted lipidomics based on LC-tandem-MS parameters prediction, quantification, and multiple statistical data mining: Evaluation of lysophosphatidylcholines as potential cancer biomarkers. Analytical Chemistry 91, 3389–3396.

PUPPYOMICS

Rogers, B., Gron, K.J., Montgomery, J., Rowley-Conwy, P., Nowell, G., Peterkin, J., Jacques, D., 2019. Isotopic analysis of the Blick Mead dog: A proxy for the dietary reconstruction and mobility of Mesolithic British hunter-gatherers. Journal of Archaeological Science: Reports 24, 712-720.

Yeomans, L., Martin, L., Richter, T., 2019. Close companions: Early evidence for dogs in northeast Jordan and the potential impact of new hunting methods. Journal of Anthropological Archaeology 53, 161-173.

Archaeological/Art Organic Chemistry

Bartl, B., Zapletal, M., Urbánek, Š., Slavíková, M.K., Trejbal, J., Hrdlička, Z., 2019. Why do historical beeswax seals become brittle over time? Studies in Conservation 64, 138-145.

Eshel, T., Erel, Y., Yahalom-Mack, N., Tirosh, O., Gilboa, A., 2019. Lead isotopes in silver reveal earliest Phoenician quest for metals in the west Mediterranean. Proceedings of the National Academy of Sciences 116, 6007-6012.

Fay, J.C., Liu, P., Ong, G.T., Dunham, M.J., Cromie, G.A., Jeffery, E.W., Ludlow, C.L., Dudley, A.M., 2019. A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. PLOS Biology 17, Article e3000147.

Feldman, M., Fernández-Domínguez, E., Reynolds, L., Baird, D., Pearson, J., Hershkovitz, I., May, H., Goring-Morris, N., Benz, M., Gresky, J., Bianco, R.A., Fairbairn, A., Mustafaoğlu, G., Stockhammer, P.W., Posth, C., Haak, W., Jeong, C., Krause, J., 2019. Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Nature Communications 10, Article 1218.

Geweely, N.S., Afifi, H.A., Ibrahim, D.M., Soliman, M.M., 2019. Efficacy of essential oils on fungi isolated from archaeological objects in Saqqara excavation, Egypt. Geomicrobiology Journal 36, 148-168.

James, H.F., Willmes, M., Boel, C.A., Courtaud, P., Chancerel, A., Ciesielski, E., Desideri, J., Bridy, A., Wood, R., Moffat, I., Fallon, S., McMorrow, L., Armstrong, R.A., Williams, I.S., Kinsley, L., Aubert, M., Eggins, S., Frieman, C.J., Grün, R., 2019. Who's been using my burial mound? Radiocarbon dating and isotopic tracing of human diet and mobility at the collective burial site, Le Tumulus des Sables, southwest France. Journal of Archaeological Science: Reports 24, 955-966.

Munkittrick, T.J.A., Varney, T.L., Pike, K.-A., Grimes, V., 2019. Life histories from the Southside Cemetery, St. John's, Newfoundland: Insights into Royal Naval diet using stable isotopes. Journal of Archaeological Science: Reports 24, 815-828.

Nardella, F., Landi, N., Degano, I., Colombo, M., Serradimigni, M., Tozzi, C., Ribechini, E., 2019. Chemical investigations of bitumen from Neolithic archaeological excavations in Italy by GC/MS combined with principal component analysis. Analytical Methods 11, 1449-1459.

O’Hare, P., Mekhaldi, F., Adolphi, F., Raisbeck, G., Aldahan, A., Anderberg, E., Beer, J., Christl, M., Fahrni, S., Synal, H.-A., Park, J., Possnert, G., Southon, J., Bard, E., ASTER Team, Muscheler, R., 2019. Multiradionuclide evidence for an extreme solar proton event around 2,610 B.P. (∼660 BC). Proceedings of the National Academy of Sciences 116, 5961-5966.

Olalde, I., Mallick, S., Patterson, N., Rohland, N., Villalba-Mouco, V., Silva, M., Dulias, K., Edwards, C.J., Gandini, F., Pala, M., Soares, P., Ferrando-Bernal, M., Adamski, N., Broomandkhoshbacht, N., Cheronet, O., Culleton, B.J., Fernandes, D., Lawson, A.M., Mah, M., Oppenheimer, J., Stewardson, K., Zhang, Z., Jiménez Arenas, J.M., Toro Moyano, I.J., Salazar-García, D.C., Castanyer, P., Santos, M., Tremoleda, J., Lozano, M., García Borja, P., Fernández-Eraso, J., Mujika-Alustiza, J.A., Barroso, C., Bermúdez, F.J., Viguera Mínguez, E., Burch, J., Coromina, N., Vivó, D., Cebrià, A., Fullola, J.M., García-Puchol, O., Morales, J.I., Oms, F.X., Majó, T., Vergès, J.M., Díaz-Carvajal, A., Ollich-Castanyer, I., López-Cachero, F.J., Silva, A.M., Alonso-Fernández, C., Delibes de Castro, G., Jiménez Echevarría, J., Moreno-Márquez, A., Pascual Berlanga, G., Ramos-García, P., Ramos-Muñoz, J., Vijande Vila, E., Aguilella Arzo, G., Esparza Arroyo, Á., Lillios, K.T., Mack, J., Velasco-Vázquez, J., Waterman, A., Benítez de Lugo Enrich, L., Benito Sánchez, M., Agustí, B., Codina, F., de Prado, G., Estalrrich, A., Fernández Flores, Á., Finlayson, C., Finlayson, G., Finlayson, S., Giles-Guzmán, F., Rosas, A., Barciela González, V., García Atiénzar, G., Hernández Pérez, M.S., Llanos, A., Carrión Marco, Y., Collado Beneyto, I., López-Serrano, D., Sanz Tormo, M., Valera, A.C., Blasco, C., Liesau, C., Ríos, P., Daura, J., de Pedro Michó, M.J., Diez-Castillo, A.A., Flores Fernández, R., Francès Farré, J., Garrido-Pena, R., Gonçalves, V.S., Guerra-Doce, E., Herrero-Corral, A.M., Juan-Cabanilles, J., López-Reyes, D., McClure, S.B., Merino Pérez, M., Oliver Foix, A., Sanz Borràs, M., Sousa, A.C., Vidal Encinas, J.M., Kennett, D.J., Richards, M.B., Werner Alt, K., Haak, W., Pinhasi, R., Lalueza-Fox, C., Reich, D., 2019. The genomic history of the Iberian Peninsula over the past 8000 years. Science 363, 1230-1234.

Penny, D., Hall, T., Evans, D., Polkinghorne, M., 2019. Geoarchaeological evidence from Angkor, Cambodia, reveals a gradual decline rather than a catastrophic 15th-century collapse. Proceedings of the National Academy of Sciences 116, 4871-4876.


Schablitsky, J.M., Witt, K.E., Madrigal, J.R., Ellegaard, M.R., Malhi, R.S., Schroeder, H., 2019. Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter. Journal of Archaeological Science 105, 11-18.

Wade, L., 2019. Did Black Death strike sub-Saharan Africa? Science 363, 1022.

White, A.J., Stevens, L.R., Lorenzi, V., Munoz, S.E., Schroeder, S., Cao, A., Bogdanovich, T., 2019. Fecal stanols show simultaneous flooding and seasonal precipitation change correlate with Cahokia’s population decline. Proceedings of the National Academy of Sciences 116, 5461-5466.


Zavodny, E., McClure, S.B., Welker, M.H., Culleton, B.J., Balen, J., Kennett, D.J., 2019. Scaling up: Stable isotope evidence for the intensification of animal husbandry in Bronze-Iron Age Lika, Croatia. Journal of Archaeological Science: Reports 23, 1055-1065.

Biochemistry

Buckley, A., MacGregor, B., Teske, A., 2019. Identification, expression and activity of candidate nitrite reductases from orange Beggiatoaceae, Guaymas Basin. Frontiers in Microbiology 10, 644. doi: 610.3389/fmicb.2019.00644.

Evans, P.N., Boyd, J.A., Leu, A.O., Woodcroft, B.J., Parks, D.H., Hugenholtz, P., Tyson, G.W., 2019. An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology 17, 219-232.

Garcia, G.P., Sutour, S., Rabehaja, D., Tissandié, L., Filippi, J.-J., Tomi, F., 2019. Essential oil of the malagasy grass Elionurus tristis Hack. contains several undescribed sesquiterpenoids. Phytochemistry 162, 29-38.

Guzman, M.S., Rengasamy, K., Binkley, M.M., Jones, C., Ranaivoarisoa, T.O., Singh, R., Fike, D.A., Meacham, J.M., Bose, A., 2019. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nature Communications 10, Article 1355.

Kashkooli, A.B., van der Krol, A., Rabe, P., Dickschat, J.S., Bouwmeester, H., 2019. Substrate promiscuity of enzymes from the sesquiterpene biosynthetic pathways from Artemisia annua and Tanacetum parthenium allows for novel combinatorial sesquiterpene production. Metabolic Engineering 54, 12-23.

Kreuter, L.J., Weinfurtner, A., Ziegler, A., Weigl, J., Hoffmann, J., Morgner, N., Müller, V., Huber, H., 2019. Purification of a crenarchaeal ATP synthase in the light of the unique bioenergetics of Ignicoccus species. Journal of Bacteriology 201, e00510-00518.

Largen, A.H., Gudde, L.R., Franke, J.D., Hulce, M., 2019. Sterol synthesis is essential for viability in the planctomycete bacterium Gemmata obscuriglobus. FEMS Microbiology Letters 366, Article fnz019.

Mason-Jones, K., Banfield, C.C., Dippold, M.A., 2019. Compound-specific 13C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria. Rapid Communications in Mass Spectrometry 33, 795-802.

McKay, L.J., Dlakić, M., Fields, M.W., Delmont, T.O., Eren, A.M., Jay, Z.J., Klingelsmith, K.B., Rusch, D.B., Inskeep, W.P., 2019. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology 4, 614-622.

Olszewska-Widdrat, A., Schiro, G., Reichel, V.E., Faivre, D., 2019. Reducing conditions favor magnetosome production in Magnetospirillum magneticum AMB-1. Frontiers in Microbiology 10, 582. doi: 510.3389/fmicb.2019.00582.

Park, S., Steen, C.J., Lyska, D., Fischer, A.L., Endelman, B., Iwai, M., Niyogi, K.K., Fleming, G.R., 2019. Chlorophyll–carotenoid excitation energy transfer and charge transfer in

Nannochloropsis oceanica for the regulation of photosynthesis. Proceedings of the National Academy of Sciences 116, 3385-3390.

Stoeva, M.K., Coates, J.D., 2019. Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding. Microbiology 165, 254-269.

Tang, K., Wang, Y., Wang, X., 2019. Recent progress on signalling molecules of coral-associated microorganisms. Science China Earth Sciences 62, 609-618.

Wang, X., Xia, K., Yang, X., Tang, C., 2019. Growth strategy of microbes on mixed carbon sources. Nature Communications 10, Article 1279.

Zuo, Z., 2019. Why algae release volatile organic compounds—the emission and roles. Frontiers in Microbiology 10, 491. doi: 410.3389/fmicb.2019.00491.

Biodegradation


Babaei, F., Habibi, A., 2018. Fast biodegradation of diesel hydrocarbons at high concentration by the sophorolipid-producing yeast Candida catenulata KP324968. Journal of Molecular Microbiology and Biotechnology 28, 240-254.

Chen, J., Liu, Y.-F., Zhou, L., Mbadinga, S.M., Yang, T., Zhou, J., Liu, J.-F., Yang, S.-Z., Gu, J.-D., Mu, B.-Z., 2019. Methanogenic degradation of branched alkanes in enrichment cultures of production water from a high-temperature petroleum reservoir. Applied Microbiology and Biotechnology 103, 2391-2401.

Hammershøj, R., Birch, H., Redman, A.D., Mayer, P., 2019. Mixture effects on biodegradation kinetics of hydrocarbons in surface water: Increasing concentrations inhibited degradation whereas multiple substrates did not. Environmental Science & Technology 53, 3087-3094.

Heckel, B., Phillips, E., Edwards, E., Sherwood Lollar, B., Elsner, M., Manefield, M.J., Lee, M., 2019. Reductive dehalogenation of trichloromethane by two different Dehalobacter restrictus strains reveal opposing dual element isotope effects. Environmental Science & Technology 53, 2332–2343.

Kimak, C., Ntarlagiannis, D., Slater, L.D., Atekwana, E.A., Beaver, C.L., Rossbach, S., Porter, A., Ustra, A., 2019. Geophysical monitoring of hydrocarbon biodegradation in highly conductive environments. Journal of Geophysical Research: Biogeosciences 124, 353-366.


Rontani, J.-F., Smik, L., Belt, S.T., Vaultier, F., Armbrecht, L., Leventer, A., Armand, L.K., 2019. Abiotic degradation of highly branched isoprenoid alkenes and other lipids in the water column off East Antarctica. Marine Chemistry 210, 34-47.

Vergara-Fernández, A., Morales, P., Scott, F., Guerrero, S., Yañez, L., Mau, S., Aroca, G., 2019. Methane biodegradation and enhanced methane solubilization by the filamentous fungi Fusarium solani. Chemosphere 226, 24-35.

Zhuang, L., Tang, Z., Ma, J., Yu, Z., Wang, Y., Tang, J., 2019. Enhanced anaerobic biodegradation of benzoate under sulfate-reducing conditions with conductive iron-oxides in sediment of Pearl River Estuary. Frontiers in Microbiology 10, 374. doi: 310.3389/fmicb.2019.00374.

BIODEGRADATION PATHWAYS/GENOMICS

Abdelhaleem, H.A.R., Zein, H.S., Azeiz, A., Sharaf, A.N., Abdelhadi, A.A., 2019. Identification and characterization of novel bacterial polyaromatic hydrocarbon-degrading enzymes as potential tools for cleaning up hydrocarbon pollutants from different environmental sources. Environmental Toxicology and Pharmacology 67, 108-116.

Borrel, G., Adam, P.S., McKay, L.J., Chen, L.-X., Sierra-García, I.N., Sieber, C.M.K., Letourneur, Q., Ghozlane, A., Andersen, G.L., Li, W.-J., Hallam, S.J., Muyzer, G., de Oliveira, V.M., Inskeep, W.P., Banfield, J.F., Gribaldo, S., 2019. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology 4, 603-613.

Iqbal, A., Mukherjee, M., Rashid, J., Khan, S.A., Ali, M.A., Arshad, M., 2019. Development of plant-microbe phytoremediation system for petroleum hydrocarbon degradation: An insight from alkb gene expression and phytotoxicity analysis. Science of The Total Environment 671, 696-704.

Li, J., Zhang, J., Yadav, M.P., Li, X., 2019. Biodegradability and biodegradation pathway of di-(2-ethylhexyl) phthalate by Burkholderia pyrrocinia B1213. Chemosphere 225, 443-450.

Liang, C., Huang, Y., Wang, Y., Ye, Q., Zhang, Z., Wang, H., 2019. Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics. Applied Microbiology and Biotechnology 103, 2427-2440.

Scoma, A., Heyer, R., Rifai, R., Dandyk, C., Marshall, I., Kerckhof, F.-M., Marietou, A., Boshker, H.T.S., Meysman, F.J.R., Malmos, K.G., Vosegaard, T., Vermeir, P., Banat, I.M., Benndorf, D., Boon, N., 2019. Reduced TCA cycle rates at high hydrostatic pressure hinder hydrocarbon degradation and obligate oil degraders in natural, deep-sea microbial communities. The ISME Journal 13, 1004-1018.

Suvorova, I.A., Gelfand, M.S., 2019. Comparative genomic analysis of the regulation of aromatic metabolism in Betaproteobacteria. Frontiers in Microbiology 10, 642. doi: 610.3389/fmicb.2019.00642.

Wang, Y., Wegener, G., Hou, J., Wang, F., Xiao, X., 2019. Expanding anaerobic alkane metabolism in the domain of Archaea. Nature Microbiology 4, 595-602.

Zhou, Z., Liang, B., Wang, L.Y., Liu, J.F., Mu, B.Z., Shim, H., Gu, J.D., 2019. Identify the core bacterial microbiome of hydrocarbon degradation and a shift of dominant

methanogenesis pathways in oil and aqueous phases of petroleum reservoirs with different temperatures from China. Biogeosciences Discussions 2019, 1-28.

Biofuels/Biomass/Bioengineering

Atalah, J., Cáceres-Moreno, P., Espina, G., Blamey, J.M., 2019. Thermophiles and the applications of their enzymes as new biocatalysts. Bioresource Technology 280, 478-488.

Crosby, J.R., Laemthong, T., Lewis, A.M., Straub, C.T., Adams, M.W.W., Kelly, R.M., 2019. Extreme thermophiles as emerging metabolic engineering platforms. Current Opinion in Biotechnology 59, 55-64.

Dai, G., Zhu, Y., Yang, J., Pan, Y., Wang, G., Reubroycharoen, P., Wang, S., 2019. Mechanism study on the pyrolysis of the typical ether linkages in biomass. Fuel 249, 146-153.

de Carvalho, L.M., Borelli, G., Camargo, A.P., de Assis, M.A., de Ferraz, S.M.F., Fiamenghi, M.B., José, J., Mofatto, L.S., Nagamatsu, S.T., Persinoti, G.F., Silva, N.V., Vasconcelos, A.A., Pereira, G.A.G., Carazzolle, M.F., 2019. Bioinformatics applied to biotechnology: A review towards bioenergy research. Biomass and Bioenergy 123, 195-224.

Figueirêdo, M.B., Jotic, Z., Deuss, P.J., Venderbosch, R.H., Heeres, H.J., 2019. Hydrotreatment of pyrolytic lignins to aromatics and phenolics using heterogeneous catalysts. Fuel Processing Technology 189, 28-38.

Flores, A., Wang, X., Nielsen, D.R., 2019. Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production. Current Opinion in Biotechnology 57, 82-87.

Hameed, S., Sharma, A., Pareek, V., Wu, H., Yu, Y., 2019. A review on biomass pyrolysis models: Kinetic, network and mechanistic models. Biomass and Bioenergy 123, 104-122.

Li, J.S., Barber, C.C., Zhang, W., 2019. Natural products from anaerobes. Journal of Industrial Microbiology & Biotechnology 46, 375-383.

Liu, C.L., Dong, H.G., Zhan, J., Liu, X., Yang, Y., 2019. Multi-modular engineering for renewable production of isoprene via mevalonate pathway in Escherichia coli. Journal of Applied Microbiology 126, 1128-1139.


Schocke, L., Bräsen, C., Siebers, B., 2019. Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms. Current Opinion in Biotechnology 59, 71-77.

Spagnuolo, M., Yaguchi, A., Blenner, M., 2019. Oleaginous yeast for biofuel and oleochemical production. Current Opinion in Biotechnology 57, 73-81.


Xu, J., Cui, Z., Nie, K., Cao, H., Jiang, M., Xu, H., Tan, T., Liu, L., 2019. A quantum mechanism study of the C-C bond cleavage to predict the bio-catalytic polyethylene degradation. Frontiers in Microbiology 10, 489. doi: 410.3389/fmicb.2019.00489.

Yan, H.-L., Li, Z.-K., Wang, Z.-C., Lei, Z.-P., Ren, S.-B., Pan, C.-X., Tian, Y.-J., Kang, S.-G., Yan, J.-C., Shui, H.-F., 2019. Characterization of soluble portions from cellulose, hemicellulose, and lignin methanolysis. Fuel 246, 394-401.

Yin, Y., Wang, J., 2019. Enhanced biohydrogen production from macroalgae by zero-valent iron nanoparticles: Insights into microbial and metabolites distribution. Bioresource Technology 282, 110-117.

Biogeochemistry

Abney, R.B., Kuhn, T.J., Chow, A., Hockaday, W., Fogel, M.L., Berhe, A.A., 2019. Pyrogenic carbon erosion after the Rim Fire, Yosemite National Park: The role of burn severity and slope. Journal of Geophysical Research: Biogeosciences 124, 432-449.

Archibald, K.M., Siegel, D.A., Doney, S.C., 2019. Modeling the impact of zooplankton diel vertical migration on the carbon export flux of the biological pump. Global Biogeochemical Cycles 33, 181-199.


Bomberg, M., Mäkinen, J., Salo, M., Kinnunen, P., 2019. High diversity in iron cycling microbial communities in acidic, iron-rich water of the Pyhäsalmi Mine, Finland. Geofluids 2019, Article 7401304.

Bucha, M., Kufka, D., Pleśniak, Ł., Krajniak, J., Kubiak, K., Marynowski, L., Błaszczyk, M., Jędrysek, M.-O., 2019. Decomposition of carbon-bearing compounds and their influence on methane formation in a lignite incubation experiment. Geomicrobiology Journal 36, 63-74.

Dale, A.W., Flury, S., Fossing, H., Regnier, P., Røy, H., Scholze, C., Jørgensen, B.B., 2019. Kinetics of organic carbon mineralization and methane formation in marine sediments (Aarhus Bay, Denmark). Geochimica et Cosmochimica Acta 252, 159-178.

Dilkes-Hoffman, L.S., Lant, P.A., Laycock, B., Pratt, S., 2019. The rate of biodegradation of PHA bioplastics in the marine environment: A meta-study. Marine Pollution Bulletin 142, 15-24.

Fu, L., Zhou, T., Wang, J., You, L., Lu, Y., Yu, L., Zhou, S., 2019. NanoFe3O4 as solid electron shuttles to accelerate acetotrophic methanogenesis by Methanosarcina barkeri. Frontiers in Microbiology 10, 388. doi: 310.3389/fmicb.2019.00388.

Kunoh, T., Kusano, Y., Takeda, M., Nakanishi, M., Matsumoto, S., Suzuki, I., Takano, M., Kunoh, H., Takada, J., 2019. Formation of gold particles via thiol groups on glycoconjugates comprising the sheath skeleton of Leptothrix. Geomicrobiology Journal 36, 251-260.

Kushkevych, I., Dordević, D., Vítězová, M., 2019. Toxicity of hydrogen sulfide toward sulfate-reducing bacteria Desulfovibrio piger Vib-7. Archives of Microbiology 201, 389-397.

Li, L., Yao, S., Xue, B., Cheng, L., Yan, R., 2019. Methane levels in five shallow lakes in China: Effect of lake paludification. Quaternary International 503, 128-135.

Markosyan, L., Badalyan, H., Vardanyan, N., Vardanyan, A., 2019. Study of colloidal polysaccharides produced by iron oxidizing bacteria Leptospirillum ferriphilum CC. Geomicrobiology Journal 36, 188-193.


Piché-Choquette, S., Constant, P., 2019. Molecular hydrogen, a neglected key driver of soil biogeochemical processes. Applied and Environmental Microbiology 85, e02418-02418.

Puri, A.W., Liu, D., Schaefer, A.L., Yu, Z., Pesesky, M.W., Greenberg, E.P., Lidstrom, M.E., 2019. Interspecies chemical signaling in a methane-oxidizing bacterial community. Applied and Environmental Microbiology 85, Article e02702-02718.

Quigley, L.N.M., Edwards, A., Steen, A.D., Buchan, A., 2019. Characterization of the interactive effects of labile and recalcitrant organic matter on microbial growth and metabolism. Frontiers in Microbiology 10, 493. doi: 410.3389/fmicb.2019.00493.

Ren, G., Yan, Y., Nie, Y., Lu, A., Wu, X., Li, Y., Wang, C., Ding, H., 2019. Natural extracellular electron transfer between semiconducting minerals and electroactive bacterial communities occurred on the rock varnish. Frontiers in Microbiology 10, 10:293. doi: 210.3389/fmicb.2019.00293.


Shi, J., Zhang, B., Qiu, R., Lai, C., Jiang, Y., He, C., Guo, J., 2019. Microbial chromate reduction coupled to anaerobic oxidation of elemental sulfur or zerovalent iron. Environmental Science & Technology 53, 3198-3207.

Singh, T., Kshirsagar, P.R., Das, A., Yadav, K., Mallik, S., Mascarenhas-Pereira, M.B.L., Thomas, T.R.A., Shivaramu, M.S., P. A, L., Khadge, N.H., Nath, B.N., Dhakephalkar, P.K., Iyer, S.D., Ray, D., Valsangkar, A.B., Garg, A., Prakash Babu, C., Waghole, R.J., Waghmare, S.S., Rajwade, J.M., Paknikar, K.M., 2019. Implications of microbial thiosulfate utilization in red clay sediments of the Central Indian Basin: The martian analogy. Geochemistry, Geophysics, Geosystems 20, 708-729.

Sun, M., Ren, G., Li, Y., Lu, A., Ding, H., 2019. Extracellular electron transfer between birnessite and electrochemically active bacteria community from red soil in Hainan, China. Geomicrobiology Journal 36, 169-178.

Thottathil, S.D., Reis, P.C.J., Prairie, Y.T., 2019. Methane oxidation kinetics in northern freshwater lakes. Biogeochemistry 143, 105-116.


Vigneron, A., Alsop, E.B., Cruaud, P., Philibert, G., King, B., Baksmaty, L., Lavallee, D., Lomans, B.P., Eloe-Fadrosh, E., Kyrpides, N.C., Head, I.M., Tsesmetzis, N., 2019. Contrasting pathways for anaerobic methane oxidation in Gulf of Mexico cold seep sediments. mSystems 4, Article e00091-00018.

Wang, J., Hua, M., Cai, C., Hu, J., Wang, J., Yang, H., Ma, F., Qian, H., Zheng, P., Hu, B., 2019. Spatial-temporal pattern of sulfate-dependent anaerobic methane oxidation in an intertidal zone of the East China Sea. Applied and Environmental Microbiology 85, Article e02638-02618.

Wang, P.-H., Correia, K., Ho, H.-C., Venayak, N., Nemr, K., Flick, R., Mahadevan, R., Edwards, E.A., 2019. An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. The ISME Journal 13, 1042-1055.


Zhai, X., Li, J.-L., Zhang, H.-H., Tan, D.-D., Yang, G.-P., 2019. Spatial distribution and biogeochemical cycling of dimethylated sulfur compounds and methane in the East China Sea during spring. Journal of Geophysical Research: Oceans 124, 1074-1090.

Zhang, K., Shi, Y., Cui, X., Yue, P., Li, K., Liu, X., Tripathi, B.M., Chu, H., 2019. Salinity is a key determinant for soil microbial communities in a desert ecosystem. mSystems 4, Article e00225-00218.

BIOFILM/MICROBIAL INDUCED CORROSION

Bar-On, Y.M., Milo, R., 2019. Towards a quantitative view of the global ubiquity of biofilms. Nature Reviews Microbiology 17, 199-200.

Belan, M.A., Brady, A.L., Kim, S.-T., Lim, D.S.S., Slater, G.F., 2019. Spatial distribution and preservation of carbon isotope biosignatures in freshwater microbialite carbonate. ACS Earth and Space Chemistry 3, 335-343.

Coutaud, M., Méheut, M., Viers, J., Rols, J.-L., Pokrovsky, O.S., 2019. Copper isotope fractionation during excretion from a phototrophic biofilm. Chemical Geology 513, 88-100.

Flemming, H.-C., Wuertz, S., 2019. Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology 17, 247-260.

Kettner, M.T., Oberbeckmann, S., Labrenz, M., Grossart, H.-P., 2019. The eukaryotic life on microplastics in brackish ecosystems. Frontiers in Microbiology 10, 538. doi: 510.3389/fmicb.2019.00538.

Lozano, G.L., Bravo, J.I., Garavito Diago, M.F., Park, H.B., Hurley, A., Peterson, S.B., Stabb, E.V., Crawford, J.M., Broderick, N.A., Handelsman, J., 2019. Introducing THOR, a model microbiome for genetic dissection of community behavior. mBio 10, Article e02846-02818.

Mohamed, A., Ha, P.T., Peyton, B.M., Mueller, R., Meagher, M., Beyenal, H., 2019. In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs. Journal of Power Sources 414, 547-556.

MICROBIAL MEDIATION OF MINERAL FORMATION/DEGRADATION

Bellenberg, S., Huynh, D., Poetsch, A., Sand, W., Vera, M., 2019. Proteomics reveal enhanced oxidative stress responses and metabolic adaptation in Acidithiobacillus ferrooxidans biofilm cells on pyrite. Frontiers in Microbiology 10, 592. doi: 510.3389/fmicb.2019.00592.

do Carmo, T.S., Moreira, F.S., Cabral, B.V., Dantas, R.C.C., de Resende, M.M., Cardoso, V.L., Ribeiro, E.J., 2019. Phosphorus recovery from phosphate rocks using phosphate-solubilizing bacteria. Geomicrobiology Journal 36, 195-203.

Etemadifar, Z., Etemadzadeh, S.S., Emtiazi, G., 2019. A novel approach for bioleaching of sulfur, iron, and silica impurities from coal by growing and resting cells of Rhodococcus spp. Geomicrobiology Journal 36, 123-129.

Gao, L., Lu, X., Liu, H., Li, J., Li, W., Song, R., Wang, R., Zhang, D., Zhu, J., 2019. Mediation of extracellular polymeric substances in microbial reduction of hematite by Shewanella oneidensis MR-1. Frontiers in Microbiology 10, 575. doi: 510.3389/fmicb.2019.00575.

Qiu, X., Yao, Y., Wang, H., Shen, A., Zhang, J., 2019. Halophilic archaea mediate the formation of proto-dolomite in solutions with various sulfate concentrations and salinities. Frontiers in Microbiology 10, 480. doi: 410.3389/fmicb.2019.00480.

Rao, A., Roncal-Herrero, T., Schmid, E., Drechsler, M., Scheffner, M., Gebauer, D., Kröger, R., Cölfen, H., 2019. On biomineralization: Enzymes switch on mesocrystal assembly. ACS Central Science 5, 357-364.


Shang, N., Ding, M., Dai, M., Si, H., Li, S., Zhao, G., 2019. Biodegradation of malachite green by an endophytic bacterium Klebsiella aerogenes S27 involving a novel oxidoreductase. Applied Microbiology and Biotechnology 103, 2141-2153.

Wells, M., McGarry, J., Gaye, M.M., Basu, P., Oremland, R.S., Stolz, J.F., 2019. Respiratory selenite reductase from Bacillus selenitireducens strain MLS10. Journal of Bacteriology 201, e00614-00618.

Xu, H., Peng, X., Bai, S., Ta, K., Yang, S., Liu, S., Jang, H.B., Guo, Z., 2019. Precipitation of calcium carbonate mineral induced by viral lysis of cyanobacteria: evidence from laboratory experiments. Biogeosciences 16, 949-960.

Yan, R., Kappler, A., Muehe, E.M., Knorr, K.-H., Horn, M.A., Poser, A., Lohmayer, R., Peiffer, S., 2019. Effect of reduced sulfur species on chemolithoautotrophic pyrite oxidation with nitrate. Geomicrobiology Journal 36, 19-29.

Zhang, F., Song, Y., Li, C., Zhang, S., Lyu, C., Fan, K., 2019. The impact of indigenous microorganisms on the mineral corrosion and mineral trapping in the SO2 co-injected CO2-saline-sandstone interaction. Geomicrobiology Journal 36, 110-122.

Zhang, Y., Huang, L., Jiang, H., Wu, G., 2019. Hyperthermophilic anaerobic nitrate-dependent Fe(II) oxidization by Tibetan hot spring microbiota and the formation of Fe minerals. Geomicrobiology Journal 36, 30-41.

Carbon Cycle


Bogard, M.J., Kuhn, C.D., Johnston, S.E., Striegl, R.G., Holtgrieve, G.W., Dornblaser, M.M., Spencer, R.G.M., Wickland, K.P., Butman, D.E., 2019. Negligible cycling of terrestrial carbon in many lakes of the arid circumpolar landscape. Nature Geoscience 12, 180-185.

Fennel, K., Alin, S., Barbero, L., Evans, W., Bourgeois, T., Cooley, S., Dunne, J., Feely, R.A., Hernandez-Ayon, J.M., Hu, X., Lohrenz, S., Muller-Karger, F., Najjar, R., Robbins, L., Shadwick, E., Siedlecki, S., Steiner, N., Sutton, A., Turk, D., Vlahos, P., Wang, Z.A., 2019. Carbon cycling in the North American coastal ocean: a synthesis. Biogeosciences 16, 1281-1304.

Gruber, N., Clement, D., Carter, B.R., Feely, R.A., van Heuven, S., Hoppema, M., Ishii, M., Key, R.M., Kozyr, A., Lauvset, S.K., Lo Monaco, C., Mathis, J.T., Murata, A., Olsen, A., Perez, F.F., Sabine, C.L., Tanhua, T., Wanninkhof, R., 2019. The oceanic sink for anthropogenic CO2 from 1994 to 2007. Science 363, 1193-1199.

Hodson, A.J., Nowak, A., Redeker, K.R., Holmlund, E.S., Christiansen, H.H., Turchyn, A.V., 2019. Seasonal dynamics of methane and carbon dioxide evasion from an open system pingo: Lagoon Pingo, Svalbard. Frontiers in Earth Science 7, 30. doi: 10.3389/feart.2019.00030.

Hutchins, R.H.S., Prairie, Y.T., del Giorgio, P.A., 2019. Large-scale landscape drivers of CO2, CH4, DOC, and DIC in boreal river networks. Global Biogeochemical Cycles 33, 125-142.

Leroy, F., Gogo, S., Guimbaud, C., Bernard-Jannin, L., Yin, X., Belot, G., Wang, S., Laggoun-Défarge, F., 2019. CO2 and CH4 budgets and global warming potential modifications in Sphagnum-dominated peat mesocosms invaded by Molinia caerulea. Biogeosciences Discussions 2019, 1-17.

Lininger, K.B., Wohl, E., Rose, J.R., Leisz, S.J., 2019. Significant floodplain soil organic carbon storage along a large high-latitude river and its tributaries. Geophysical Research Letters 46, 2121-2129.

Longbottom, T.L., Hockaday, W.C., 2019. Molecular and isotopic composition of modern soils derived from kerogen-rich bedrock and implications for the global C cycle. Biogeochemistry 143, 239-255.

Martínez-Mena, M., Almagro, M., García-Franco, N., de Vente, J., García, E., Boix Fayos, C., 2019. Fluvial sedimentary deposits as carbon sinks: organic carbon pools and stabilization mechanisms across a Mediterranean catchment. Biogeosciences 16, 1035-1051.

O'Sullivan, M., Spracklen, D.V., Batterman, S.A., Arnold, S.R., Gloor, M., Buermann, W., 2019. Have synergies between nitrogen deposition and atmospheric CO2 driven the recent enhancement of the terrestrial carbon sink? Global Biogeochemical Cycles 33, 163-180.

Romeijn, P., Comer-Warner, S.A., Ullah, S., Hannah, D.M., Krause, S., 2019. Streambed organic matter controls on carbon dioxide and methane emissions from streams. Environmental Science & Technology 53, 2364–2374.

Treat, C.C., Kleinen, T., Broothaerts, N., Dalton, A.S., Dommain, R., Douglas, T.A., Drexler, J.Z., Finkelstein, S.A., Grosse, G., Hope, G., Hutchings, J., Jones, M.C., Kuhry, P., Lacourse, T., Lähteenoja, O., Loisel, J., Notebaert, B., Payne, R.J., Peteet, D.M., Sannel, A.B.K., Stelling, J.M., Strauss, J., Swindles, G.T., Talbot, J., Tarnocai, C., Verstraeten, G., Williams, C.J., Xia, Z., Yu, Z., Väliranta, M., Hättestrand, M., Alexanderson, H., Brovkin, V., 2019. Widespread global peatland establishment and persistence over the last 130,000 y. Proceedings of the National Academy of Sciences 116, 4822-4827.

Wanyama, I., Pelster, D.E., Butterbach-Bahl, K., Verchot, L.V., Martius, C., Rufino, M.C., 2019. Soil carbon dioxide and methane fluxes from forests and other land use types in an African tropical montane region. Biogeochemistry 143, 171-190.

Winkler, A.J., Myneni, R.B., Alexandrov, G.A., Brovkin, V., 2019. Earth system models underestimate carbon fixation by plants in the high latitudes. Nature Communications 10, Article 885.

Yang, M., Bell, T.G., Brown, I.J., Fishwick, J.R., Kitidis, V., Nightingale, P.D., Rees, A.P., Smyth, T.J., 2019. Insights from year-long measurements of air–water CH4 and CO2 exchange in a coastal environment. Biogeosciences 16, 961-978.

Zhang, C., Cheng, S., Li, Y., Zhang, W., Xiao, S., 2019. Diel methane flux from a subtropical eutrophic pond in November based on continuous monitoring. Acta Geochimica 38, 232-240.

Zhang, Y., Luo, M., Hu, Y., Wang, H., Chen, D., 2019. An areal assessment of subseafloor carbon cycling in cold seeps and hydrate-bearing areas in the northern South China Sea. Geofluids 2019, Article 2573937.

Zhuang, G.-C., Peña-Montenegro, T.D., Montgomery, A., Montoya, J.P., Joye, S.B., 2019. Significance of acetate as a microbial carbon and energy source in the water column of Gulf of Mexico: Implications for marine carbon cycling. Global Biogeochemical Cycles 33, 223-235.

Climate Change

Lasher, G.E., Axford, Y., 2019. Medieval warmth confirmed at the Norse Eastern Settlement in Greenland. Geology 47, 267-270.

Lunt, P.H., Fyfe, R.M., Tappin, A.D., 2019. Role of recent climate change on carbon sequestration in peatland systems. Science of The Total Environment 667, 348-358.

Novak, T., Godrijan, J., Pfannkuchen, D.M., Djakovac, T., Medić, N., Ivančić, I., Mlakar, M., Gašparović, B., 2019. Global warming and oligotrophication lead to increased lipid production in marine phytoplankton. Science of The Total Environment 668, 171-183.


Wang, C., Wang, Z., Kong, Y., Zhang, F., Yang, K., Zhang, T., 2019. Most of the northern hemisphere permafrost remains under climate change. Scientific Reports 9, Article 3295.

Carbon Sequestration

Barik, S.S., Singh, R.K., Jena, P.S., Tripathy, S., Sharma, K., Prusty, P., 2019. Spatio-temporal variations in ecosystem and CO2 sequestration in coastal lagoon: A foraminiferal perspective. Marine Micropaleontology 147, 43-56.

Gambelli, A.M., Castellani, B., Nicolini, A., Rossi, F., 2019. Experimental study on natural gas hydrate exploitation: Optimization of methane recovery, carbon dioxide storage and deposit structure preservation. Journal of Petroleum Science and Engineering 177, 594-601.

González-Nicolás, A., Cihan, A., Petrusak, R., Zhou, Q., Trautz, R., Riestenberg, D., Godec, M., Birkholzer, J.T., 2019. Pressure management via brine extraction in geological CO2 storage: Adaptive optimization strategies under poorly characterized reservoir conditions. International Journal of Greenhouse Gas Control 83, 176-185.

Liu, P., Zhang, T., Sun, S., 2019. A tutorial review of reactive transport modeling and risk assessment for geologic CO2 sequestration. Computers & Geosciences 127, 1-11.

McCutcheon, J., Power, I.M., Shuster, J., Harrison, A.L., Dipple, G.M., Southam, G., 2019. Carbon sequestration in biogenic magnesite and other magnesium carbonate minerals. Environmental Science & Technology 53, 3225-3237.

Myers, M.B., Roberts, J.J., White, C., Stalker, L., 2019. An experimental investigation into quantifying CO2 leakage in aqueous environments using chemical tracers. Chemical Geology 511, 91-99.

Peck, W.D., Ayash, S.C., Klapperich, R.J., Gorecki, C.D., 2019. The North Dakota integrated carbon storage complex feasibility study. International Journal of Greenhouse Gas Control 84, 47-53.

Roberts, J.J., Leplastrier, A., Feitz, A.J., Shipton, Z.K., Bell, A.F., Karolytė, R., 2019. Structural controls on the location and distribution of CO2 emission at a natural CO2 spring in Daylesford, Australia. International Journal of Greenhouse Gas Control 84, 36-46.

Seo, S., Mastiani, M., Hafez, M., Kunkel, G., Ghattas Asfour, C., Garcia-Ocampo, K.I., Linares, N., Saldana, C., Yang, K., Kim, M., 2019. Injection of in-situ generated CO2 microbubbles into deep saline aquifers for enhanced carbon sequestration. International Journal of Greenhouse Gas Control 83, 256-264.



Zhang, K., Jiang, H., Qin, G., 2019. Utilization of zeolite as a potential multi-functional proppant for CO2 enhanced shale gas recovery and CO2 sequestration: A molecular simulation study on the competitive adsorption of CH4 and CO2 in zeolite and organic matter. Fuel 249, 119-129.

Coal/Lignite/Peat Geochemistry


Dwivedi, K.K., Chatterjee, P.K., Karmakar, M.K., Pramanick, A.K., 2019. Pyrolysis characteristics and kinetics of Indian low rank coal using thermogravimetric analysis. International Journal of Coal Science & Technology 6, 102-112.

Feng, S., He, J., Tian, J., Lu, X., Yang, B., 2019. The characteristic and evolution of coal-forming swamp in Hanshuiquan district, Santanghu Coalfield, Xinjiang, NW China, during the Middle Jurassic: evidence from coal petrography, coal facies and sporopollen. International Journal of Coal Science & Technology 6, 1-14.

Raymond, A., Lambert, L.L., Costanza, S.H., 2019. Are coal balls rare? A cyclostratigraphic analysis of coal-ball occurrence in North America. International Journal of Coal Geology 206, 65-79.


Wang, X., Wang, X., Pan, Z., Yin, X., Chai, P., Pan, S., Yang, Q., 2019. Abundance and distribution pattern of rare earth elements and yttrium in vitrain band of high-rank coal from the Qinshui basin, northern China. Fuel 248, 93-103.

Zheng, S., Yao, Y., Liu, D., Cai, Y., Liu, Y., 2019. Nuclear magnetic resonance surface relaxivity of coals. International Journal of Coal Geology 205, 1-13.

COAL BED METHANE

Golsanami, N., Sun, J., Liu, Y., Yan, W., Chen, L., Jiang, L., Dong, H., Zong, C., Wang, H., 2019. Distinguishing fractures from matrix pores based on the practical application of rock physics inversion and NMR data: A case study from an unconventional coal reservoir in China. Journal of Natural Gas Science and Engineering 65, 145-167.

Sharma, A., Jani, K., Thite, V., Dhar, S.K., Shouche, Y., 2019. Geochemistry shapes bacterial communities and their metabolic potentials in Tertiary coalbed. Geomicrobiology Journal 36, 179-187.

Xie, J., Liang, Y., Zou, Q., Wang, Z., Li, X., 2019. Prediction model for isothermal adsorption curves based on adsorption potential theory and adsorption behaviors of methane on granular coal. Energy & Fuels 33, 1910-1921.


Yan, M., Bai, Y., Li, S.-G., Lin, H.-F., Yan, D.-J., Shu, C.-M., 2019. Factors influencing the gas adsorption thermodynamic characteristics of low-rank coal. Fuel 248, 117-126.

Cosmochemistry/Planetary Geochemistry

Abotalib, A.Z., Heggy, E., 2019. A deep groundwater origin for recurring slope lineae on Mars. Nature Geoscience 12, 235-241.

Aponte, J.C., Whitaker, D., Powner, M.W., Elsila, J.E., Dworkin, J.P., 2019. Analyses of aliphatic aldehydes and ketones in carbonaceous chondrites. ACS Earth and Space Chemistry 3, 463-472.

Castillo-Rogez, J.C., Hesse, M.A., Formisano, M., Sizemore, H., Bland, M., Ermakov, A.I., Fu, R.R., 2019. Conditions for the long-term preservation of a deep brine reservoir in Ceres. Geophysical Research Letters 46, 1963-1972.

Etiope, G., Oehler, D.Z., 2019. Methane spikes, background seasonality and non-detections on Mars: A geological perspective. Planetary and Space Science 168, 52-61.

Herkenhoff, K.E., Squyres, S.W., Arvidson, R.E., Cole, S.B., Sullivan, R., Yingst, A., Cabrol, N., Lee, E.M., Richie, J., Sucharski, B., Bell III, J.F., Calef, F., Chapman, M., Edgar, L., Franklin, B., Geissler, P., Hurowitz, J., Jensen, E., Johnson, J.R., Kirk, R., Lanagan, P., Leff, C., Maki, J., Mullins, K., Redding, B., Rice, M., Sims, M., Soderblom, L., Spanovich, N., Springer, R., Sunda, A., Vaughan, A., 2019. Overview of Spirit microscopic imager results. Journal of Geophysical Research: Planets 124, 528-584.

Kebukawa, Y., Ito, M., Zolensky, M.E., Greenwood, R.C., Rahman, Z., Suga, H., Nakato, A., Chan, Q.H.S., Fries, M., Takeichi, Y., Takahashi, Y., Mase, K., Kobayashi, K., 2019. A novel organic-rich meteoritic clast from the outer solar system. Scientific Reports 9, Article 3169.

Küppers, M., 2019. The mystery of Ceres' activity. Journal of Geophysical Research: Planets 124, 205-208.


Rabinovitch, J., Katz, I., 2019. Surface deposition of molecular contaminants in the Mars 2020 rover wake. Planetary and Space Science 168, 1-14.

Salese, F., Pondrelli, M., Neeseman, A., Schmidt, G., Ori, G.G., 2019. Geological evidence of planet-wide groundwater system on Mars. Journal of Geophysical Research: Planets 124, 374-395.

Sugiura, K., Kobayashi, H., Inutsuka, S.-i., 2019. Collisional elongation: Possible origin of extremely elongated shape of 1I/‘Oumuamua. Icarus 328, 14-22.

Summons, R.E., Miller, K.E., Kotrc, B., Belmahadi, I., Buch, A., Eigenbrode, J.L., Freissinet, C., Glavin, D.P., Szopa, C., 2019. Reply to Comment by F. Kenig, L. Chou, and D. J. Wardrop on “Evaluation of the Tenax trap in the sample analysis at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater” by Miller et al., 2015. Journal of Geophysical Research: Planets 124, 648-650.

Temel, O., Karatekin, Ö., Gloesener, E., Mischna, M.A., van Beeck, J., 2019. Atmospheric transport of subsurface, sporadic, time-varying methane releases on Mars. Icarus 325, 39-54.

Thakar, Y., Bhavsar, R., Swadia, M., Vinodkumar, M., Mason, N., Limbachiya, C., 2019. Electron interactions with astro chemical compounds. Planetary and Space Science 168, 95-103.

Tokano, T., Lorenz, R.D., 2019. Modeling of seasonal lake level fluctuations of Titan's seas/lakes. Journal of Geophysical Research: Planets 124, 617-635.

Uesugi, M., Ito, M., Yabuta, H., Naraoka, H., Kitajima, F., Takano, Y., Mita, H., Kebukawa, Y., Nakato, A., Karouji, Y., 2019. Further characterization of carbonaceous materials in Hayabusa-returned samples to understand their origin. Meteoritics & Planetary Science 54, 638-666.

Vuitton, V., Yelle, R.V., Klippenstein, S.J., Hörst, S.M., Lavvas, P., 2019. Simulating the density of organic species in the atmosphere of Titan with a coupled ion-neutral photochemical model. Icarus 324, 120-197.

ASTROBIOLOGY

Bloetscher, F., 2019. Using predictive Bayesian Monte Carlo- Markov Chain methods to provide a probablistic solution for the Drake equation. Acta Astronautica 155, 118-130.

Carroll-Nellenback, J., Frank, A., Wright, J., Scharf, C., 2019. The Fermi Paradox and the aurora effect: Exo-civilization settlement, expansion and steady states. arXiv:1902.04450 [physics.pop-ph].

Chan, M.A., Bowen, B.B., Corsetti, F.A., Farrand, W.H., Law, E.S., Newsom, H.E., Spear, J.R., Thompson, D.R., 2019. Exploring, mapping, and data management integration of habitable environments in astrobiology. Frontiers in Microbiology 10, 147. doi: 110.3389/fmicb.2019.00147.


Warren-Rhodes, K.A., Lee, K.C., Archer, S.D.J., Cabrol, N., Ng-Boyle, L., Wettergreen, D., Zacny, K., Pointing, S.B., The NASA Life in the Atacama Project Team, 2019. Subsurface microbial habitats in an extreme desert Mars-analog environment. Frontiers in Microbiology 10, 69. doi: 10.3389/fmicb.2019.00069.

BASALT: ASTROBIOLOGY VOL. 19

Love, S.G., 2018. BASALT: The future of Mars, on Earth today. Astrobiology 19, 243-244.

Lim, D.S.S., Abercromby, A.F.J., Kobs Nawotniak, S.E., Lees, D.S., Miller, M.J., Brady, A.L., Miller, M.J., Mirmalek, Z., Sehlke, A., Payler, S.J., Stevens, A.H., Haberle, C.W., Beaton, K.H., Chappell, S.P., Hughes, S.S., Cockell, C.S., Elphic, R.C., Downs, M.T., Heldmann, J.L., 2019. The BASALT research program: Designing and developing mission elements in support of human scientific exploration of Mars. Astrobiology 19, 245-259.

Hughes, S.S., Haberle, C.W., Kobs Nawotniak, S.E., Sehlke, A., Garry, W.B., Elphic, R.C., Payler, S.J., Stevens, A.H., Cockell, C.S., Brady, A.L., Heldmann, J.L., Lim, D.S.S., 2018. Basaltic terrains in Idaho and Hawai‘i as planetary analogs for Mars geology and astrobiology. Astrobiology 19, 260-283.

Cockell, C.S., Harrison, J.P., Stevens, A.H., Payler, S.J., Hughes, S.S., Kobs Nawotniak, S.E., Brady, A.L., Elphic, R.C., Haberle, C.W., Sehlke, A., Beaton, K.H., Abercromby, A.F.J., Schwendner, P., Wadsworth, J., Landenmark, H., Cane, R., Dickinson, A.W., Nicholson, N., Perera, L., Lim, D.S.S., 2019. A low-diversity microbiota inhabits extreme terrestrial basaltic terrains and their fumaroles: Implications for the exploration of Mars. Astrobiology 19, 284-299.

Beaton, K.H., Chappell, S.P., Abercromby, A.F.J., Miller, M.J., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Payler, S.J., Hughes, S.S., Lim, D.S.S., 2019. Using science-driven analog research to investigate extravehicular activity science operations concepts and capabilities for human planetary exploration. Astrobiology 19, 300-320.

Beaton, K.H., Chappell, S.P., Abercromby, A.F.J., Miller, M.J., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Payler, S.J., Hughes, S.S., Lim, D.S.S., 2019. Assessing the acceptability of science operations concepts and the level of mission enhancement of capabilities for human Mars exploration extravehicular activity. Astrobiology 19, 321-346.

Brady, A.L., Kobs Nawotniak, S.E., Hughes, S.S., Payler, S.J., Stevens, A.H., Cockell, C.S., Elphic, R.C., Sehlke, A., Haberle, C.W., Slater, G.F., Lim, D.S.S., 2019. Strategic planning insights for future science-driven extravehicular activity on Mars. Astrobiology 19, 347-368.

Stevens, A.H., Kobs Nawotniak, S.E., Garry, W.B., Payler, S.J., Brady, A.L., Miller, M.J., Beaton, K.H., Cockell, C.S., Lim, D.S.S., 2019. Tactical scientific decision-making during crewed astrobiology Mars missions. Astrobiology 19, 369-386.

Payler, S.J., Mirmalek, Z., Hughes, S.S., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Cockell, C.S., Lim, D.S.S., 2019. Developing intra-EVA science support team practices for a human mission to Mars. Astrobiology 19, 387-400.

Sehlke, A., Mirmalek, Z., Burtt, D., Haberle, C.W., Santiago-Materese, D., Kobs Nawotniak, S.E., Hughes, S.S., Garry, W.B., Bramall, N., Brown, A.J., Heldmann, J.L., Lim, D.S.S., 2019. Requirements for portable instrument suites during human scientific exploration of Mars. Astrobiology 19, 401-425.

Kobs Nawotniak, S.E., Miller, M.J., Stevens, A.H., Marquez, J.J., Payler, S.J., Brady, A.L., Hughes, S.S., Haberle, C.W., Sehlke, A., Beaton, K.H., Chappell, S.P., Elphic, R.C., Lim,

D.S.S., 2019. Opportunities and challenges of promoting scientific dialog throughout execution of future science-driven extravehicular activity. Astrobiology 19, 426-439.

Marquez, J.J., Miller, M.J., Cohen, T., Deliz, I., Lees, D.S., Zheng, J., Lee, Y.J., Kanefsky, B., Norheim, J., Deans, M., Hillenius, S., 2019. Future needs for science-driven geospatial and temporal extravehicular activity planning and execution. Astrobiology 19, 440-461.

Seibert, M.A., Lim, D.S.S., Miller, M.J., Santiago-Materese, D., Downs, M.T., 2019. Developing future deep-space telecommunication architectures: A historical look at the benefits of analog research on the development of solar system internetworking for future human spaceflight. Astrobiology 19, 462-477.

Miller, M.J., Miller, M.J., Santiago-Materese, D., Seibert, M.A., Lim, D.S.S., 2019. A flexible telecommunication architecture for human planetary exploration based on the BASALT science-driven Mars analog. Astrobiology 19, 478-496.

Kenig, F., Chou, L., Wardrop, D.J., 2019. Comment on “Evaluation of the Tenax trap in the sample analysis at Mars instrument suite on the curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater” by Miller et al. (2015). Journal of Geophysical Research: Planets 124, 644-647.

King, A.J., Russell, S.S., Schofield, P.F., Humphreys-Williams, E.R., Strekopytov, S., Abernethy, F.A.J., Verchovsky, A.B., Grady, M.M., 2019. The alteration history of the Jbilet Winselwan CM carbonaceous chondrite: An analog for C-type asteroid sample return. Meteoritics & Planetary Science 54, 521-543.

Environmental Geochemistry

Ashok, A., Cusack, M., Saderne, V., Krishnakumar, P.K., Rabaoui, L., Qurban, M.A., Duarte, C.M., Agustí, S., 2019. Accelerated burial of petroleum hydrocarbons in Arabian Gulf blue carbon repositories. Science of The Total Environment 669, 205-212.

Feng, J., Liu, M., Zhao, J., Hu, P., Zhang, F., Sun, J.-H., 2019. Historical trends and spatial distributions of polycyclic aromatic hydrocarbons in the upper reach of the Huai River, China: Evidence from the sedimentary record. Applied Geochemistry 103, 59-67.



Kappenberg, A., Braun, M., Amelung, W., Lehndorff, E., 2019. Fire condensates and charcoals: Chemical composition and fuel source identification. Organic Geochemistry 130, 43-50.

Kuwayama, T., Charrier-Klobas, J.G., Chen, Y., Vizenor, N.M., Blake, D.R., Pongetti, T., Conley, S.A., Sander, S.P., Croes, B., Herner, J.D., 2019. Source apportionment of ambient methane enhancements in Los Angeles, California, to evaluate emission inventory estimates. Environmental Science & Technology 53, 2961-2970.

Lindaas, J., Farmer, D.K., Pollack, I.B., Abeleira, A., Flocke, F., Fischer, E.V., 2019. Acyl peroxy nitrates link oil and natural gas emissions to high ozone abundances in the Colorado Front Range during summer 2015. Journal of Geophysical Research: Atmospheres 124, 2336-2350.

Liu, L., Ryu, B., Sun, Z., Wu, N., Cao, H., Geng, W., Zhang, X., Jia, Y., Xu, C., Guo, L., Wang, L., 2019. Monitoring and research on environmental impacts related to marine natural gas hydrates: Review and future perspective. Journal of Natural Gas Science and Engineering 65, 82-107.

Parviainen, A., Loukola-Ruskeeniemi, K., 2019. Environmental impact of mineralised black shales. Earth-Science Reviews 192, 65-90.

Reagan, M.T., Moridis, G.J., Keen, N.D., Lee, K.J., Natter, M., Bjerstedt, T., Shedd, W.W., 2019. Transport and fate of natural gas and brine escaping from a hydrocarbon reservoir through a failed deepwater well in the oceanic subsurface of the Gulf of Mexico. Transport in Porous Media 127, 459-480.


Yu, Y., Katsoyiannis, A., Bohlin-Nizzetto, P., Brorström-Lundén, E., Ma, J., Zhao, Y., Wu, Z., Tych, W., Mindham, D., Sverko, E., Barresi, E., Dryfhout-Clark, H., Fellin, P., Hung, H., 2019. Polycyclic aromatic hydrocarbons not declining in Arctic air despite global emission reduction. Environmental Science & Technology 53, 2375-2382.

Zhang, L., Wu, S., Zhao, L., Lu, X., Pierce, E.M., Gu, B., 2019. Mercury sorption and desorption on organo-mineral particulates as a source for microbial methylation. Environmental Science & Technology 53, 2426–2433.

BIOREMEDIATION



Dangelmayr, M.A., Figueroa, L.A., Williams, K.H., Long, P.E., 2019. Characterizing organic carbon dynamics during biostimulation of a uranium contaminated field site. Biogeochemistry 143, 117-132.

Dashti, N., Ali, N., Salamah, S., Khanafer, M., Al-Shamy, G., Al-Awadhi, H., Radwan, S.S., 2019. Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation. MicrobiologyOpen 8, e00630.

Gielnik, A., Pechaud, Y., Huguenot, D., Cébron, A., Riom, J.-M., Guibaud, G., Esposito, G., van Hullebusch, E.D., 2019. Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils. Science of The Total Environment 670, 271-281.

Hashmat, A.J., Afzal, M., Fatima, K., Anwar-ul-Haq, M., Khan, Q.M., Arias, C.A., Brix, H., 2019. Characterization of hydrocarbon-degrading bacteria in constructed wetland microcosms used to treat crude oil polluted water. Bulletin of Environmental Contamination and Toxicology 102, 358-364.


Kim, J., Chang, W., 2019. Modified soil respiration model (URESP) extended to sub-zero temperatures for biostimulated petroleum hydrocarbon-contaminated sub-Arctic soils. Science of The Total Environment 667, 400-411.



Sun, S., Wang, Y., Zang, T., Wei, J., Wu, H., Wei, C., Qiu, G., Li, F., 2019. A biosurfactant-producing Pseudomonas aeruginosa S5 isolated from coking wastewater and its application for bioremediation of polycyclic aromatic hydrocarbons. Bioresource Technology 281, 421-428.

Villela, H.D.M., Peixoto, R.S., Soriano, A.U., Carmo, F.L., 2019. Microbial bioremediation of oil contaminated seawater: A survey of patent deposits and the characterization of the top genera applied. Science of The Total Environment 666, 743-758.

Xia, M., Fu, D., Chakraborty, R., Singh, R.P., Terry, N., 2019. Enhanced crude oil depletion by constructed bacterial consortium comprising bioemulsifier producer and petroleum hydrocarbon degraders. Bioresource Technology 282, 456-463.

Yu, W., Chen, H., Song, J., Zhao, C., Du, X., Guo, C., Song, Q., 2019. Microbial community from arid desert oilfield in response to accurate bio-stimulation remediation. Petroleum Science and Technology 37, 337-345.

DEEPWATER HORIZON/MACONDO/OTHER OIL SPILLS

Adhikari, P.L., Maiti, K., Bam, W., 2019. Fate of particle-bound polycyclic aromatic hydrocarbons in the river-influenced continental margin of the northern Gulf of Mexico. Marine Pollution Bulletin 141, 350-362.

Chen, D., Wang, A., Li, Y., Hou, Y., Wang, Z., 2019. Biosurfactant-modified palygorskite clay as solid-stabilizers for effective oil spill dispersion. Chemosphere 226, 1-7.


Farooq, U., Nourani, M., Ivol, F., Årrestad, A.B., Øye, G., 2019. Adsorption of crude oil components on mineral surfaces followed by quartz crystal microbalance and contact angle measurements: The effect of oil composition, simulated weathering and dispersants. Energy & Fuels 33, 2359-2365.

Han, B., Song, Z., Li, Q., Zheng, L., 2019. Evaluation of new diagnostic ratios of naphthalenes and fluorenes by identifying severely weathered oils collected in laboratory simulations and coastal weathering experiments. Archives of Environmental Contamination and Toxicology 76, 508-517.

Penko, L., Bajt, O., 2019. Aliphatic and polycyclic aromatic hydrocarbons in surface seawater of the Gulf of Trieste (northern Adriatic). Marine Pollution Bulletin 142, 103-111.

Perrot, V., Landing, W.M., Grubbs, R.D., Salters, V.J.M., 2019. Mercury bioaccumulation in tilefish from the northeastern Gulf of Mexico 2 years after the Deepwater Horizon oil spill: Insights from Hg, C, N and S stable isotopes. Science of The Total Environment 666, 828-838.

Rogers, K.L., Bosman, S.H., Lardie-Gaylord, M., McNichol, A., Rosenheim, B.E., Montoya, J.P., Chanton, J.P., 2019. Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. PLOS ONE 14, Article e0212433.

Suja, L.D., Chen, X., Summers, S., Paterson, D.M., Gutierrez, T., 2019. Chemical dispersant enhances microbial exopolymer (EPS) production and formation of marine oil/dispersant snow in surface waters of the subarctic northeast Atlantic. Frontiers in Microbiology 10, 553. doi: 510.3389/fmicb.2019.00553.


MICROPLASTICS


Ferreira, I., Venâncio, C., Lopes, I., Oliveira, M., 2019. Nanoplastics and marine organisms: What has been studied? Environmental Toxicology and Pharmacology 67, 1-7.

Guo, X., Wang, J., 2019. The chemical behaviors of microplastics in marine environment: A review. Marine Pollution Bulletin 142, 1-14.

Heidbreder, L.M., Bablok, I., Drews, S., Menzel, C., 2019. Tackling the plastic problem: A review on perceptions, behaviors, and interventions. Science of The Total Environment 668, 1077-1093.


Malizia, A., Monmany-Garzia, A.C., 2019. Terrestrial ecologists should stop ignoring plastic pollution in the Anthropocene time. Science of The Total Environment 668, 1025-1029.

Oliveira, M., Almeida, M., 2019. The why and how of micro(nano)plastic research. TrAC Trends in Analytical Chemistry 114, 196-201.

Pico, Y., Alfarhan, A., Barcelo, D., 2019. Nano- and microplastic analysis: Focus on their occurrence in freshwater ecosystems and remediation technologies. TrAC Trends in Analytical Chemistry 113, 409-425.

Rios Mendoza, L.M., Balcer, M., 2019. Microplastics in freshwater environments: A review of quantification assessment. TrAC Trends in Analytical Chemistry 113, 402-408.

Rochman, C.M., Brookson, C., Bikker, J., Djuric, N., Earn, A., Bucci, K., Athey, S., Huntington, A., McIlwraith, H., Munno, K., De Frond, H., Kolomijeca, A., Erdle, L., Grbic, J., Bayoumi, M., Borrelle, S.B., Wu, T., Santoro, S., Werbowski, L.M., Zhu, X., Giles, R.K., Hamilton, B.M., Thaysen, C., Kaura, A., Klasios, N., Ead, L., Kim, J., Sherlock, C., Ho, A., Hung, C., 2019. Rethinking microplastics as a diverse contaminant suite. Environmental Toxicology and Chemistry 38, 703-711.

OIL SAND PROCESS WATERS/TAILING PONDS



Benally, C., Messele, S.A., Gamal El-Din, M., 2019. Adsorption of organic matter in oil sands process water (OSPW) by carbon xerogel. Water Research 154, 402-411.


Landis, M.S., Studabaker, W.B., Pancras, J.P., Graney, J.R., White, E.M., Edgerton, E.S., 2019. Source apportionment of ambient fine and coarse particulate matter polycyclic aromatic hydrocarbons at the Bertha Ganter-Fort McKay community site in the Oil Sands Region of Alberta, Canada. Science of The Total Environment 666, 540-558.

Schuster, J.K., Harner, T., Su, K., Eng, A., Wnorowski, A., Charland, J.-P., 2019. Temporal and spatial trends of polycyclic aromatic compounds in air across the Athabasca oil sands region reflect inputs from open pit mining and forest fires. Environmental Science & Technology Letters 6, 178-183.


UNCONVENTIONALSHALE GAS-CBM RESOURCES

Hanson, A.J., Luek, J.L., Tummings, S.S., McLaughlin, M.C., Blotevogel, J., Mouser, P.J., 2019. High total dissolved solids in shale gas wastewater inhibit biodegradation of alkyl and nonylphenol ethoxylate surfactants. Science of The Total Environment 668, 1094-1103.

Robert, J., McGuire, C.C., Nagel, S., Lawrence, B.P., Andino, F.D.J., 2019. Developmental exposure to chemicals associated with unconventional oil and gas extraction alters immune homeostasis and viral immunity of the amphibian Xenopus. Science of The Total Environment 671, 644-654.

Evolution/Paleontology/Palynology

Chen, Z.-Q., Tu, C., Pei, Y., Ogg, J., Fang, Y., Wu, S., Feng, X., Huang, Y., Guo, Z., Yang, H., 2019. Biosedimentological features of major microbe-metazoan transitions (MMTs) from Precambrian to Cenozoic. Earth-Science Reviews 189, 21-50.

Daley, A.C., 2019. A treasure trove of Cambrian fossils. Science 363, 1284-1285.

Fu, D., Tong, G., Dai, T., Liu, W., Yang, Y., Zhang, Y., Cui, L., Li, L., Yun, H., Wu, Y., Sun, A., Liu, C., Pei, W., Gaines, R.R., Zhang, X., 2019. The Qingjiang biota—A Burgess Shale–type fossil Lagerstätte from the early Cambrian of South China. Science 363, 1338-1342.

Hua, H., Cai, Y., Xiao, S., Li, G., 2019. Diverse biomineralizing animals in the terminal Ediacaran Period herald the Cambrian explosion. Geology 47, 380-384.


Paterson, J.R., Edgecombe, G.D., Lee, M.S.Y., 2019. Trilobite evolutionary rates constrain the duration of the Cambrian explosion. Proceedings of the National Academy of Sciences 116, 4394-4399.

Pratt, B.R., Kimmig, J., 2019. Extensive bioturbation in a middle Cambrian Burgess Shale–type fossil Lagerstätte in northwestern Canada. Geology 47, 231-234.

Rishworth, G.M., Edwards, M.J.K., Cónsole-Gonella, C., Perissinotto, R., 2019. Modern active microbialite-metazoan relationships in peritidal systems on the Eastern Cape coast of South Africa: Ecological significance and implication for the palaeontological record. Journal of African Earth Sciences 153, 1-8.

Soltis, P.S., Folk, R.A., Soltis, D.E., 2019. Darwin review: angiosperm phylogeny and evolutionary radiations. Proceedings of the Royal Society B: Biological Sciences 286, Article 20190099.

Sutherland, J.T.F., Moon, B., C., Stubbs, T., L., Benton, M., J., 2019. Does exceptional preservation distort our view of disparity in the fossil record? Proceedings of the Royal Society B: Biological Sciences 286, 20190091.

Topper, T.P., Guo, J., Clausen, S., Skovsted, C.B., Zhang, Z., 2019. A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria. Nature Communications 10, Article 1366.

Ullmann, P.V., Pandya, S.H., Nellermoe, R., 2019. Patterns of soft tissue and cellular preservation in relation to fossil bone tissue structure and overburden depth at the Standing Rock Hadrosaur Site, Maastrichtian Hell Creek Formation, South Dakota, USA. Cretaceous Research 99, 1-13.

Yamagata, K., Nagai, K., Miyamoto, H., Anzai, M., Kato, H., Miyamoto, K., Kurosaka, S., Azuma, R., Kolodeznikov, I.I., Protopopov, A.V., Plotnikov, V.V., Kobayashi, H., Kawahara-Miki, R., Kono, T., Uchida, M., Shibata, Y., Handa, T., Kimura, H., Hosoi, Y., Mitani, T., Matsumoto, K., Iritani, A., 2019. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Scientific Reports 9, Article 4050.

Zhao, C., Wang, Y., Chan, K.X., Marchant, D.B., Franks, P.J., Randall, D., Tee, E.E., Chen, G., Ramesh, S., Phua, S.Y., Zhang, B., Hills, A., Dai, F., Xue, D., Gilliham, M., Tyerman, S., Nevo, E., Wu, F., Zhang, G., Wong, G.K.S., Leebens-Mack, J.H., Melkonian, M., Blatt, M.R., Soltis, P.S., Soltis, D.E., Pogson, B.J., Chen, Z.-H., 2019. Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land. Proceedings of the National Academy of Sciences 116, 5015-5020.

ORIGINS OF LIFE/MICROBIAL GENOMICS

Bäckström, D., Yutin, N., Jørgensen, S.L., Dharamshi, J., Homa, F., Zaremba-Niedwiedzka, K., Spang, A., Wolf, Y.I., Koonin, E.V., Ettema, T.J.G., 2019. Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism. mBio 10, Article e02497-02418.

Barge, L.M., Flores, E., Baum, M.M., VanderVelde, D.G., Russell, M.J., 2019. Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems. Proceedings of the National Academy of Sciences 116, 4828-4833.

Berghuis, B.A., Yu, F.B., Schulz, F., Blainey, P.C., Woyke, T., Quake, S.R., 2019. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proceedings of the National Academy of Sciences 116, 5037-5044.

Dalai, P., Sahai, N., 2019. Mineral–lipid interactions in the origins of life. Trends in Biochemical Sciences 44, 331-341.

Degli Esposti, M., Mentel, M., Martin, W., Sousa, F.L., 2019. Oxygen reductases in alphaproteobacterial genomes: Physiological evolution from low to high oxygen environments. Frontiers in Microbiology 10, 499. doi: 410.3389/fmicb.2019.00499.

Jaffe, A.L., Castelle, C.J., Banfield, J.F., Dupont, C.L., 2018. Lateral gene transfer shapes the distribution of RuBisCO among candidate Phyla Radiation bacteria and DPANN archaea. Molecular Biology and Evolution 36, 435-446.

Legendre, M., Alempic, J.-M., Philippe, N., Lartigue, A., Jeudy, S., Poirot, O., Ta, N.T., Nin, S., Couté, Y., Abergel, C., Claverie, J.-M., 2019. Pandoravirus celtis illustrates the microevolution processes at work in the giant Pandoraviridae genomes. Frontiers in Microbiology 10, 430. doi: 410.3389/fmicb.2019.00430.

Lu, H.-P., Yeh, Y.-C., Shiah, F.-K., Gong, G.-C., Hsieh, C.-h., 2019. Evolutionary constraints on species diversity in marine bacterioplankton communities. The ISME Journal 13, 1032-1041.


Moelling, K., Broecker, F., 2019. Viruses and evolution – viruses first? A personal perspective. Frontiers in Microbiology 10, 523. doi: 510.3389/fmicb.2019.00523.

O’Malley, M.A., Leger, M.M., Wideman, J.G., Ruiz-Trillo, I., 2019. Concepts of the last eukaryotic common ancestor. Nature Ecology & Evolution 3, 338-344.

Palmer, M., Venter, S.N., Coetzee, M.P.A., Steenkamp, E.T., 2019. Prokaryotic species are sui generis evolutionary units. Systematic and Applied Microbiology 42, 145-158.

Russell, S.L., 2019. Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis. FEMS Microbiology Letters 366, Article fnz013.

Sambamoorthy, G., Sinha, H., Raman, K., 2019. Evolutionary design principles in metabolism. Proceedings of the Royal Society B: Biological Sciences 286, Artcile 20190098.

Schoelmerich, M.C., Müller, V., 2019. Energy conservation by a hydrogenase-dependent chemiosmotic mechanism in an ancient metabolic pathway. Proceedings of the National Academy of Sciences 116, 6329.

Ward, L.M., Rasmussen, B., Fischer, W.W., 2019. Primary productivity was limited by electron donors prior to the advent of oxygenic photosynthesis. Journal of Geophysical Research: Biogeosciences 124, 211-226.

Xiao, J., Fan, L., Wu, D., Xu, Y., Lai, D., Martin, W.F., Zhu, R., Zhang, C., 2019. Archaea, the tree of life, and cellular evolution in eukaryotes. Science China Earth Sciences 62, 489-506.

Zitnik, M., Sosič, R., Feldman, M.W., Leskovec, J., 2019. Evolution of resilience in protein interactomes across the tree of life. Proceedings of the National Academy of Sciences 116, 4426-4433.

HOMINID EVOLUTION

Callaway, E., 2019. Siberia’s ancient ghost clan starts to surrender its secrets. Nature 566, 444-446.

Haeusler, M., Trinkaus, E., Fornai, C., Müller, J., Bonneau, N., Boeni, T., Frater, N., 2019. Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal. Proceedings of the National Academy of Sciences 116, 4923-4927.

Jaouen, K., Richards, M.P., Le Cabec, A., Welker, F., Rendu, W., Hublin, J.-J., Soressi, M., Talamo, S., 2019. Exceptionally high δ15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores. Proceedings of the National Academy of Sciences 116, 4928-4933.

Fluid Inclusions

Han, C., Lin, C., Lu, X., Tian, J., Ren, L., Ma, C., 2019. Petrological and geochemical constraints on fluid types and formation mechanisms of the Ordovician carbonate reservoirs in Tahe Oilfield, Tarim Basin, NW China. Journal of Petroleum Science and Engineering 178, 106-120.

Lao, H., Wang, Y., Shan, Y., Hao, X., Li, Q., 2019. Hydrocarbon downward accumulation from an upper oil source to the oil reservoir below in an extensional basin: A case study of Chezhen Depression in the Bohai Bay Basin. Marine and Petroleum Geology 103, 516-525.

Li, G., Qin, Y., Shen, J., Wu, M., Li, C., Wei, K., Zhu, C., 2019. Geochemical characteristics of tight sandstone gas and hydrocarbon charging history of Linxing area in Ordos Basin, China. Journal of Petroleum Science and Engineering 177, 198-207.

Li, Y., Yang, J., Pan, Z., Meng, S., Wang, K., Niu, X., 2019. Unconventional natural gas accumulations in stacked deposits: A discussion of Upper Paleozoic coal-bearing strata in the east margin of the Ordos Basin, China. Acta Geologica Sinica - English Edition 93, 111-129.

Li, Y., Zha, M., Gao, C., Ding, X., Wang, X., Zhang, Y., Yang, L., 2019. Geochemistry and origin of heavy oils in the south part of Zhanhua Depression, east China. Marine and Petroleum Geology 103, 499-515.

Ping, H., Chen, H., George, S.C., Li, C., Hu, S., 2019. Relationship between the fluorescence colour of oil inclusions and thermal maturity in the Dongying Depression, Bohai Bay Basin, China: Part 2. Fluorescence evolution of oil in the context of petroleum generation, expulsion and cracking under geological conditions. Marine and Petroleum Geology 103, 306-319.

Volk, H., George, S.C., 2019. Using petroleum inclusions to trace petroleum systems – A review. Organic Geochemistry 129, 99-123.

General Interest


Díaz-Urrutia, C., Ott, T., 2019. Activation of methane to CH3+: A selective industrial route to

methanesulfonic acid. Science 363, 1326-1329.

Gal, J.-F., 2019. An excursion into the history of chromatography: Mikhail Tswett, from Asti, Italy, to Tartu, Estonia. Chromatographia 82, 519-521.

Grubel, K., Chouyyok, W., Heldebrant, D.J., Linehan, J.C., Bays, J.T., 2019. Octane-on-demand: Onboard separation of oxygenates from gasoline. Energy & Fuels 33, 1869-1881.

Jiang, H., Wei, L., Fan, X., Xu, J., Shyy, W., Zhao, T., 2019. A novel energy storage system incorporating electrically rechargeable liquid fuels as the storage medium. Science Bulletin 64, 270-280.

Khattak, H.K., Bianucci, P., Slepkov, A.D., 2019. Linking plasma formation in grapes to microwave resonances of aqueous dimers. Proceedings of the National Academy of Sciences 116, 4000-4005.

Pomerantz, A.E., Bostrom, N.W., Kleinberg, R.L., Crace, E., Weng, T.-C., Sokaras, D., Nordlund, D., 2019. Electronic structure of naturally occurring aromatic carbon. Energy & Fuels 33, 2099-2105.

Su, L., Ajo-Franklin, C.M., 2019. Reaching full potential: bioelectrochemical systems for storing renewable energy in chemical bonds. Current Opinion in Biotechnology 57, 66-72.

Geology

Chen, Z.-Q., Hu, X., Montañez, I.P., Ogg, J.G., 2019. Sedimentology as a key to understanding Earth and life processes. Earth-Science Reviews 189, 1-5.

Ibarra, D.E., Rugenstein, J.K.C., Bachan, A., Baresch, A., Lau, K.V., Thomas, D.L., Lee, J.-E., Boyce, C.K., Chamberlain, C.P., 2019. Modeling the consequences of land plant evolution on silicate weathering. American Journal of Science 319, 1-43.

Pires, L.O., Winter, A., Trevisan, O.V., 2019. Dolomite cores evaluated by NMR. Journal of Petroleum Science and Engineering 176, 1187-1197.

Rickard, D., 2019. How long does it take a pyrite framboid to form? Earth and Planetary Science Letters 513, 64-68.

Rickard, D., 2019. Sedimentary pyrite framboid size-frequency distributions: A meta-analysis. Palaeogeography, Palaeoclimatology, Palaeoecology 522, 62-75.

Suosaari, E.P., Oehlert, A.M., Milano, G.R., Eberli, G.P., Reid, R.P., Playford, P.E., Steffensen, C.K., Andres, M.S., Suosaari, G.V., 2019. Stromatolite provinces of Hamelin Pool: Physiographic controls on stromatolites and associated lithofacies. Journal of Sedimentary Research 89, 207-226.

Trower, E.J., Lamb, M.P., Fischer, W.W., 2019. The origin of carbonate mud. Geophysical Research Letters 46, 2696-2703.

JOURNAL OF THE GEOLOGICAL SOCIETY 176. GEOLOGIC CARBON

Frezzotti, M.L., Villa, I.M., Iannantuoni, G., 2019. Introduction to the Thematic set: Carbon forms, paths and processes in the Earth. Journal of the Geological Society 176, 335-336.


Sverjensky, D.A., 2019. Thermodynamic modelling of fluids from surficial to mantle conditions. Journal of the Geological Society 176, 348-374.

Stagno, V., 2019. Carbon, carbides, carbonates and carbonatitic melts in the Earth's interior. Journal of the Geological Society 176, 375-387.

Tumiati, S., Malaspina, N., 2019. Redox processes and the role of carbon-bearing volatiles from the slab–mantle interface to the mantle wedge. Journal of the Geological Society 176, 388-397.

Moore, L.R., Bodnar, R.J., 2019. A pedagogical approach to estimating the CO2 budget of magmas. Journal of the Geological Society 176, 398-407.

Frondini, F., Cardellini, C., Caliro, S., Beddini, G., Rosiello, A., Chiodini, G., 2019. Measuring and interpreting CO2 fluxes at regional scale: the case of the Apennines, Italy. Journal of the Geological Society 176, 408-416.

BOLIDE IMPACTS/CRATER GEOCHEMISTRY

Ackerman, L., Skála, R., Křížová, Š., Žák, K., Magna, T., 2019. The quest for an extraterrestrial component in Muong Nong-type and splash-form Australasian tektites from

Laos using highly siderophile elements and Re-Os isotope systematics. Geochimica et Cosmochimica Acta 252, 179-189.

Coldwell, B.C., Pankhurst, M.J., 2019. Evaluating the influence of meteorite impact events on global potassium feldspar availability to the atmosphere since 600 Ma. Journal of the Geological Society 176, 209-224.

Tsikalas, F., Eldholm, O., 2019. Malvinas (Falkland) Plateau structure versus Mjølnir crater: Geophysical workflow template for proposed marine impact craters. Meteoritics & Planetary Science 54, 544-557.

Urrutia-Fucugauchi, J., Pérez-Cruz, L., Morgan, J., Gulick, S., Wittmann, A., Lofi, J., Party, I.-I.E.S., 2019. Peering inside the peak ring of the Chicxulub Impact Crater—its nature and formation mechanism. Geology Today 35, 68-72.

Hydrates

Almenningen, S., Gauteplass, J., Hauge, L.P., Barth, T., Fernø, M.A., Ersland, G., 2019. Measurements of CH4 and CO2 relative permeability in hydrate-bearing sandstone. Journal of Petroleum Science and Engineering 177, 880-888.

Berndt, C., Chi, W.C., Jegen, M., Lebas, E., Crutchley, G., Muff, S., Hölz, S., Sommer, M., Lin, S., Liu, C.S., Lin, A.T., Klaeschen, D., Klaucke, I., Chen, L., Hsu, H.H., Kunath, P., Elger, J., McIntosh, K.D., Feseker, T., 2019. Tectonic controls on gas hydrate distribution off SW Taiwan. Journal of Geophysical Research: Solid Earth 124, 1164-1184.


Fu, W., Wang, Z., Yue, X., Zhang, J., Sun, B., 2019. Experimental study of methane hydrate formation in water-continuous flow loop. Energy & Fuels 33, 2176-2185.



Lasich, M., Tumba, K., 2019. Single-site Langmuir-type adsorption in structure-I clathrate hydrates: A molecular simulation study using a general self-consistent force field. Fluid Phase Equilibria 489, 111-116.

Li, S., Li, Y., Yang, L., Chen, Y., Shao, Y., Sun, J., Xu, R., 2019. Prediction of phase equilibrium of methane hydrate below 272.2 K based on different equations of state. Fluid Phase Equilibria 490, 61-67.

Liu, L., Ryu, B., Sun, Z., Wu, N., Cao, H., Geng, W., Zhang, X., Jia, Y., Xu, C., Guo, L., Wang, L., 2019. Monitoring and research on environmental impacts related to marine natural gas

hydrates: Review and future perspective. Journal of Natural Gas Science and Engineering 65, 82-107.

Malagar, B.R.C., Lijith, K.P., Singh, D.N., 2019. Formation & dissociation of methane gas hydrates in sediments: A critical review. Journal of Natural Gas Science and Engineering 65, 168-184.

Naullage, P.M., Bertolazzo, A.A., Molinero, V., 2019. How do surfactants control the agglomeration of clathrate hydrates? ACS Central Science 5, 428-439.

Owari, S., Tomaru, H., Matsumoto, R., 2019. Long-term, continuous OsmoSampler results for interstitial waters from an active gas venting site at a shallow gas hydrate field, Umitaka Spur, eastern margin of the Japan Sea. Applied Geochemistry 104, 25-32.


Sun, R., Fan, Z., Yang, M., Pang, W., Li, Y., Song, Y., 2019. Experimental investigation into the dissociation of methane hydrate near ice-freezing point induced by depressurization and the concomitant metastable phases. Journal of Natural Gas Science and Engineering 65, 125-134.

Sun, X., Wang, L., Luo, H., Song, Y., Li, Y., 2019. Numerical modeling for the mechanical behavior of marine gas hydrate-bearing sediments during hydrate production by depressurization. Journal of Petroleum Science and Engineering 177, 971-982.

Waage, M., Portnov, A., Serov, P., Bünz, S., Waghorn, K.A., Vadakkepuliyambatta, S., Mienert, J., Andreassen, K., 2019. Geological controls on fluid flow and gas hydrate pingo development on the Barents Sea margin. Geochemistry, Geophysics, Geosystems 20, 630-650.

Ye, J., Wei, J., Liang, J., Lu, J., Lu, H., Zhang, W., 2019. Complex gas hydrate system in a gas chimney, South China Sea. Marine and Petroleum Geology 104, 29-39.


Isotope Geochemistry

Andrae, J.W., McInerney, F.A., Tibby, J., Henderson, A.C.G., Hall, P.A., Marshall, J.C., McGregor, G.B., Barr, C., Greenway, M., 2019. Variation in leaf wax n-alkane characteristics with climate in the broad-leaved paperbark (Melaleuca quinquenervia). Organic Geochemistry 130, 33-42.

Badger, M.P.S., Chalk, T.B., Foster, G.L., Bown, P.R., Gibbs, S.J., Sexton, P.F., Schmidt, D.N., Pälike, H., Mackensen, A., Pancost, R.D., 2019. Insensitivity of alkenone carbon isotopes to atmospheric CO2 at low to moderate CO2 levels. Climate of the Past 15, 539-554.


Bore, E.K., Halicki, S., Kuzyakov, Y., Dippold, M.A., 2019. Structural and physiological adaptations of soil microorganisms to freezing revealed by position-specific labeling and compound-specific 13C analysis. Biogeochemistry 143, 207-219.


Halloran, L.J.S., Brunner, P., Hunkeler, D., 2019. COMPEST, a PEST-COMSOL interface for inverse multiphysics modelling: Development and application to isotopic fractionation of groundwater contaminants. Computers & Geosciences 126, 107-119.


Jurikova, H., Liebetrau, V., Raddatz, J., Fietzke, J., Trotter, J., Rocholl, A., Krause, S., McCulloch, M., Rüggeberg, A., Eisenhauer, A., 2019. Boron isotope composition of the cold-water coral Lophelia pertusa along the Norwegian margin: Zooming into a potential pH-proxy by combining bulk and high-resolution approaches. Chemical Geology 513, 143-152.

Liu, J., Selby, D., Zhou, H., Pujol, M., 2019. Further evaluation of the Re-Os systematics of crude oil: Implications for Re-Os geochronology of petroleum systems. Chemical Geology 513, 1-22.

Parzanini, C., Parrish, C.C., Hamel, J.F., Mercier, A., 2019. Reviews and syntheses: Insights into deep-sea food webs and global environmental gradients revealed by stable isotopes (δ15N, δ13C) and fatty acids trophic biomarkers. Biogeosciences Discussions 2019, 1-41.

Shtangeeva, I., Buša, L., Viksna, A., 2019. Carbon and nitrogen stable isotope ratios of soils and grasses as indicators of soil characteristics and biological taxa. Applied Geochemistry 104, 19-24.

Sime, L.C., Hopcroft, P.O., Rhodes, R.H., 2019. Impact of abrupt sea ice loss on Greenland water isotopes during the last glacial period. Proceedings of the National Academy of Sciences 116, 4099-4104.

Wu, Y., Zhang, Z., Sun, L., Li, Y., Zhang, M., Ji, L., 2019. Stable isotope reversal and evolution of gas during the hydrous pyrolysis of continental kerogen in source rocks under supercritical conditions. International Journal of Coal Geology 205, 105-114.

CLUMPED ISOTOPES

Veillard, C.M.A., John, C.M., Krevor, S., Najorka, J., 2019. Rock-buffered recrystallization of Marion Plateau dolomites at low temperature evidenced by clumped isotope thermometry and X-ray diffraction analysis. Geochimica et Cosmochimica Acta 252, 190-212.

Xi, K., Cao, Y., Lin, M., Liu, K., Wu, S., Yuan, G., Yang, T., 2019. Applications of light stable isotopes (C, O, H) in the study of sandstone diagenesis: A review. Acta Geologica Sinica - English Edition 93, 213-226.

METHODS/INSTRUMENTATION

Fetter, N., Blichert-Toft, J., Télouk, P., Albarède, F., 2019. Extraction of Pb and Zn from crude oil for high-precision isotopic analysis by MC-ICP-MS. Chemical Geology 511, 112-122.

Mathematical Geochemistry/Phase Behavior

Lee, J., Kim, K.-I., Min, K.-B., Rutqvist, J., 2019. TOUGH-UDEC: A simulator for coupled multiphase fluid flows, heat transfers and discontinuous deformations in fractured porous media. Computers & Geosciences 126, 120-130.

Marshall, B.D., Bokis, C.P., 2019. A PC-SAFT model for hydrocarbons I: Mapping aromatic π-π interactions onto a dipolar free energy. Fluid Phase Equilibria 489, 83-89.

Seyyedattar, M., Zendehboudi, S., Butt, S., 2019. Invited review - Molecular dynamics simulations in reservoir analysis of offshore petroleum reserves: A systematic review of theory and applications. Earth-Science Reviews 192, 194-213.

Valsala, R., Govindarajan, S.K., 2019. Co-colloidal BTEX and microbial transport in a saturated porous system: Numerical modeling and sensitivity analysis. Transport in Porous Media 127, 269-294.

Wu, J., Xu, Y., 2019. Effect of asphaltene content in bitumen on thermodynamic properties of light hydrocarbons dissolving in bitumen. Fluid Phase Equilibria 490, 22-32.

Microbiology/Extremophiles

Barreteau, H., Vandervennet, M., Guédon, L., Point, V., Canaan, S., Rebuffat, S., Peduzzi, J., Carré-Mlouka, A., 2019. Haloarcula sebkhae sp. nov., an extremely halophilic archaeon from Algerian hypersaline environment. International Journal of Systematic and Evolutionary Microbiology 69, 732-738.



Gray, D.A., Dugar, G., Gamba, P., Strahl, H., Jonker, M.J., Hamoen, L.W., 2019. Extreme slow growth as alternative strategy to survive deep starvation in bacteria. Nature Communications 10, Article 890.

Zhu, G., Wang, S., Wang, C., Zhou, L., Zhao, S., Li, Y., Li, F., Jetten, M.S.M., Lu, Y., Schwark, L., 2019. Resuscitation of anammox bacteria after >10,000 years of dormancy. The ISME Journal 13, 1098-1109.

MICROBIAL ECOSYSTEMS

Amend, A., Burgaud, G., Cunliffe, M., Edgcomb, V.P., Ettinger, C.L., Gutiérrez, M.H., Heitman, J., Hom, E.F.Y., Ianiri, G., Jones, A.C., Kagami, M., Picard, K.T., Quandt, C.A., Raghukumar, S., Riquelme, M., Stajich, J., Vargas-Muñiz, J., Walker, A.K., Yarden, O., Gladfelter, A.S., 2019. Fungi in the marine environment: Open questions and unsolved problems. mBio 10, Article e01189-01118.

Arab, M., Bakour, S., Lalaoui, R., Aissaoui, N., Nas, F., Hoceini, A., Fournier, P.-E., Klouche-Khelil, N., 2019. Diversity of aerobic bacilli analysis using molecular and culture-based approaches in Debagh hot spring. Geomicrobiology Journal 36, 137-147.



Burkert, A., Douglas, T.A., Waldrop, M.P., Mackelprang, R., 2019. Changes in the active, dead, and dormant microbial community structure across a Pleistocene permafrost chronosequence. Applied and Environmental Microbiology 85, Article e02646-02618.

Carlson, H.K., Price, M.N., Callaghan, M., Aaring, A., Chakraborty, R., Liu, H., Kuehl, J.V., Arkin, A.P., Deutschbauer, A.M., 2019. The selective pressures on the microbial community in a metal-contaminated aquifer. The ISME Journal 13, 937-949.

Hanson, C.A., Müller, A.L., Loy, A., Dona, C., Appel, R., Jørgensen, B.B., Hubert, C.R.J., 2019. Historical factors associated with past environments influence the biogeography of thermophilic endospores in Arctic marine sediments. Frontiers in Microbiology 10, 245. doi: 210.3389/fmicb.2019.00245.


Levy-Booth, D.J., Giesbrecht, I.J.W., Kellogg, C.T.E., Heger, T.J., D’Amore, D.V., Keeling, P.J., Hallam, S.J., Mohn, W.W., 2019. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil. The ISME Journal 13, 950-963.

Liu, M., Xue, Y., Yang, J., 2019. Rare plankton subcommunities are far more affected by DNA extraction kits than abundant plankton. Frontiers in Microbiology 10, 454. doi: 410.3389/fmicb.2019.00454.

Liu, Q., Liu, H.-C., Zhou, Y.-G., Xin, Y.-H., 2019. Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Systematic and Applied Microbiology 42, 168-177.



Mahato, N.K., Sharma, A., Singh, Y., Lal, R., 2019. Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Archives of Microbiology 201, 377-388.


Parkes, R.J., Berlendis, S., Roussel, E.G., Bahruji, H., Webster, G., Oldroyd, A., Weightman, A.J., Bowker, M., Davies, P.R., Sass, H., 2019. Rock-crushing derived hydrogen directly supports a methanogenic community: significance for the deep biosphere. Environmental Microbiology Reports 11, 165-172.

Payler, S.J., Biddle, J.F., Sherwood Lollar, B., Fox-Powell, M.G., Edwards, T., Ngwenya, B.T., Paling, S.M., Cockell, C.S., 2019. An ionic limit to life in the deep subsurface. Frontiers in Microbiology 10, 426. doi: 410.3389/fmicb.2019.00426.

Peoples, L.M., Grammatopoulou, E., Pombrol, M., Xu, X., Osuntokun, O., Blanton, J., Allen, E.E., Nunnally, C.C., Drazen, J.C., Mayor, D.J., Bartlett, D.H., 2019. Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology 10, 347. doi: 310.3389/fmicb.2019.00347.


Rincón-Molina, C.I., Hernández-García, J.A., Rincón-Rosales, R., Gutiérrez-Miceli, F.A., Ramírez-Villanueva, D.A., González-Terreros, E., Peña-Ocaña, B.A., Palomeque-Domínguez, H., Dendooven, L., Ruíz-Valdiviezo, V.M., 2019. Structure and diversity of the bacterial communities in the acid and thermophilic crater-lake of the volcano “El Chichón”, Mexico. Geomicrobiology Journal 36, 97-109.

Rojas-Jimenez, K., Rieck, A., Wurzbacher, C., Jürgens, K., Labrenz, M., Grossart, H.-P., 2019. A salinity threshold separating fungal communities in the Baltic Sea. Frontiers in Microbiology 10, 680. doi: 610.3389/fmicb.2019.00680.

Román, S., Ortiz-Álvarez, R., Romano, C., Casamayor, E.O., Martin, D., 2019. Microbial community structure and functionality in the deep sea floor: Evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain). Frontiers in Marine Science 6, 108. doi: 110.3389/fmars.2019.00108.


Souza, V., Moreno-Letelier, A., Travisano, M., Alcaraz, L.D., Olmedo, G., Eguiarte, L.E., 2018. The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis. eLife 7, Article e38278.


Wemheuer, F., von Hoyningen-Huene, A.J.E., Pohlner, M., Degenhardt, J., Engelen, B., Daniel, R., Wemheuer, B., 2019. Primary production in the water column as major structuring element of the biogeographical distribution and function of archaea in deep-sea sediments of the Central Pacific Ocean. Archaea 2019, Article 3717239,.

Winkler, P., Kaiser, K., Jahn, R., Mikutta, R., Fiedler, S., Cerli, C., Kölbl, A., Schulz, S., Jankowska, M., Schloter, M., Müller-Niggemann, C., Schwark, L., Woche, S.K., Kümmel, S., Utami, S.R., Kalbitz, K., 2019. Tracing organic carbon and microbial community structure in mineralogically different soils exposed to redox fluctuations. Biogeochemistry 143, 31-54.




PETROLEUM DEGRADERS

An, B.A., Shen, Y., Voordouw, J., Voordouw, G., 2019. Halophilic methylotrophic methanogens may contribute to the high ammonium concentrations found in shale oil and shale gas reservoirs. Frontiers in Energy Research 7, 23. doi: 10.3389/fenrg.2019.00023.



Fernandes, C., Kankonkar, H., Meena, R.M., Menezes, G., Shenoy, B.D., Khandeparker, R., 2019. Metagenomic analysis of tarball-associated bacteria from Goa, India. Marine Pollution Bulletin 141, 398-403.



Jiang, M.-z., Qiu, Z.-j., Zhang, G.-w., Gao, S.-y., You, X.-y., Ma, Y.-f., 2019. Mucilaginibacter xinganensis sp. nov., a phenanthrene-degrading bacterium isolated from wetland soil. Antonie van Leeuwenhoek 112, 641-649.



Luo, C., Wang, W., Zhang, H., Yu, X., Wang, G., 2019. Microbial treatment of waxy crude oil for mitigating wax precipitation and improving liquidity. Petroleum Science and Technology 37, 471-478.

Morono, Y., Wishart, J.R., Ito, M., Ijiri, A., Hoshino, T., Torres, M., Verba, C., Terada, T., Inagaki, F., Colwell, F.S., 2019. Microbial metabolism and community dynamics in hydraulic fracturing fluids recovered from deep hydrocarbon-rich shale. Frontiers in Microbiology 10, 376. doi: 310.3389/fmicb.2019.00376.

Potts, L.D., Perez Calderon, L.J., Gubry-Rangin, C., Witte, U., Anderson, J.A., 2019. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. Marine Pollution Bulletin 142, 169-177.


Song, Z., Chen, S., Zhao, F., Zhu, W., 2019. Whole metagenome of injected and produced fluids reveal the heterogenetic characteristics of the microbial community in a water-flooded oil reservoir. Journal of Petroleum Science and Engineering 176, 1198-1207.


Tena-Garitaonaindia, M., Llamas, I., Toral, L., Sampedro, I., 2019. Chemotaxis of halophilic bacterium Halomonas anticariensis FP35 towards the environmental pollutants phenol and naphthalene. Science of The Total Environment 669, 631-636.

Tianyuan, W., Li, Y., Jianlong, X., Lixin, H., Qingfeng, C., Yuandong, M., 2019. A mathematical model for microbial enhanced oil recovery considering the double-bacterial competition mechanism. Journal of Petroleum Science and Engineering 178, 336-343.




Zhou, Z., Liang, B., Wang, L.Y., Liu, J.F., Mu, B.Z., Shim, H., Gu, J.D., 2019. Identify the core bacterial microbiome of hydrocarbon degradation and a shift of dominant methanogenesis pathways in oil and aqueous phases of petroleum reservoirs with different temperatures from China. Biogeosciences Discussions 2019, 1-28.

Oil & Gas Exploration

Baig, I., Faleide, J.I., Mondol, N.H., Jahren, J., 2019. Burial and exhumation history controls on shale compaction and thermal maturity along the Norwegian North Sea basin margin areas. Marine and Petroleum Geology 104, 61-85.

Baniasad, A., Sachse, V., Littke, R., Soleimany, B., 2019. Burial, temperature and maturation history of Cretaceous source rocks in the Nw Persian Gulf, offshore SW Iran: 3D basin modelling. Journal of Petroleum Geology 42, 125-144.

Barabasch, J., Ducros, M., Hawie, N., Bou Daher, S., Nader, F.H., Littke, R., 2019. Integrated 3D forward stratigraphic and petroleum system modeling of the Levant Basin, Eastern Mediterranean. Basin Research 31, 228-252.

Bhattacharya, S., Carr, T.R., 2019. Integrated data-driven 3D shale lithofacies modeling of the Bakken Formation in the Williston basin, North Dakota, United States. Journal of Petroleum Science and Engineering 177, 1072-1086.

Galasso, F., Fernandes, P., Montesi, G., Marques, J., Spina, A., Pereira, Z., 2019. Thermal history and basin evolution of the Moatize - Minjova Coal Basin (N'Condédzi sub-basin, Mozambique) constrained by organic maturation levels. Journal of African Earth Sciences 153, 219-238.

Jones, D.J.R., McCarthy, D.J., Dodd, T.J.H., 2019. Tectonostratigraphy and the petroleum systems in the Northern sector of the North Falkland Basin, South Atlantic. Marine and Petroleum Geology 103, 150-162.


Luo, B., Xia, M., Wang, H., Fan, Y., Xu, L., Liu, R., Zhan, W., 2019. Hydrocarbon accumulation conditions of Permian volcanic gas reservoirs in the western Sichuan Basin. Natural Gas Industry 39, 9-16.

Ma, X., Yang, Y., Zhang, J., Xie, J., 2019. A major discovery in Permian volcanic rock gas reservoir exploration in the Sichuan Basin and its implications Natural Gas Industry 39, 1-8.

Omodeo-Salé, S., Ondrak, R., Arribas, J., Mas, R., Guimerà, J., Martínez, L., 2019. Petroleum systems modelling in a fold-and-thrust belt setting: The inverted Cameros Basin, north-central Spain. Journal of Petroleum Geology 42, 145-171.

Osli, L.N., Shalaby, M.R., Islam, M.A., 2019. Hydrocarbon generation modeling and source rock characterization of the Cretaceous–Paleocene Taratu Formation, Great South Basin, New Zealand. Journal of Petroleum Exploration and Production Technology 9, 125-139.

Peng, W., Liu, Q., Feng, Z., Fang, C., Gong, D., Li, P., Lyu, Y., Wang, P., 2019. First discovery and significance of liquid mercury in a thermal simulation experiment on humic kerogen. Energy & Fuels 33, 1817-1824.

Oil & Gas Generation/Expulsion

Bai, F., Zhao, J., Liu, Y., 2019. An investigation into the characteristics and kinetics of oil shale oxy-fuel combustion by thermogravimetric analysis. Oil Shale 36, 1–18.

Chang, Z., Chu, M., 2019. The chemical composition and pyrolysis characteristics of thermal bitumen derived from pyrolyzing Huadian oil shale, China. Oil Shale 36, 62–75.

Liu, Q., Zhu, D., Meng, Q., Liu, J., Wu, X., Zhou, B., Fu, Q., Jin, Z., 2019. The scientific connotation of oil and gas formations under deep fluids and organic-inorganic interaction. Science China Earth Sciences 62, 507-528.

Lu, Z., Zhao, X., Liu, Z., Liu, Q., 2019. Mutual influences between organic matter and minerals during oil shale pyrolysis. Energy & Fuels 33, 1850-1858.

Ping, H., Chen, H., George, S.C., Li, C., Hu, S., 2019. Relationship between the fluorescence colour of oil inclusions and thermal maturity in the Dongying Depression, Bohai Bay Basin, China: Part 2. Fluorescence evolution of oil in the context of petroleum generation, expulsion and cracking under geological conditions. Marine and Petroleum Geology 103, 306-319.

Vakhin, A.V., Onishchenko, Y.V., Chemodanov, A.E., Sitnov, S.A., Mukhamatdinov, I.I., Nazimov, N.A., Sharifullin, A.V., 2019. The composition of aromatic destruction products of Domanic shale kerogen after aquathermolysis. Petroleum Science and Technology 37, 390-395.

Veski, R., Veski, S., 2019. Aliphatic dicarboxylic acids from oil shale organic matter ‒ historic review. Oil Shale 36, 76–95.

Wu, L., Horsfield, B., 2019. Initial insights into releasing bound biomarkers from kerogen matrices using microscale sealed vessel catalytic hydrogenation (MSSV-HY). Organic Geochemistry 130, 22-32.

Wu, L., Wang, P., Geng, A., 2019. Later stage gas generation in shale gas systems based on pyrolysis in closed and semi-closed systems. International Journal of Coal Geology 206, 80-90.


You, Y., Wang, X., Han, X., Jiang, X., 2019. Kerogen pyrolysis model based on its chemical structure for predicting product evolution. Fuel 246, 149-159.

Zhang, Z., Zhao, L., Zhuang, L., Li, Y., Zhang, H., 2019. The effect of acid treatment on pyrolysis of Longkou oil shale. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 1605-1614.

Oil & Gas Geochemistry

Agyingi, C.M., Abanda, P.A., Fozao, K.F., Njoh, O.A., Epanty, A.F., Tangko, N.C., Kwangkam, F.N., Eseme, E., 2019. Geochemistry of seep and produced oil samples from southern Cameroon. Journal of Petroleum Geology 42, 193-206.

Bai, Y., Zhang, H., 2019. Organic geochemistry characterization of the Yan 9 crude oils and oil-source rock correlations in Jingbian Oil Field, Ordos Basin. Petroleum Science and Technology 37, 543-550.

Barakat, A.O., Mostafa, A.R., El-Gayar, M.S., Omar, M.F., 2019. Organic geochemical characterization of crude oils based on alkanes and acyclic isoprenoids distribution. Petroleum Science and Technology 37, 243-254.

Cheng, X., Hou, D., Zhao, Z., Chen, X., Diao, H., 2019. Sources of natural gases in the Xihu sag, East China Sea Basin: Insights from stable carbon isotopes and confined system pyrolysis. Energy & Fuels 33, 2166-2175.

Ellis, G.S., Zhang, T., Kralert, P.G., Tang, Y., 2019. Kinetics of elemental sulfur reduction by petroleum hydrocarbons and the implications for hydrocarbon thermal chemical alteration. Geochimica et Cosmochimica Acta 251, 192-216.

Faboya, O.L., Sonibare, O.O., Liao, Z., 2019. Biomarkers and isotopic characteristics of crude oils from a central Niger delta depobelt field, Nigeria. Petroleum Science and Technology 37, 346-353.

Ganeeva, Y.M., Barskaya, E.E., Okhotnikova, E.S., Timirgalieva, A.H., Yusupova, T.N., 2019. Study of hydrocarbons adsorbed in asphaltenes of Domanic Formation bitumoid. Petroleum Science and Technology 37, 479-485.

Hakimi, M.H., Alaug, A.S., Alramisy, G.A., Ahmed, A.F., 2019. Petroleum that has migrated into an outcropping of the Jurassic Ayad Salt Dome of Shabwah depression, Yemen. Petroleum Science and Technology 37, 296-304.


Han, Y., John, G.F., Clement, T.P., 2019. Understanding the thermal degradation patterns of hopane biomarker compounds present in crude oil. Science of The Total Environment 667, 792-798.

Hao, G., Shan, X., Li, F., Tong, L., Liu, Y., Wang, S., Zhang, J., Zhao, C., 2019. Characteristics of geochemistry and biodegradation for oil sand extracts in western slope of Songliao Basin Acta Petrolei Sinica 40, 308-321.

Huo, F., Wang, X., Xu, Z., Huang, H., Li, J., 2019. Characteristics and genesis of the Ordovician crude oil in the RePu area, Halahatang sag, Tarim Basin, China. Petroleum Science and Technology 37, 581-588.

Kara-Gülbay, R., Korkmaz, S., Erdoğan, M.S., Kadınkız, G., 2019. Biomarker geochemistry of crude oils and Neogene bituminous shales in the Yeniköy area, Ereğli-Ulukișla Basin, Central Anatolia, Turkey. Journal of Petroleum Geology 42, 173-191.

Kayukova, G.P., Kosachev, I.P., Mikhailova, A.N., Vakhin, A.V., Isakov, D.R., 2019. Hydrothermal transformation of heavy oil and organic matter from carbonate rocks of oil fields of Tatarstan. Petroleum Science and Technology 37, 528-534.

Lakhova, A., Soldatova, R., Petrov, S., Nosova, A., Safiulina, A., 2019. Transformation of heavy oil in hydrothermal impact. Petroleum Science and Technology 37, 611-616.



Li, X., Wu, B., 2019. Understanding to the composition and structure of organic chlorides in petroleum and its distillates. Petroleum Science and Technology 37, 119-126.


Lin, Y.-J., Cao, T., Chacón-Patiño, M.L., Rowland, S.M., Rodgers, R.P., Yen, A., Biswal, S.L., 2019. Microfluidic study of the deposition dynamics of asphaltene subfractions enriched with island and archipelago motifs. Energy & Fuels 33, 1882-1891.


Małachowska, A., Mastalerz, M., Hampton, L., Hupka, J., Drobniak, A., 2019. Origin of bitumen fractions in the Jurassic-early Cretaceous Vaca Muerta Formation in Argentina: insights from

organic petrography and geochemical techniques. International Journal of Coal Geology 205, 155-165.

Mikhailova, A.N., Kayukova, G.P., Vakhin, A.V., Eskin, A.A., Vandyukova, I.I., 2019. Composition features of hydrocarbons and rocks of Domanic deposits of different oil fields in the Tatarstan territory. Petroleum Science and Technology 37, 374-381.

Mou, W., Zhang, Z., Li, S., Yan, C., Guo, R., Zhang, J., Li, S., 2019. The application of sterane in the oil-sources correlation of near-source and multi-source: a case study of CH-8 oil reservoir in Central Ordos Basin, China. Petroleum Science and Technology 37, 701-709.

Roy, P.S., Ryu, C., Dong, S.K., Park, C.S., 2019. Development of a natural gas methane number prediction model. Fuel 246, 204-211.




Xiao, H., Li, M., Liu, J., Mao, F., Cheng, D., Yang, Z., 2019. Oil-oil and oil-source rock correlations in the Muglad Basin, Sudan and South Sudan: New insights from molecular markers analyses. Marine and Petroleum Geology 103, 351-365.

Xiao, Q., Sun, Y., He, S., Liu, J., Zhu, C., 2019. Thermal stability of 2-thiadiamondoids determined by pyrolysis experiments in a closed system and its geochemical implications. Organic Geochemistry 130, 14-21.

Zhou, X., Gao, G., Lü, X., Zhao, L., Dong, Y., Xu, X., Gan, J., 2019. Petroleum source and accumulation of WZ12 oils in the Weixi'nan sag, south China sea, China. Journal of Petroleum Science and Engineering 177, 681-698.


Paleoclimatology/Paleoceanography


Ausín, B., Magill, C., Haghipour, N., Fernández, Á., Wacker, L., Hodell, D., Baumann, K.-H., Eglinton, T.I., 2019. (In)coherent multiproxy signals in marine sediments: Implications for high-resolution paleoclimate reconstruction. Earth and Planetary Science Letters 515, 38-46.

Azmy, K., 2019. Carbon-isotope stratigraphy of the uppermost Cambrian in eastern Laurentia: implications for global correlation. Geological Magazine 156, 759-771.

Botsyun, S., Sepulchre, P., Donnadieu, Y., Risi, C., Licht, A., Caves Rugenstein, J.K., 2019. Revised paleoaltimetry data show low Tibetan Plateau elevation during the Eocene. Science 363, Article eaaq1436.

Chen, J., Zhao, L., Algeo, T.J., Zhou, L., Zhang, L., Qiu, H., 2019. Evaluation of paleomarine redox conditions using Mo-isotope data in low-[Mo] sediments: A case study from the Lower Triassic of South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 178-193.

de Bar, M.W., Dorhout, D.J.C., Hopmans, E.C., Rampen, S.W., Sinninghe Damsté, J.S., Schouten, S., 2019. Corrigendum to “Constraints on the application of long chain diol proxies in the Iberian Atlantic margin” [Org. Geochem. 101 (2016) 184–195]. Organic Geochemistry 130, 51-52.

Fung, M.K., Schaller, M.F., Hoff, C.M., Katz, M.E., Wright, J.D., 2019. Widespread and intense wildfires at the Paleocene-Eocene boundary. Geochemical Perspectives Letters 10, 1-6.

Gal, J.-K., Kim, J.-H., Kim, S., Lee, S.H., Yoo, K.-C., Shin, K.-H., 2019. Application of the newly developed nutrient diol index (NDI) as a sea surface nutrient proxy in the East Sea for the last 240 years. Quaternary International 503, 146-152.

Hasenfratz, A.P., Jaccard, S.L., Martínez-García, A., Sigman, D.M., Hodell, D.A., Vance, D., Bernasconi, S.M., Kleiven, H.F., Haumann, F.A., Haug, G.H., 2019. The residence time of Southern Ocean surface waters and the 100,000-year ice age cycle. Science 363, 1080-1084.

Hay, W.W., DeConto, R.M., de Boer, P., Flögel, S., Song, Y., Stepashko, A., 2019. Possible solutions to several enigmas of Cretaceous climate. International Journal of Earth Sciences 108, 587-620.

Hennhoefer, D., Al Suwaidi, A., Bottini, C., Helja, E., Steuber, T., 2019. The Albian to Turonian carbon isotope record from the Shilaif Basin (United Arab Emirates) and its regional and intercontinental correlation. Sedimentology 66, 536-555.

Li, H., Yu, J., McElwain, J.C., Yiotis, C., Chen, Z.-Q., 2019. Reconstruction of atmospheric CO2

concentration during the late Changhsingian based on fossil conifers from the Dalong Formation in South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 37-48.

Li, M., Hinnov, L., Kump, L., 2019. Acycle: Time-series analysis software for paleoclimate research and education. Computers & Geosciences 127, 12-22.

Li, M., Huang, C., Ogg, J., Zhang, Y., Hinnov, L., Wu, H., Chen, Z.-Q., Zou, Z., 2019. Paleoclimate proxies for cyclostratigraphy: Comparative analysis using a Lower Triassic marine section in South China. Earth-Science Reviews 189, 125-146.

McNeill, L.C., Shillington, D.J., Carter, G.D.O., Everest, J.D., Gawthorpe, R.L., Miller, C., Phillips, M.P., Collier, R.E.L., Cvetkoska, A., De Gelder, G., Diz, P., Doan, M.-L., Ford, M., Geraga, M., Gillespie, J., Hemelsdaël, R., Herrero-Bervera, E., Ismaiel, M., Janikian, L., Kouli, K., Le Ber, E., Li, S., Maffione, M., Mahoney, C., Machlus, M.L., Michas, G., Nixon, C.W., Oflaz, S.A., Omale, A.P., Panagiotopoulos, K., Pechlivanidou, S., Sauer, S., Seguin, J., Sergiou, S., Zakharova, N.V., Green, S., 2019. High-resolution record reveals climate-driven environmental and sedimentary changes in an active rift. Scientific Reports 9, Article 3116.

Meng, F.-W., Zhang, Z.-l., Yan, X.-q., Ni, P., Liu, W.-H., Fan, F., Xie, G.-W., 2019. Stromatolites in Middle Ordovician carbonate–evaporite sequences and their carbon and sulfur isotopes stratigraphy, Ordos Basin, northwestern China. Carbonates and Evaporites 34, 11-20.

Muschitiello, F., D’Andrea, W.J., Schmittner, A., Heaton, T.J., Balascio, N.L., deRoberts, N., Caffee, M.W., Woodruff, T.E., Welten, K.C., Skinner, L.C., Simon, M.H., Dokken, T.M., 2019. Deep-water circulation changes lead North Atlantic climate during deglaciation. Nature Communications 10, Article 1272.

Oksman, M., Juggins, S., Miettinen, A., Witkowski, A., Weckström, K., 2019. The biogeography and ecology of common diatom species in the northern North Atlantic, and their implications for paleoceanographic reconstructions. Marine Micropaleontology 148, 1-28.

Penman, D.E., Keller, A., D'Haenens, S., Kirtland Turner, S., Hull, P.M., 2019. Atlantic deep-sea cherts associated with Eocene hyperthermal events. Paleoceanography and Paleoclimatology 34, 287-299.

Reynolds, D.J., Hall, I.R., Slater, S.M., 2019. An integrated carbon and oxygen isotope approach to reconstructing past environmental variability in the northeast Atlantic Ocean. Palaeogeography, Palaeoclimatology, Palaeoecology 523, 48-61.

Salacup, J.M., Farmer, J.R., Herbert, T.D., Prell, W.L., 2019. Alkenone paleothermometry in coastal settings: Evaluating the potential for highly resolved time series of sea surface temperature. Paleoceanography and Paleoclimatology 34, 164-181.

Schreuder, L.T., Hopmans, E.C., Castañeda, I.S., Schefuß, E., Mulitza, S., Sinninghe Damsté, J.S., Schouten, S., 2019. Late Quaternary biomass burning in Northwest Africa and interactions with climate, vegetation, and humans. Paleoceanography and Paleoclimatology 34, 153-163.

Scorrer, S., Azmy, K., Stouge, S., 2018. Carbon-isotope stratigraphy of the Furongian Berry Head Formation (Port au Port Group) and Tremadocian Watts Bight Formation (St. George Group), western Newfoundland, and the correlative significance. Canadian Journal of Earth Sciences 56, 223-234.

Sluijs, A., Peterse, F., Middelburg, J.J., Cramwinckel, M.J., Bijl, P.K., van der Ploeg, R., Schouten, S., Bohaty, S.M., Röhl, U., 2019. Harmful algae and export production collapse in the equatorial Atlantic during the zenith of Middle Eocene Climatic Optimum warmth. Geology 47, 247-250.

Szymczak-Żyła, M., Krajewska, M., Witak, M., Ciesielski, T.M., Ardelan, M.V., Jenssen, B.M., Goslar, T., Winogradow, A., Filipkowska, A., Lubecki, L., Zamojska, A., Kowalewska, G., 2019. Present and past-millennial eutrophication in the Gulf of Gdańsk (southern Baltic Sea). Paleoceanography and Paleoclimatology 34, 136-152.

Turney, C.S.M., McGregor, H.V., Francus, P., Abram, N., Evans, M.N., Goosse, H., von Gunten, L., Kaufman, D., Linderholm, H., Loutre, M.F., Neukom, R., 2019. Introduction to the special issue “Climate of the past 2000 years: regional and trans-regional syntheses”. Climate of the Past 15, 611-615.

Vasiliev, I., Karakitsios, V., Bouloubassi, I., Agiadi, K., Kontakiotis, G., Antonarakou, A., Triantaphyllou, M., Gogou, A., Kafousia, N., de Rafélis, M., Zarkogiannis, S., Kaczmar, F., Parinos, C., Pasadakis, N., 2019. Large sea surface temperature, salinity, and productivity-

preservation changes preceding the onset of the Messinian Salinity Crisis in the eastern Mediterranean Sea. Paleoceanography and Paleoclimatology 34, 182-202.

Weiss, A.M., Martindale, R.C., 2019. Paleobiological traits that determined scleractinian coral survival and proliferation during the Late Paleocene and Early Eocene hyperthermals. Paleoceanography and Paleoclimatology 34, 252-274.

Yang, Y., Zhang, D., Lan, B., Abdusalih, N., Feng, Z., 2019. Peat δ13Ccelluose-signified moisture variations over the past ∼2200 years in the southern Altai Mountains, northwestern China. Journal of Asian Earth Sciences 174, 59-67.

Yi, H., Xia, G., Li, G., Yi, F., Zhang, S., Cai, Z., Jiao, H., Wu, C., 2019. The carbon isotope fluctuations across the Lower–Middle Jurassic boundary and the paleoclimate changes. Acta Geologica Sinica - English Edition 93, 244-245.

Zeng, F., Yang, H., 2019. Temperature changes reconstructed from branched GDGTs on the central Loess Plateau during the past 130–5 ka. Quaternary International 503, 3-9.

EXTINCTION EVENTS

Cao, Y., Song, H., Algeo, T.J., Chu, D., Du, Y., Tian, L., Wang, Y., Tong, J., 2019. Intensified chemical weathering during the Permian-Triassic transition recorded in terrestrial and marine successions. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 166-177.

Chen, J., Song, H., He, W., Tong, J., Wang, F., Wu, S., 2019. Size variation of brachiopods from the Late Permian through the Middle Triassic in South China: Evidence for the Lilliput Effect following the Permian-Triassic extinction. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 248-257.

Chen, Z.-Q., Algeo, T.J., Schoepfer, S.D., 2019. The Permian–Triassic transition in the eastern Paleo-Tethys and adjacent regions: Environmental and biotic changes in ocean and on land. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 1-7.

Chiarenza, A.A., Mannion, P.D., Lunt, D.J., Farnsworth, A., Jones, L.A., Kelland, S.-J., Allison, P.A., 2019. Ecological niche modelling does not support climatically-driven dinosaur diversity decline before the Cretaceous/Paleogene mass extinction. Nature Communications 10, Article 1091.

Chu, D., Tong, J., Benton, M.J., Yu, J., Huang, Y., 2019. Mixed continental-marine biotas following the Permian-Triassic mass extinction in South and North China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 95-107.

Faggetter, L.E., Wignall, P.B., Pruss, S.B., Jones, D.S., Grasby, S., Widdowson, M., Newton, R.J., 2019. Mercury chemostratigraphy across the Cambrian Series 2 – Series 3 boundary: evidence for increased volcanic activity coincident with extinction? Chemical Geology 510, 188-199.

Feng, X., Chen, Z.-Q., Benton, M.J., Wu, S., Bottjer, D.J., Thompson, J.R., 2019. A diverse trackway-dominated marine ichnoassemblage from the Lower Triassic in the northern Paleotethys: Ichnology and implications for biotic recovery. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 124-140.

Feng, X., Chen, Z.-Q., Bottjer, D.J., Wu, S., Zhao, L., Xu, Y., Shi, G.R., Huang, Y., Fang, Y., Tu, C., 2019. Unusual shallow marine matground-adapted benthic biofacies from the Lower Triassic of the northern Paleotethys: Implications for biotic recovery following the end-Permian mass extinction. Earth-Science Reviews 189, 194-219.

Fu, X., Wang, J., Song, C., Wang, Z., Zeng, S., Wang, D., 2019. The Permian-Triassic transition in ocean island setting: Environmental disturbances and new high-resolution carbon-isotope record from the Qiangtang Basin, NW China. Palaeogeography, Palaeoclimatology, Palaeoecology 522, 40-51.

Gastaldo, R.A., 2019. Ancient plants escaped the end-Permian mass extinction. Nature 567, 38-39.

Gastaldo, R.A., Neveling, J., Geissman, J.W., Li, J., 2019. A multidisciplinary approach to review the vertical and lateral facies relationships of the purported vertebrate-defined terrestrial Permian–Triassic boundary interval at Bethulie, Karoo Basin, South Africa. Earth-Science Reviews 189, 220-243.

Hart, M.B., Leighton, A.D., Hampton, M., Smart, C.W., 2019. Global bioevents and the Cretaceous/Paleogene boundary in Texas and Alabama: Stratigraphy, correlation and ocean acidification. Global and Planetary Change 175, 129-143.

Hong, H., Zhao, L., Fang, Q., Algeo, T.J., Wang, C., Yu, J., Gong, N., Yin, K., Ji, K., 2019. Volcanic sources and diagenetic alteration of Permian–Triassic boundary K-bentonites in Guizhou Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 141-153.

Huang, Y., Chen, Z.-Q., Zhao, L., Stanley, G.D., Yan, J., Pei, Y., Yang, W., Huang, J., 2019. Restoration of reef ecosystems following the Guadalupian–Lopingian boundary mass extinction: Evidence from the Laibin area, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 8-22.

Ji, C., Wu, Z., Fang, C., Yi, H., Xia, G., 2019. High temperature, high reducibility and low productivity of the paleoceanographic environment in the P/T, Tethys. Acta Geologica Sinica - English Edition 93, 248-249.

Lei, Y., Shen, J., Algeo, T.J., Servais, T., Feng, Q., Yu, J., 2019. Phytoplankton (acritarch) community changes during the Permian-Triassic transition in South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 84-94.

Lyu, Z., Orchard, M.J., Chen, Z.-Q., Wang, X., Zhao, L., Han, C., 2019. Uppermost Permian to Lower Triassic conodont successions from the Enshi area, western Hubei Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 49-64.

MacDougall, M.J., Brocklehurst, N., Fröbisch, J., 2019. Species richness and disparity of parareptiles across the end-Permian mass extinction. Proceedings of the Royal Society B: Biological Sciences 286, Article 20182572.

Muscente, A.D., Bykova, N., Boag, T.H., Buatois, L.A., Mángano, M.G., Eleish, A., Prabhu, A., Pan, F., Meyer, M.B., Schiffbauer, J.D., Fox, P., Hazen, R.M., Knoll, A.H., 2019. Ediacaran biozones identified with network analysis provide evidence for pulsed extinctions of early complex life. Nature Communications 10, Article 911.

Pavlov, V.E., Fluteau, F., Latyshev, A.V., Fetisova, A.M., Elkins-Tanton, L.T., Black, B.A., Burgess, S.D., Veselovskiy, R.V., 2019. Geomagnetic secular variations at the Permian-Triassic boundary and pulsed magmatism during eruption of the Siberian Traps. Geochemistry, Geophysics, Geosystems 20, 773-791.

Pei, Y., Chen, Z.-Q., Fang, Y., Kershaw, S., Wu, S., Luo, M., 2019. Volcanism, redox conditions, and microbialite growth linked with the end-Permian mass extinction: Evidence from the Xiajiacao section (western Hubei Province), South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 194-208.

Pino, M., Abarzúa, A.M., Astorga, G., Martel-Cea, A., Cossio-Montecinos, N., Navarro, R.X., Lira, M.P., Labarca, R., LeCompte, M.A., Adedeji, V., Moore, C.R., Bunch, T.E., Mooney, C., Wolbach, W.S., West, A., Kennett, J.P., 2019. Sedimentary record from Patagonia, southern Chile supports cosmic-impact triggering of biomass burning, climate change, and megafaunal extinctions at 12.8 ka. Scientific Reports 9, Article 4413.

Roopnarine, P.D., Angielczyk, K.D., Weik, A., Dineen, A., 2019. Ecological persistence, incumbency and reorganization in the Karoo Basin during the Permian-Triassic transition. Earth-Science Reviews 189, 244-263.

Smolarek-Lach, J., Marynowski, L., Trela, W., Wignall, P.B., 2019. Mercury spikes indicate a volcanic trigger for the Late Ordovician mass extinction event: An example from a deep shelf of the Peri-Baltic region. Scientific Reports 9, Article 3139.

Soliman, A., Slimani, H., 2019. The Cretaceous–Paleogene (K/Pg) boundary in the Dababiya Borehole, southern Egypt: An organic-walled dinoflagellate cyst approach. Cretaceous Research 98, 230-249.

Song, T., Tong, J., Tian, L., Chu, D., Huang, Y., 2019. Taxonomic and ecological variations of Permian-Triassic transitional bivalve communities from the littoral clastic facies in southwestern China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 108-123.

Tian, L., Tong, J., Xiao, Y., Benton, M.J., Song, H., Song, H., Liang, L., Wu, K., Chu, D., Algeo, T.J., 2019. Environmental instability prior to end-Permian mass extinction reflected in biotic and facies changes on shallow carbonate platforms of the Nanpanjiang Basin (South China). Palaeogeography, Palaeoclimatology, Palaeoecology 519, 23-36.

Wang, G., Zhan, R., Percival, I.G., 2019. The end-Ordovician mass extinction: A single-pulse event? Earth-Science Reviews 192, 15-33.

Wang, T., Burne, R.V., Yuan, A., Wang, Y., Yi, Z., 2019. The evolution of microbialite forms during the Early Triassic transgression: A case study in Chongyang of Hubei Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 209-220.

Wang, X., Cawood, P.A., Zhao, H., Zhao, L., Grasby, S.E., Chen, Z.-Q., Zhang, L., 2019. Global mercury cycle during the end-Permian mass extinction and subsequent Early Triassic recovery. Earth and Planetary Science Letters 513, 144-155.

Wang, X., Cawood, P.A., Zhao, L., Chen, Z.-Q., Lyu, Z., Ma, B., 2019. Convergent continental margin volcanic source for ash beds at the Permian-Triassic boundary, South China: Constraints from trace elements and Hf-isotopes. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 154-165.

Young, S.A., Kleinberg, A., Owens, J.D., 2019. Geochemical evidence for expansion of marine euxinia during an early Silurian (Llandovery–Wenlock boundary) mass extinction. Earth and Planetary Science Letters 513, 187-196.

Precambrian Geochemistry

Fru, E.C., Somogyi, A., Medjoubi, K., El Albani, A., Aubineau, J., Konhauser, K.O., Robbins, L.J., Lalonde, S.V., 2019. The rise of oxygen-driven arsenic cycling at ca. 2.48 Ga. Geology 47, 243-246.

Kreitsmann, T., Külaviir, M., Lepland, A., Paiste, K., Paiste, P., Prave, A.R., Sepp, H., Romashkin, A.E., Rychanchik, D.V., Kirsimäe, K., 2019. Hydrothermal dedolomitisation of carbonate rocks of the Paleoproterozoic Zaonega Formation, NW Russia — Implications for the preservation of primary C isotope signals. Chemical Geology 512, 43-57.

Prince, J.K.G., Rainbird, R.H., Wing, B.A., 2019. Evaporite deposition in the mid-Neoproterozoic as a driver for changes in seawater chemistry and the biogeochemical cycle of sulfur. Geology 47, 375-379.


Wang, S.-J., Rudnick, R.L., Gaschnig, R.M., Wang, H., Wasylenki, L.E., 2019. Methanogenesis sustained by sulfide weathering during the Great Oxidation Event. Nature Geoscience 12, 296-300.

ORGANICS/MICROFOSSILS/MICROBIAL EVOLUTION


Liu, J., Zhou, Z., Liu, X., Ren, S., Wang, J., Wang, H., Zhou, C.a., Liu, Y., 2019. Geological conditions of the Mesoproterozoic shale gas accumulation in Yanshan area, North China Acta Petrolei Sinica 40, 268-278.

Liu, Q., Zhu, D., Jin, Z., Meng, Q., Li, S., 2019. Influence of volcanic activities on redox chemistry changes linked to the enhancement of the ancient Sinian source rocks in the Yangtze craton. Precambrian Research 327, 1-13.

Muscente, A.D., Bykova, N., Boag, T.H., Buatois, L.A., Mángano, M.G., Eleish, A., Prabhu, A., Pan, F., Meyer, M.B., Schiffbauer, J.D., Fox, P., Hazen, R.M., Knoll, A.H., 2019.

Ediacaran biozones identified with network analysis provide evidence for pulsed extinctions of early complex life. Nature Communications 10, Article 911.

Rooney, A.D., Penman, D.E., 2019. Coupled carbon and silica cycle perturbations during the Marinoan snowball Earth deglaciation. Geology 47, 317-320.

Sharma, M., Shukla, B., 2019. Akinetes from Late Paleoproterozoic Salkhan Limestone (>1600 Ma) of India: A proxy for understanding life in extreme conditions. Frontiers in Microbiology 10, 397. doi: 310.3389/fmicb.2019.0039.

Strbak, O., Dobrota, D., 2019. Archean iron-based metabolism analysis and the photoferrotrophy-driven hypothesis of microbial magnetotaxis origin. Geomicrobiology Journal 36, 278-290.

PALEOCLIMATOLOGY/PALEOCEANOGRAPHY

George, B.G., Ray, J.S., Kumar, S., 2018. Geochemistry of carbonate formations of the Chhattisgarh Supergroup, central India: implications for Mesoproterozoic global events. Canadian Journal of Earth Sciences 56, 335-346.

Ostrander, C.M., Nielsen, S.G., Owens, J.D., Kendall, B., Gordon, G.W., Romaniello, S.J., Anbar, A.D., 2019. Fully oxygenated water columns over continental shelves before the Great Oxidation Event. Nature Geoscience 12, 186-191.


Spalding, C., Fischer, W.W., 2019. A shorter Archean day-length biases interpretations of the early Earth's climate. Earth and Planetary Science Letters 514, 28-36.

Sundman, A., Koeksoy, E., Byrne, J.M., Kappler, A., Planer-Friedrich, B., Lohmayer, R., Halevy, I., Konhauser, K.O., 2019. Formation of green rust and elemental sulfur in an analogue for oxygenated ferro-euxinic transition zones of Precambrian oceans. Geology 47, 211-214.

Zhou, C., Lang, X., Huyskens, M.H., Yin, Q.-Z., Xiao, S., 2019. Calibrating the terminations of Cryogenian global glaciations. Geology 47, 251-254.

CRUSTAL EVOLUTION

Hartnady, M.I.H., Kirkland, C.L., 2019. A gradual transition to plate tectonics on Earth between 3.2 to 2.7 billion years ago. Terra Nova 31, 129-134.

Production/Engineering Geochemistry


Dąbrowski, K.M., Kuczyński, S., Barbacki, J., Włodek, T., Smulski, R., Nagy, S., 2019. Downhole measurements and determination of natural gas composition using Raman spectroscopy. Journal of Natural Gas Science and Engineering 65, 25-31.

Feng, S., Cui, C., Li, K., Zhang, L., Shi, Q., Zhao, S., Xu, C., 2019. Molecular composition modelling of petroleum fractions based on a hybrid structural unit and bond-electron matrix (SU-BEM) framework. Chemical Engineering Science 201, 145-156.

Fustic, M., Strobl, R., Fowler, M., Jablonski, B.V., Martinius, A.W., 2019. Impact of reservoir heterogeneity on oil migration and the origin of oil-water contacts: McMurray Formation type section, Alberta, Canada. Marine and Petroleum Geology 103, 216-230.

Hu, Z., Gao, H., Ramisetti, S.B., Zhao, J., Nourafkan, E., Glover, P.W.J., Wen, D., 2019. Carbon quantum dots with tracer-like breakthrough ability for reservoir characterization. Science of The Total Environment 669, 579-589.



Schüth, F., 2019. Making more from methane. Science 363, 1282-1283.


Stratiev, D., Shishkova, I., Tankov, I., Pavlova, A., 2019. Challenges in characterization of residual oils. A review. Journal of Petroleum Science and Engineering 178, 227-250.

Sun, Y., Kang, S., Wang, S., He, L., Guo, W., Li, Q., Deng, S., 2019. Subcritical water extraction of Huadian oil shale at 300 °C. Energy & Fuels 33, 2106-2114.


Xue, X., Jiang, H., Ouyang, F., Zhou, X., 2019. Molecular reconstruction of naphtha by maximum information entropy method. Petroleum Science and Technology 37, 535-542.


ASPHALTENES

Dong, X., Zhang, Y., Milton, J., Yerabolu, R., Easterling, L., Kenttämaa, H.I., 2019. Investigation of the relative abundances of single-core and multicore compounds in asphaltenes by using high-resolution in-source collision-activated dissociation and medium-energy collision-activated dissociation mass spectrometry with statistical considerations. Fuel 246, 126-132.

Jiang, B., Zhang, R., Yang, N., Zhang, L., Sun, Y., 2019. Asphaltene aggregation and assembly behaviors in organic solvents with water and inhibitor. Energy & Fuels 33, 1955-1968.


McKenna, A.M., Chacón-Patiño, M.L., Weisbrod, C.R., Blakney, G.T., Rodgers, R.P., 2019. Molecular-level characterization of asphaltenes isolated from distillation cuts. Energy & Fuels 33, 2018-2029.


Raj, G., Larkin, E., Lesimple, A., Commins, P., Whelan, J., Naumov, P., 2019. In situ monitoring of the inhibition of asphaltene adsorption by a surfactant on carbon steel surface. Energy & Fuels 33, 2030-2036.

Rezvani, H., Kazemzadeh, Y., Sharifi, M., Riazi, M., Shojaei, S., 2019. A new insight into Fe3O4-based nanocomposites for adsorption of asphaltene at the oil/water interface: An experimental interfacial study. Journal of Petroleum Science and Engineering 177, 786-797.

Syed, F.I., Boukhatem, M., Al Kiyoumi, A.A., 2019. Lean HC gas injection pilots analysis and IPR back calculation to examine the impact of asphaltene deposition on flow performance. Petroleum Research 4, 84-95.

Taheri-Shakib, J., Hosseini, S.A., Kazemzadeh, E., Keshavarz, V., Rajabi-Kochi, M., Naderi, H., 2019. Experimental and mathematical model evaluation of asphaltene fractionation based on adsorption in porous media: Dolomite reservoir rock. Fuel 245, 570-585.

Tirjoo, A., Bayati, B., Rezaei, H., Rahmati, M., 2019. Molecular dynamics simulations of asphaltene aggregation under different conditions. Journal of Petroleum Science and Engineering 177, 392-402.


Yaseen, S., Mansoori, G.A., 2019. Microscopic details of asphaltenes aggregation onset during waterflooding. Petroleum Science and Technology 37, 573-580.

INTERFACES/EOR

Al-Otaibi, F.M., Zhou, X., Kokal, S.L., 2019. Laboratory evaluation of different modes of supercritical carbon dioxide miscible flooding for carbonate rocks. SPE Reservoir Evaluation & Engineering 22, 137-149.

Alqam, M.H., Abu-Khamsin, S.A., Sultan, A.S., Okasha, T.M., Yildiz, H.O., 2019. Effect of rock mineralogy and oil composition on wettability alteration and interfacial tension by brine and carbonated water. Energy & Fuels 33, 1983-1989.

Bayestehparvin, B., Farouq Ali, S.M., Abedi, J., 2019. Solvent-based and solvent-assisted recovery processes: State of the art. SPE Reservoir Evaluation & Engineering 22, 29-49.

Ding, M., Wang, Y., Wang, Y., Gao, M., Liu, D., Chen, W., 2019. Experimental investigation of bypassed-oil recovery via CO2 soaking and huff and puff injection: Effects of miscibility and bypassed-oil size. Fuel 248, 152-160.

Druetta, P., Picchioni, F., 2019. Polymer and nanoparticles flooding as a new method for Enhanced Oil Recovery. Journal of Petroleum Science and Engineering 177, 479-495.

Guo, K., Lv, Y., He, L., Luo, X., Yang, D., 2019. Separation characteristics of water-in-oil emulsion under the coupling of electric field and magnetic field. Energy & Fuels 33, 2565-2574.

Jahanbani Veshareh, M., Ganji Azad, E., Deihimi, T., Niazi, A., Ayatollahi, S., 2019. Isolation and screening of Bacillus subtilis MJ01 for MEOR application: biosurfactant characterization, production optimization and wetting effect on carbonate surfaces. Journal of Petroleum Exploration and Production Technology 9, 233-245.

Mansour, E.M., Al-Sabagh, A.M., Desouky, S.M., Zawawy, F.M., Ramzi, M., 2019. A laboratory investigation of carbon dioxide-enhanced oil recovery by focusing on CO2-oil physical properties. Egyptian Journal of Petroleum 28, 21-26.

Mohajeri, M., Reza Rasaei, M., Hekmatzadeh, M., 2019. Experimental study on using SiO2 nanoparticles along with surfactant in an EOR process in micromodel. Petroleum Research 4, 59-70.

Pang, S., Pu, W., Xie, J., Chu, Y., Wang, C., Shen, C., 2019. Investigation into the properties of water-in-heavy oil emulsion and its role in enhanced oil recovery during water flooding. Journal of Petroleum Science and Engineering 177, 798-807.

Phukan, R., Gogoi, S.B., Tiwari, P., 2019. Enhanced oil recovery by alkaline-surfactant-alternated-gas/CO2 flooding. Journal of Petroleum Exploration and Production Technology 9, 247-260.

Ren, B., Duncan, I., 2019. Modeling oil saturation evolution in residual oil zones: Implications for CO2 EOR and sequestration. Journal of Petroleum Science and Engineering 177, 528-539.



Wang, M., Wang, L., Zhou, W., Yu, W., 2019. Lean gas Huff and Puff process for Eagle Ford Shale: Methane adsorption and gas trapping effects on EOR. Fuel 248, 143-151.

Xie, J., Chu, Y., Shi, Y., Han, X., Li, X., Wang, L., Guo, Y., 2019. Studies of chromatographic separation and self-emulsification of crude oil. Petroleum Science and Technology 37, 220-225.


HEAVY OIL PRODUCTION


Kuznetsov, O., Agrawal, D., Suresh, R., Feng, X., Behles, J., Khabashesku, V., 2019. Experimental evaluation of colloidal nanosilica for improving bitumen recovery from mined oil-sand ore. SPE Reservoir Evaluation & Engineering 22, 50-60.

Sie, C.-Y., Nguyen, B., Castellanos Diaz, O., Verlaan, M., Nguyen, Q.P., 2019. Viscous oil recovery and in-situ deasphalting in fractured reservoirs – Part 2: Effect of solvent type and temperature. Fuel 247, 294-301.

Tajik, S., Shahrabadi, A., Rashidi, A., 2019. Silica-graphene nanohybrid supported MoS2 nanocatalyst for hydrogenation reaction and upgrading heavy oil. Journal of Petroleum Science and Engineering 177, 822-828.

Recent Sediments


Fiskal, A., Deng, L., Michel, A., Eickenbusch, P., Han, X., Lagostina, L., Zhu, R., Sander, M., Schroth, M.H., Bernasconi, S.M., Dubois, N., Lever, M.A., 2019. Effects of eutrophication on sedimentary organic carbon cycling in five temperate lakes. Biogeosciences Discussions 2019, 1-35.

Fuchsman, C.A., Paul, B., Staley, J.T., Yakushev, E.V., Murray, J.W., 2019. Detection of transient denitrification during a high organic matter event in the Black Sea. Global Biogeochemical Cycles 33, 143-162.


Vadsaria, T., Ramstein, G., Dutay, J.C., Li, L., Ayache, M., Richon, C., 2019. Simulating the occurrence of the last sapropel event (S1): Mediterranean Basin ocean dynamics simulations using Nd isotopic composition modeling. Paleoceanography and Paleoclimatology 34, 237-251.

Wu, X., Xing, L., Jiang, Y., Zhang, X., Xiang, R., Zhou, L., 2019. High-resolution reconstruction of sedimentary organic matter variability during the Holocene in the mud area of the Yellow Sea using multiple organic geochemical proxies. Quaternary International 503, 178-188.

Xiong, Y., Guilbaud, R., Peacock, C.L., Cox, R.P., Canfield, D.E., Krom, M.D., Poulton, S.W., 2019. Phosphorus cycling in Lake Cadagno, Switzerland: A low sulfate euxinic ocean analogue. Geochimica et Cosmochimica Acta 251, 116-135.


Zhuang, G.-C., Montgomery, A., Samarkin, V.A., Song, M., Liu, J., Schubotz, F., Teske, A., Hinrichs, K.-U., Joye, S.B., 2019. Generation and utilization of volatile fatty acids and alcohols in hydrothermally altered sediments in the Guaymas Basin, Gulf of California. Geophysical Research Letters 46, 2637-2646.

ATMOSPHERIC GEOCHEMISTRY

Alwe, H.D., Millet, D.B., Chen, X., Raff, J.D., Payne, Z.C., Fledderman, K., 2019. Oxidation of volatile organic compounds as the major source of formic acid in a mixed forest canopy. Geophysical Research Letters 46, 2940-2948.

Giorio, C., Bortolini, C., Kourtchev, I., Tapparo, A., Bogialli, S., Kalberer, M., 2019. Direct target and non-target analysis of urban aerosol sample extracts using atmospheric pressure photoionisation high-resolution mass spectrometry. Chemosphere 224, 786-795.

Jiang, H., Frie, A.L., Lavi, A., Chen, J., Zhang, H., Bahreini, R., Lin, Y.-H., 2019. Brown carbon formation from nighttime chemistry of unsaturated heterocyclic volatile organic compounds. Environmental Science & Technology Letters 6, 184-190.

Malfatti, F., Lee, C., Tinta, T., Pendergraft, M.A., Celussi, M., Zhou, Y., Sultana, C.M., Rotter, A., Axson, J.L., Collins, D.B., Santander, M.V., Anides Morales, A.L., Aluwihare, L.I., Riemer, N., Grassian, V.H., Azam, F., Prather, K.A., 2019. Detection of active microbial enzymes in nascent sea spray aerosol: Implications for atmospheric chemistry and climate. Environmental Science & Technology Letters 6, 171-177.

Roose, A., Toubin, C., Dusanter, S., Riffault, V., Duflot, D., 2019. Classical molecular dynamics study of small-chain carboxylic acid aerosol particles. ACS Earth and Space Chemistry 3, 380-389.


Vione, D., Albinet, A., Barsotti, F., Mekic, M., Jiang, B., Minero, C., Brigante, M., Gligorovski, S., 2019. Formation of substances with humic-like fluorescence properties, upon photoinduced oligomerization of typical phenolic compounds emitted by biomass burning. Atmospheric Environment 206, 197-207.


Yu, Q., Chen, J., Qin, W., Cheng, S., Zhang, Y., Ahmad, M., Ouyang, W., 2019. Characteristics and secondary formation of water-soluble organic acids in PM1, PM2.5 and PM10 in Beijing during haze episodes. Science of The Total Environment 669, 175-184.

HYDROSPHERE GEOCHEMISTRY

Amir, M., Paul, D., Samal, R.N., 2019. Sources of organic matter in Chilika lagoon, India inferred from stable C and N isotopic compositions of particulates and sediments. Journal of Marine Systems 194, 81-90.

Belcher, A., Henson, S.A., Manno, C., Hill, S.L., Atkinson, A., Thorpe, S.E., Fretwell, P., Ireland, L., Tarling, G.A., 2019. Krill faecal pellets drive hidden pulses of particulate organic carbon in the marginal ice zone. Nature Communications 10, Article 889.

Bikkina, P., Kawamura, K., Bikkina, S., Kunwar, B., Tanaka, K., Suzuki, K., 2019. Hydroxy fatty acids in remote marine aerosols over the Pacific Ocean: Impact of biological activity and wind speed. ACS Earth and Space Chemistry 3, 366-379.


Chaichana, S., Jickells, T., Johnson, M., 2019. Interannual variability in the summer dissolved organic matter inventory of the North Sea: implications for the continental shelf pump. Biogeosciences 16, 1073-1096.

Cisternas-Novoa, C., Le Moigne, F.A.C., Engel, A., 2019. Composition and vertical flux of particulate organic matter to the oxygen minimum zone of the central Baltic Sea: impact of a sporadic North Sea inflow. Biogeosciences 16, 927-947.

Coble, A.A., Koenig, L.E., Potter, J.D., Parham, L.M., McDowell, W.H., 2019. Homogenization of dissolved organic matter within a river network occurs in the smallest headwaters. Biogeochemistry 143, 85-104.

Dean, J.F., Garnett, M.H., Spyrakos, E., Billett, M.F., 2019. The potential hidden age of dissolved organic carbon exported by peatland streams. Journal of Geophysical Research: Biogeosciences 124, 328-341.

Dehwah, A.H.A., Anderson, D.M., Li, S., Mallon, F.L., Batang, Z., Alshahri, A.H., Hegy, M., Missimer, T.M., 2019. Transparent exopolymer particle binding of organic and inorganic particles in the Red Sea: Implications for downward transport of biogenic materials. Biogeosciences Discussions 2019, 1-40.


Islam, M.S., Sun, J., Li, X., Leng, X., 2019. Seasonal sinking rates of transparent exopolymer particles (TEP) concentrations with associated carbon flux in adjacent Bohai Sea and Yellow Sea. Biogeosciences Discussions 2019, 1-43.

Juhls, B., Overduin, P.P., Hölemann, J., Hieronymi, M., Matsuoka, A., Heim, B., Fischer, J., 2019. Dissolved organic matter at the fluvial-marine transition in the Laptev Sea using in situ data and ocean color remote sensing. Biogeosciences Discussions 2019, 1-37.

Lemieux, A.J., Hamilton, S.M., Clark, I.D., 2018. Allochthonous sources of iodine and organic carbon in an eastern Ontario aquifer. Canadian Journal of Earth Sciences 56, 209-222.


Lin, H.-T., Repeta, D.J., Xu, L., Rappé, M.S., 2019. Dissolved organic carbon in basalt-hosted deep subseafloor fluids of the Juan de Fuca Ridge flank. Earth and Planetary Science Letters 513, 156-165.

Minor, E.C., Tennant, C.J., Brown, E.T., 2019. A seasonal to interannual view of inorganic and organic carbon and pH in western Lake Superior. Journal of Geophysical Research: Biogeosciences 124, 405-419.

Negandhi, K., Edwards, G., Kelleway, J.J., Howard, D., Safari, D., Saintilan, N., 2019. Blue carbon potential of coastal wetland restoration varies with inundation and rainfall. Scientific Reports 9, Article 4368.

O’Mara, N.A., Dunne, J.P., 2019. Hot spots of carbon and alkalinity cycling in the coastal oceans. Scientific Reports 9, Article 4434.

Raidla, V., Pärn, J., Schloemer, S., Aeschbach, W., Czuppon, G., Ivask, J., Marandi, A., Sepp, H., Vaikmäe, R., Kirsimäe, K., 2019. Origin and formation of methane in groundwater of glacial origin from the Cambrian-Vendian aquifer system in Estonia. Geochimica et Cosmochimica Acta 251, 247-264.



Sarma, V.V.S.S., Yadav, K., Behera, S., 2019. Role of eddies on organic matter production and f-ratios in the Bay of Bengal. Marine Chemistry 210, 13-23.

Sehnal, L., Procházková, T., Smutná, M., Kohoutek, J., Lepšová-Skácelová, O., Hilscherová, K., 2019. Widespread occurrence of retinoids in water bodies associated with cyanobacterial blooms dominated by diverse species. Water Research 156, 136-147.

Song, F., Wu, F., Feng, W., Liu, S., He, J., Li, T., Zhang, J., Wu, A., Amarasiriwardena, D., Xing, B., Bai, Y., 2019. Depth-dependent variations of dissolved organic matter composition and humification in a plateau lake using fluorescence spectroscopy. Chemosphere 225, 507-516.

Wang, J., Hilton, R.G., Jin, Z., Zhang, F., Densmore, A.L., Gröcke, D.R., Xu, X., Li, G., West, A.J., 2019. The isotopic composition and fluxes of particulate organic carbon exported from the eastern margin of the Tibetan Plateau. Geochimica et Cosmochimica Acta 252, 1-15.



SOIL GEOCHEMISTRY

Aaltonen, H., Köster, K., Köster, E., Berninger, F., Zhou, X., Karhu, K., Biasi, C., Bruckman, V., Palviainen, M., Pumpanen, J., 2019. Forest fires in Canadian permafrost region: the combined effects of fire and permafrost dynamics on soil organic matter quality. Biogeochemistry 143, 257-274.


Baveye, P.C., Wander, M., 2019. The (bio)chemistry of soil humus and humic substances: Why is the “new view” still considered novel after more than 80 years? Frontiers in Environmental Science 7, 27. doi: 10.3389/fenvs.2019.00027.


Dandare, S.U., Young, J.M., Kelleher, B.P., Allen, C.C.R., 2019. The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy. Science of The Total Environment 671, 19-27.






Robertson, A.D., Paustian, K., Ogle, S., Wallenstein, M.D., Lugato, E., Cotrufo, M.F., 2019. Unifying soil organic matter formation and persistence frameworks: the MEMS model. Biogeosciences 16, 1225-1248.






Remote Sensing-Hydrocarbon Seepage


Alden, C.B., Coburn, S.C., Wright, R.J., Baumann, E., Cossel, K., Perez, E., Hoenig, E., Prasad, K., Coddington, I., Rieker, G.B., 2019. Single-blind quantification of natural gas leaks from 1 km distance using frequency combs. Environmental Science & Technology 53, 2908–2917.

Cyr, F., Tedetti, M., Besson, F., Bhairy, N., Goutx, M., 2019. A glider-compatible optical sensor for the detection of polycyclic aromatic hydrocarbons in the marine environment. Frontiers in Marine Science 6, 110. doi: 110.3389/fmars.2019.00110.

Guan, H., Xu, L., Wang, Q., Chen, D., Wu, N., Mao, S., 2019. Lipid biomarkers and their stable carbon isotopes in ancient seep carbonates from SW Taiwan, China. Acta Geologica Sinica - English Edition 93, 167-174.

He, W., Zhou, J., 2019. Structural features and formation conditions of mud diapirs in the Andaman Sea Basin. Geological Magazine 156, 659-668.


Kioka, A., Tsuji, T., Otsuka, H., Ashi, J., 2019. Methane concentration in mud conduits of submarine mud volcanoes: A coupled geochemical and geophysical approach. Geochemistry, Geophysics, Geosystems 20, 792-813.



Source Rocks/Depositional Environments

Abarghani, A., Ostadhassan, M., Gentzis, T., Carvajal-Ortiz, H., Ocubalidet, S., Bubach, B., Mann, M., Hou, X., 2019. Correlating Rock-Eval™ Tmax with bitumen reflectance from organic petrology in the Bakken Formation. International Journal of Coal Geology 205, 87-104.

Amirhossein, F., Youse, A.N., 2018. A new method to classification of total organic carbon by petrophysical logs in Australia. Archives of Petroleum & Environmental Biotechnology 2018, Article APEB-141.

Ayyıldız, T., Varol, B., Karakaş, Z., Sözeri, K., 2019. Basic geochemical characteristics of lacustrine rocks in the Neogene Kağızman–Tuzluca Basin, Northeastern Turkey. Journal of Petroleum Exploration and Production Technology 9, 141-157.


Barakat, M.A., Abd El-Gawad, E.A., Gaber, M.A.W., Lotfy, M.A., Abd El Ghany, A.A., 2019. Mineralogical and geochemical studies of oil shale deposits in the Cretaceous/Paleogene succession at Quseir area, Egypt. Egyptian Journal of Petroleum 28, 11-19.

DeReuil, A.A., Birgenheier, L.P., 2019. Sediment dispersal and organic carbon preservation in a dynamic mudstone-dominated system, Juana Lopez Member, Mancos Shale. Sedimentology 66, 1002-1041.

Duman, A., Bozcu, A., 2019. Source rock potential of the Sayındere formation in the Şambayat oil field, SE Turkey. Petroleum Science and Technology 37, 171-180.

Ganeeva, Y.M., Okhotnikova, E.S., Barskaya, E.E., Yusupova, T.N., Foss, L.E., Sotnikov, O.C., Remeev, M.M., Khisamov, R.S., 2019. The composition of organic matter of Domanic deposit of the Bavly field. Petroleum Science and Technology 37, 317-322.

Godfray, G., Seetharamaiah, J., 2019. Geochemical and well logs evaluation of the Triassic source rocks of the Mandawa basin, SE Tanzania: Implication on richness and hydrocarbon generation potential. Journal of African Earth Sciences 153, 9-16.

Goodarzi, F., Haeri-Ardakani, O., Gentzis, T., Pedersen, P.K., 2019. Organic petrology and geochemistry of Tournaisian-age Albert Formation oil shales, New Brunswick, Canada. International Journal of Coal Geology 205, 43-57.

Hakimi, M.H., Alaug, A.S., Al Faifi, H.J., Alramisy, G.A., Lashin, A.A., 2019. Late Jurassic Safer Salt Member in the Al-Jawf sub-basin of NW Sabatayn Basin, Yemen: geochemical evaluation of organic-rich oil-source rock potential. Petroleum Science and Technology 37, 645-654.

Hattori, K., Desrochers, A., Pedro, J., 2018. Provenance and depositional environment of organic-rich calcareous black shale of the Late Ordovician Macasty Formation, western Anticosti Basin, eastern Canada. Canadian Journal of Earth Sciences 56, 321-334.

Jiang, C., Zhang, S., Reyes, J., 2019. Black shale xenolith in a Jurassic−Cretaceous kimberlite and organic-rich Upper Ordovician shale on Baffin Island, Canada: A comparison of their organic matter. Marine and Petroleum Geology 103, 202-215.

Jiang, X., Liu, L., Sun, H., Huang, S., Geng, M., Chen, S., Li, N., Shen, P., 2019. Differential distribution of high-quality lacustrine source rocks controlled by climate and tectonics: a case study from Bozhong sag Acta Petrolei Sinica 40, 165-175.

Jin, Q., Hou, Q., Cheng, F., Wang, S., Zhang, R., Wang, F., 2019. Evaluation method of effective source rock in mature exploration area: a case study of Liaodong Bay. Acta Petrolei Sinica 40, 257-267.

Khatibi, S., Ostadhassan, M., Hackley, P., Tuschel, D., Abarghani, A., Bubach, B., 2019. Understanding organic matter heterogeneity and maturation rate by Raman spectroscopy. International Journal of Coal Geology 206, 46-64.

Krim, N., Tribovillard, N., Riboulleau, A., Bout-Roumazeilles, V., Bonnel, C., Imbert, P., Aubourg, C., Hoareau, G., Fasentieux, B., 2019. Reconstruction of palaeoenvironmental conditions of the Vaca Muerta formation in the southern part of the Neuquén Basin (Tithonian-Valanginian): Evidences of initial short-lived development of anoxia. Marine and Petroleum Geology 103, 176-201.

Lee, C., Love, G.D., Hopkins, M.J., Kröger, B., Franeck, F., Finnegan, S., 2019. Lipid biomarker and stable isotopic profiles through Early-Middle Ordovician carbonates from Spitsbergen, Norway. Organic Geochemistry 131, 5-18.

Li, D., Li, R., Tan, C., Zhao, D., Xue, T., Zhao, B., Khaled, A., Liu, F., Xu, F., 2019. Origin of silica, paleoenvironment, and organic matter enrichment in the Lower Paleozoic Niutitang and Longmaxi formations of the northwestern Upper Yangtze Plate: Significance for hydrocarbon exploration. Marine and Petroleum Geology 103, 404-421.

Liu, B., Vrabec, M., Markič, M., Püttmann, W., 2019. Reconstruction of paleobotanical and paleoenvironmental changes in the Pliocene Velenje Basin, Slovenia, by molecular and stable isotope analysis of lignites. International Journal of Coal Geology 206, 31-45.

Luan, G., Dong, C., Azmy, K., Lin, C., Ma, C., Ren, L., Zhu, Z., 2019. Origin of bedding-parallel fibrous calcite veins in lacustrine black shale: A case study from Dongying Depression, Bohai Bay Basin. Marine and Petroleum Geology 102, 873-885.

Luo, G., Yang, H., Algeo, T.J., Hallmann, C., Xie, S., 2019. Lipid biomarkers for the reconstruction of deep-time environmental conditions. Earth-Science Reviews 189, 99-124.


Matava, T., Matt, V., Flannery, J., 2019. New insights on measured and calculated vitrinite reflectance. Basin Research 31, 213-227.

Niu, X., Yang, X., Yan, D., Zhuang, X., Wang, B., Huo, S., Xu, X., 2019. Development background of Mesozoic high-quality source rocks: Evidence from microfossils in North Carnarvon Basin, Australia. Petroleum Research 4, 71-83.

Sakran, S., Shehata, A.A., Osman, O., El-Sherbiny, M., 2019. Superposed tectonic regimes in west Beni Suef basin, Nile Valley, Egypt: Implications to source rock maturation and hydrocarbon entrapment. Journal of African Earth Sciences 154, 1-19.

Schieber, J., Miclăuș, C., Seserman, A., Liu, B., Teng, J., 2019. When a mudstone was actually a “sand”: Results of a sedimentological investigation of the bituminous marl formation (Oligocene), Eastern Carpathians of Romania. Sedimentary Geology 384, 12-28.

Schneider, A.C., Mutterlose, J., Blumenberg, M., Heimhofer, U., Luppold, F.W., 2019. Palynofacies, micropalaeontology, and source rock evaluation of non-marine Jurassic–Cretaceous boundary deposits from northern Germany - Implications for palaeoenvironment and hydrocarbon potential. Marine and Petroleum Geology 103, 526-548.

Shan, X., Du, S., Guo, X., 2019. Characteristics and evaluation of the high-quality source rocks of Cretaceous continental shale oil in Tonghua Basin, China. Acta Geologica Sinica - English Edition 93, 146-154.

Shekarifard, A., Daryabandeh, M., Rashidi, M., Hajian, M., Röth, J., 2019. Petroleum geochemical properties of the oil shales from the Early Cretaceous Garau Formation, Qalikuh locality, Zagros Mountains, Iran. International Journal of Coal Geology 206, 1-18.

Wang, F., Yin, S., 2019. Hydrocarbon generation potential of the C-P continental source rocks in the Qinshui Basin. Petroleum Science and Technology 37, 208-214.

Wang, X., Zhu, Y., Lash, G.G., Wang, Y., 2019. Multi-proxy analysis of organic matter accumulation in the Upper Ordovician–Lower Silurian black shale on the Upper Yangtze Platform, south China. Marine and Petroleum Geology 103, 473-484.

Wei, H., Jiang, X., 2019. Early Cretaceous ferruginous and its control on the lacustrine organic matter accumulation: Constrained by multiple proxies from the Bayingebi Formation in the Bayingebi Basin, inner Mongolia, NW China. Journal of Petroleum Science and Engineering 178, 162-179.

Wu, W., Wang, H., Yu, J., Pan, J., 2019. Geochemical characteristics of the Carboniferous-Permian source rocks in Western Henan, China. Petroleum Science and Technology 37, 519-527.

Yang, H., Chen, Z.-Q., Kershaw, S., Liao, W., Lü, E., Huang, Y., 2019. Small microbialites from the basal Triassic mudstone (Tieshikou, Jiangxi, South China): Geobiologic features, biogenicity, and paleoenvironmental implications. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 221-235.

Zou, C., Zhu, R., Chen, Z.-Q., Ogg, J.G., Wu, S., Dong, D., Qiu, Z., Wang, Y., Wang, L., Lin, S., Cui, J., Su, L., Yang, Z., 2019. Organic-matter-rich shales of China. Earth-Science Reviews 189, 51-78.

Unconventional Resources

An, Y., Althaus, S.M., Liu, H.-H., Chen, J.-H., 2019. Nuclear magnetic resonance measurement of methane diffusion in organic-rich shales. Fuel 247, 160-163.


Bowers, G.M., Schaef, H.T., Miller, Q.R.S., Walter, E.D., Burton, S.D., Hoyt, D.W., Horner, J.A., Loring, J.S., McGrail, B.P., Kirkpatrick, R.J., 2019. 13C nuclear magnetic resonance spectroscopy of methane and carbon dioxide in a natural shale. ACS Earth and Space Chemistry 3, 324-328.



Freedman, R., Rose, D., Sun, B., Brown, R.L., Malizia, T., 2019. Novel method for evaluating shale-gas and shale-tight-oil reservoirs using advanced well-log data. SPE Reservoir Evaluation & Engineering 22, 282-301.

Hakimi, M.H., Alaug, A.S., Mohialdeen, I.M.J., Kahal, A.Y., Abdulelah, H., Hadad, Y.T., Yahya, M.M.A., 2019. Late Jurassic Arwa Member in south-eastern Al-Jawf sub-basin, NW

Sabatayn Basin of Yemen: Geochemistry and basin modeling reveal shale-gas potential. Journal of Natural Gas Science and Engineering 64, 133-151.

Huang, X., Li, T., Gao, H., Zhao, J., Wang, C., 2019. Comparison of SO2 with CO2 for recovering shale resources using low-field nuclear magnetic resonance. Fuel 245, 563-569.

Huang, X., Zhao, Y.-P., Wang, X., Pan, L., 2019. Adsorption-induced pore blocking and its mechanisms in nanoporous shale due to interactions with supercritical CO2. Journal of Petroleum Science and Engineering 178, 74-81.


Hulin, C., Mercury, L., 2019. Capillarity-driven supersolubility in dual-porosity systems. Geochimica et Cosmochimica Acta 252, 144-158.


Lee, J.H., Jeong, M.S., Lee, K.S., 2019. Incorporation of multi-phase solubility and molecular diffusion in a geochemical evaluation of the CO2 huff-n-puff process in liquid-rich shale reservoirs. Fuel 247, 77-86.

Li, M., Chen, Z., Ma, X., Cao, T., Qian, M., Jiang, Q., Tao, G., Li, Z., Song, G., 2019. Shale oil resource potential and oil mobility characteristics of the Eocene-Oligocene Shahejie Formation, Jiyang Super-Depression, Bohai Bay Basin of China. International Journal of Coal Geology 204, 130-143.

Li, X., Liu, P., Liu, R., 2019. Methane adsorption characteristics of shale from different basins and its geological significance. Petroleum Science and Technology 37, 261-267.



Liao, D., Lu, B., Chen, Y., 2019. An evaluation method of geological sweet spots of shale gas reservoir: a case study of the Jiaoshiba gas field,Sichuan Basin. Acta Petrolei Sinica 40, 144-151.


Mahlstedt, N., Horsfield, B., 2019. Thermovaporisation: A screening tool for the gas-sorptive properties of source rocks. Organic Geochemistry 131, 1-4.

Misch, D., Gross, D., Hawranek, G., Horsfield, B., Klaver, J., Mendez-Martin, F., Urai, J.L., Vranjes-Wessely, S., Sachsenhofer, R.F., Schmatz, J., Li, J., Zou, C., 2019. Solid bitumen in

shales: Petrographic characteristics and implications for reservoir characterization. International Journal of Coal Geology 205, 14-31.

Mohagheghian, E., Hassanzadeh, H., Chen, Z., 2019. Estimation of shale apparent permeability for multimechanistic, multicomponent gas production using rate transient analysis. Energy & Fuels 33, 1990-1997.

Myshakin, E.M., Singh, H., Sanguinito, S., Bromhal, G., Goodman, A.L., 2019. Flow regimes and storage efficiency of CO2 injected into depleted shale reservoirs. Fuel 246, 169-177.

Nie, H., Wang, H., He, Z., Wang, R., Zhang, P., Peng, Y., 2019. Formation mechanism,distribution and exploration prospect of normal pressure shale gas reservoir: a case study of Wufeng Formation-Longmaxi Formation in Sichuan Basin and its periphery. Acta Petrolei Sinica 40, 131-143,164.


Qian, K., Ning, J., Liu, X., Zhang, Y., 2019. A rock physics driven Bayesian inversion for TOC in the Fuling shale gas reservoir. Marine and Petroleum Geology 102, 886-898.

Wang, H., Wu, W., Chen, T., Yu, J., Pan, J., 2019. Pore structure and fractal analysis of shale oil reservoirs: A case study of the Paleogene Shahejie Formation in the Dongying Depression, Bohai Bay, China. Journal of Petroleum Science and Engineering 177, 711-723.


Wang, T., Tian, S., Li, G., Sheng, M., Ren, W., Liu, Q., Tan, Y., Zhang, P., 2019. Experimental study of water vapor adsorption behaviors on shale. Fuel 248, 168-177.

Wang, X., Sheng, J.J., 2019. Multi-scaled pore network modeling of gas-water flow in shale formations. Journal of Petroleum Science and Engineering 177, 899-908.

Wang, Y., Liu, L., Sheng, Y., Wang, X., Zheng, S., Luo, Z., 2019. Investigation of supercritical methane adsorption of overmature shale in Wufeng-Longmaxi Formation, southern Sichuan Basin, China. Energy & Fuels 33, 2078-2089.

Wang, Z., 2019. Reservoir formation conditions and key efficient exploration & development technologies for marine shale gas fields in Fuling area, South China Acta Petrolei Sinica 40, 370-382.

Wang, Z., Shi, B., Wen, Z., Tong, X., Song, C., He, Z., Liu, X., 2019. Shale oil and gas exploration potential in the Tanezzuft Formation, Ghadames Basin, North Africa. Journal of African Earth Sciences 153, 83-90.

Yekeen, N., Padmanabhan, E., Idris, A.K., Chauhan, P.S., 2019. Nanoparticles applications for hydraulic fracturing of unconventional reservoirs: A comprehensive review of recent advances and prospects. Journal of Petroleum Science and Engineering 178, 41-73.

Yi, J., Bao, H., Zheng, A., Zhang, B., Shu, Z., Li, J., Wang, C., 2019. Main factors controlling marine shale gas enrichment and high-yield wells in South China: A case study of the Fuling shale gas field. Marine and Petroleum Geology 103, 114-125.

Yuan, Y., Rezaee, R., 2019. Fractal analysis of the pore structure for clay bound water and potential gas storage in shales based on NMR and N2 gas adsorption. Journal of Petroleum Science and Engineering 177, 756-765.

Zeng, K., Jiang, P., Lun, Z., Xu, R., 2019. Molecular simulation of carbon dioxide and methane adsorption in shale organic nanopores. Energy & Fuels 33, 1785-1796.

Zhang, C., Zhao, L., Yu, D., Liu, G., Pei, Y., Huang, F., Liu, B., 2019. The evaluation on physical property and fracture conductivity of a new self-generating solid proppant. Journal of Petroleum Science and Engineering 177, 841-848.



Zhang, K., Song, Y., Jiang, S., Jiang, Z., Jia, C., Huang, Y., Wen, M., Liu, W., Wang, P., Li, X., Liu, T., Xie, X., Shan, C., #x, an, Liu, X., Wang, X., 2019. Accumulation mechanism of marine shale gas reservoir in anticlines: A case study of the southern Sichuan Basin and Xiuwu Basin in the Yangtze region. Geofluids 2019, Article 5142712.

Zhang, Y., Di, Y., Yu, W., Sepehrnoori, K., 2019. A comprehensive model for investigation of carbon dioxide enhanced oil recovery with nanopore confinement in the Bakken tight oil reservoir. SPE Reservoir Evaluation & Engineering 22, 122-136.

Abstracts

Aaltonen, H., Köster, K., Köster, E., Berninger, F., Zhou, X., Karhu, K., Biasi, C., Bruckman, V., Palviainen, M., Pumpanen, J., 2019. Forest fires in Canadian permafrost region: the combined effects of fire and permafrost dynamics on soil organic matter quality. Biogeochemistry 143, 257-274.

https://doi.org/10.1007/s10533-019-00560-x

Wildfires burn approximately 1% of boreal forest yearly, being one of the most significant factors affecting soil organic matter (SOM) pools. Boreal forests are largely situated in the permafrost zone, which contains half of global soil carbon (C). Wildfires advance thawing of permafrost by burning the insulating organic layer and decreasing surface albedo, thus increasing soil temperatures. Fires also affect SOM quality through chemical and physical changes, such as the formation of resistant C compounds. The long-term post-fire effects on SOM quality, degradability and isotopic composition are not well known in permafrost forests. We studied the effect of forest fires on the proportional sizes of SOM pools with chemical fractionation (extracting with water, ethanol and acid) of soil samples (5, 30 and 50 cm depths) collected from a fire chronosequence in the upland mineral soils of the Canadian permafrost zone. We also determined the 13C and 15N isotopic composition of soil after fire. In the topsoil horizon (5 cm) recent fire areas contained a smaller fraction of labile SOM and were slightly more enriched with 15N and 13C than older fire areas. The SOM fraction ratios reverted towards pre-fire status with succession. Changes in SOM were less apparent deeper in the soil. Best predictors for the size of recalcitrant SOM fraction were active layer depth, vegetation biomass and soil C/N ratio, whereas microbial biomass was best predicted by the size of the recalcitrant SOM

fraction. Results indicated that SOM in upland mineral soils at the permafrost surface could be mainly recalcitrant and its decomposition not particularly sensitive to changes resulting from fire.

Abarghani, A., Ostadhassan, M., Gentzis, T., Carvajal-Ortiz, H., Ocubalidet, S., Bubach, B., Mann, M., Hou, X., 2019. Correlating Rock-Eval™ Tmax with bitumen reflectance from organic petrology in the Bakken Formation. International Journal of Coal Geology 205, 87-104.

http://www.sciencedirect.com/science/article/pii/S0166516218308103

The Bakken Formation is a major unconventional shale play in North America, which lacks an independent calibration for accurately correlate thermal maturity from programmed pyrolysis (via temperature of maximum pyrolysis yield, Tmax) with optical methods (e.g., bitumen reflectance). In the present study, several samples from the upper and lower members of the Bakken Formation in North Dakota were analyzed by detailed organic petrography, bitumen reflectance, and Rock-Eval 6 pyrolysis. Organic petrography showed that the organic matter consists of various types of bitumen, amorphous matrix bituminite, liptodetrinite, acanthomorphic acritarch, marine alginite, granular micrinite, and inertinite macerals. Fluorescence color under UV light of macerals from the liptinite group was used to confirm the thermal maturity level. Due to the scarcity/absence of primary vitrinite, RO measurements on solid bitumen particles were converted to equivalent vitrinite reflectance (VRO-Eq) using a published correlation equation from the coeval New Albany Shale. Overall, geochemical analysis from Rock-Eval pyrolysis reveals almost similar trends for the upper and lower members, which allowed proposing a single correlation for VRO-Eq to Tmax for the Bakken Shale. Comparing the observed relationship for the Bakken Shale with the previously established models for the Devonian Duvernay Shale (Canada) and the Mississippian Barnett Shale (United States) shows discrepancies. Results confirmed the necessity of developing a specific equation for the Bakken Shale members to relate vitrinite and solid bitumen reflectance data to Tmax from Rock-Eval pyrolysis. Furthermore, the outcome of this study indicated that linear trends cannot accurately represent the relationship between these two parameters, considering the kerogen kinetics and non-linear relationship between transformation ratio (TR) and Tmax. Therefore, a polynomial correlation, a better fit to the data, was proposed to more accurately represent the nature of this relationship.



Polycyclic aromatic hydrocarbons (PAHs) are recalcitrant hazardous environmental contaminants. Various strategies, including chemical and physical like oxidation, fixation, leaching, and electrokinetic or biological-based techniques are used for remediation of polluted sites. Bioremediation of PAHs, via PAH-degrading endophytic and rhizospheric microbes, represent a time-/cost-effective way for ecorestoration. Four bacterial strains were isolated from contaminated soil on MSM supplemented with anthracene, alpha-naphthalene or catechol as sole carbon sources. These isolates were identified with 16S rRNA as Bacillus anthracis, B. cereus, B. mojavensis and B. subtilis. The degradation efficiency on the selected aromatic compounds was tested by HPLC analysis. B. subtilis showed the highest degradation efficiency of anthracene (99%) after five days of incubation. B. subtilis showed the highest catechol 1, 2 dioxygenase activity in MSM supplemented with anthracene. The enzyme was purified by gel filtration chromatography and characterized (70 kD, Km 2.7 μg and Vmax 178U/mg protein). The catechol 1,2 dioxygenase gene from the identified four

bacterial strains were isolated and submitted to GenBank (accession numbers MG255165-MG255168). The gene expression level of catechol 1,2 dioxygenase was upregulated 23.2-fold during the 72 h of incubation period. Furthermore, B. subtilis is a promising strain to be used in bioremediation of aromatic compounds-contaminated environments.


https://doi.org/10.1029/2018JG004787

Pyrogenic carbon (PyC) is an incomplete combustion by‐product with longer soil residence times compared with nonpyrogenic components of the soil carbon (C) pool and can be preferentially eroded in fire‐affected landscapes. To investigate geomorphic and fire‐related controls on PyC erosion, sediment fences were established in three combinations of slope (high 13.9–37.3%; moderate 0–6.7%) and burn severity (high; moderate) plots within the perimeter of the Rim Fire in 2013, Yosemite National Park, California, USA. After each major precipitation event following the fire, we determined transport rates of total sediment, fine and coarse sediment fractions, and C and nitrogen (N). We measured stable isotope (δ13C and δ15N) compositions and 13C‐nuclear magnetic resonance spectra of soils and eroded sediments. The highest total and fine (<2 mm) sediment transport in high severity burned areas correlated with initial discharge peaks from an adjacent stream, while moderate burn severity sites had considerably more of the >2 mm fraction transported than high burn severity sites. The δ13C and δ15N values and 13C‐nuclear magnetic resonance analyses indicated that sediment eroded from moderate severity burn areas included fresh organic matter that was not as significantly affected by the fire, whereas sediments from high severity burn areas were preferentially enriched in PyC. Our results indicate that along a single hillslope after the Rim Fire, burn severity acted as a primary control on PyC transport postfire, with slope angle likely playing a secondary role. The preferential erosion of PyC has major implications for the long‐term persistence of PyC within the soil system.

Abotalib, A.Z., Heggy, E., 2019. A deep groundwater origin for recurring slope lineae on Mars. Nature Geoscience 12, 235-241.

https://doi.org/10.1038/s41561-019-0327-5

The recurring slope lineae on Mars have been hypothesized to originate from snow melting, deliquescence, dry flow or shallow groundwater. Except for the dry flow origin, these hypotheses imply the presence of surficial or near-surface volatiles, placing the exploration and characterization of potential habitable environments within the reach of existing technology. Here we present observations from the High Resolution Imaging Science Experiment, heat-flow modelling and terrestrial analogues, which indicate that the source of recurring slope lineae could be natural discharge along geological structures from briny aquifers within the cryosphere, at depths of approximately 750 m. Spatial correlation between recurring slope lineae source regions and multi-scale fractures (such as joints and faults) in the southern mid-latitudes and in Valles Marineris suggests that recurring slope lineae preferably emanate from tectonic and impact-related fractures. We suggest that deep groundwater occasionally surfaces on Mars in present-day conditions.

Ackerman, L., Skála, R., Křížová, Š., Žák, K., Magna, T., 2019. The quest for an extraterrestrial component in Muong Nong-type and splash-form Australasian tektites from Laos using highly

siderophile elements and Re-Os isotope systematics. Geochimica et Cosmochimica Acta 252, 179-189.


Extremely low and variable concentrations of osmium (Os) and other highly siderophile elements (HSE) in most tektites make it challenging to establish direct links between these impact-related materials and their possible extraterrestrial contribution. New Os concentrations (2–43 ppt) and 187Os/188Os ratios (0.131–0.68) in a suite of fifteen well-characterized Australasian tektites from Laos (Muong Nong and splash-form types) with variable Ni enrichment indicate a maximum of ∼0.005% addition of a chondritic impactor. This is similar to some Australasian tektites from Vietnam with similarly low siderophile contents, but significantly lower than found in previous studies of more Ni-rich Australasian splash-form tektites and microtektites from different parts of the Australasian strewn field (e.g., Indonesia, South China Sea). The contents of HSE and Re–Os isotopic compositions of layered Muong Nong-type Australasian tektites are highly variable, suggesting mingling of crustal-derived (siderophile element-poor) and extraterrestrial (siderophile element-rich) materials. The absence of a direct correlation between HSE and Ni contents is interpreted to result from a fractionation process related to their different vaporization/condensation temperatures. The low Os abundance in most of the analyzed Australasian tektites, combined with non-radiogenic 187Os/188Os far below average upper continental crust, may provide a direct test to distinguish continental versus seawater impact scenario. In the absence of any specific low-Os target, a particular process of Os loss following impact is required. We envisage a scenario where evaporative loss of >>90% Os in the form of Os oxides from the overheated tektite melt is aided by volatile species derived from dissociated seawater and/or saline pore water embedded in sediments off-shore Indochina, consistent with elevated contents of halogens in Australasian tektites. This water-assisted Os loss could also play significant role for Central European tektites, while the continental surface with limited amount of water would prevent from more efficient HSE loss as could be the case for Ivory Coast tektites.

Adhikari, P.L., Maiti, K., Bam, W., 2019. Fate of particle-bound polycyclic aromatic hydrocarbons in the river-influenced continental margin of the northern Gulf of Mexico. Marine Pollution Bulletin 141, 350-362.

http://www.sciencedirect.com/science/article/pii/S0025326X19301468

This study utilizes suspended particles and seafloor sediments collected from the northern Gulf of Mexico (GOM) continental margin to study the fate, transport, residence times and accumulation rates of particle-bound polycyclic aromatic hydrocarbons (PAHs). Total particulate-PAHs and particulate organic carbon (POC) varied between 0.9 and 7.0 ng/L, and 4–131 μg/L, respectively. Particulate-PAHs were positively correlated with POC, while both particulate-PAHs and POC were negatively correlated with salinity (P-value < 0.05). These results show that the river-derived particle influx and associated POC are important vectors for transport and fate of particulate-PAHs in the river-dominated northern GOM continental ecosystems. The composition of underlying seafloor sediment-PAHs were not correlated to the water column particulate-PAHs, which is attributed to re-mineralization, sediment resuspension/redistribution and different timescales of comparison. The 210Pb-derived residence time of particles and associated particulate-PAHs in water column varied between 2 and 39 days. Residence times of particulate-PAHs were significantly correlated with seafloor sediment-PAHs accumulation rates, shorter water column residence times leading to higher PAHs accumulation rates.


https://doi.org/10.1111/jpg.12731

Crude oil samples from surface seeps in the Douala Basin (southern Cameroon) and from producing fields in the nearby Rio del Rey and Kribi‐Campo sub‐basins were analysed for bulk and molecular geochemical parameters by inductively coupled plasma – mass spectrometry (ICP‐MS), gas chromatography – mass spectrometry (GC‐MS) and isotope ratio mass spectrometry (IRMS). The aims of the study were to assess the composition of the oils, to evaluate the relationship between the seep oils and the oils from producing fields, and to highlight the significance of the data for oil exploration in the region. Chromatograms of the saturate fractions of the oils exhibit biodegradation ranging from very light (PM1 on the scale of Peters and Moldowan, 1993) in oil from the offshore Lokele field in the Rio del Rey sub‐basin, to severe (PM 6+) for seep oils from the Douala Basin. A plot of Pr/n‐C17 (1.3– 5.0) versus Ph/n‐C18 (0.8–2.6) for the samples further supports mild biodegradation in some samples (Lokele, Kole, Ebome), and demonstrates that the oils from the Lokele and Kole fields (Rio Del Rey sub‐basin) and from Ebome field (Kribi‐Campo sub‐basin) originated from mixed organic matter with a dominant marine contribution. The Pr/Ph ratio (1.8–2.3) for the Lokele, Kole and Ebome oil samples, and the V/(V+Ni) ratios (< 0.5) for the seep oils (Douala Basin) and the oils from the Lokele, Kole and Ebome fields, indicate derivation from source rocks deposited in oxic – dysoxic environments. The CPI (1.0–1.1) demonstrates that the Lokele and Ebome oils originated from mature source rocks, with the ratios of C31 22S/(S+R) (0.57 to 0.63) and C30‐βαH/C30‐αβH (0.18–0.23) for the Lokele, Kole and Moudi samples indicating early oil window maturity. Both V/(V+Ni) ratios (0.06–0.22) and δ13C (‐26.96 to ‐24.89 ‰) were used for correlation of the oils, with the seep oils from the Douala Basin showing the closest relationship to the oil from the Lokele field. The presence of mature Type II / III source rocks in different basins in southern Cameroon suggests significant potential for oil exploration in the region.

Akai, T., Alhammadi, A.M., Blunt, M.J., Bijeljic, B., 2019. Modeling oil recovery in mixed-wet rocks: Pore-scale comparison between experiment and simulation. Transport in Porous Media 127, 393-414.

https://doi.org/10.1007/s11242-018-1198-8

To examine the need to incorporate in situ wettability measurements in direct numerical simulations, we compare waterflooding experiments in a mixed-wet carbonate from a producing reservoir and results of direct multiphase numerical simulations using the color-gradient lattice Boltzmann method. We study the experiments of Alhammadi et al. (Sci Rep 7(1):10753, 2017. https://doi.org/10.1038/s41598-017-10992-w) where the pore-scale distribution of remaining oil was imaged using micro-CT scanning. In the experiment, in situ contact angles were measured using an automated algorithm (AlRatrout et al. in Adv Water Resour 109:158–169, 2017. https://doi.org/10.1016/j.advwatres.2017.07.018), which indicated a mixed-wet state with spatially non-uniform angles. In our simulations, the pore structure was obtained from segmented images of the sample used in the experiment. Furthermore, in situ measured angles were also incorporated into our simulations using our previously developed wetting boundary condition (Akai et al. in Adv Water Resour 116(March):56–66, 2018. https://doi.org/10.1016/j.advwatres.2018.03.014). We designed six simulations with different contact angle assignments based on experimentally measured values. Both a constant contact angle based on the average value of the measured values and non-uniform contact angles informed by the measured values gave a good agreement for fluid pore occupancy between the simulation and the experiment. However, the constant contact angle assignment predicted 54% higher water effective permeability after waterflooding than that estimated for the experimental result,

whereas the non-uniform contact angle assignment gave less than 1% relative error. This means that to correctly predict fluid conductivity in mixed-wet rocks, a spatially heterogeneous wettability state needs to be taken into account. The novelty of this work is to provide a direct pore-scale comparison between experiments and simulations employing experimentally measured contact angles, and to demonstrate how to use measured contact angle data to improve the predictability of direct numerical simulation, highlighting the difference between the contact angle required for the simulation of dynamic displacement process and the contact angle measured at equilibrium after waterflooding.


https://doi.org/10.1007/s13202-018-0525-5

Geological investigation have led to discovery of huge tar sand deposits within Afowo Formation of the Turonian–Maastrichtianage (95.9–66.0 Ma) in the Nigerian sector of the Eastern Dahomey Basin. This study aims at determining the feasibility of exploiting the major hydrocarbon resource steam assisted gravity drainage enhanced recovery technique. Samples from three core holes were dry sievied to determine the particle size distribution and their sections studied using a petrographic microscope. Clay mineral content was determined using X-ray diffraction scanning electron microscopy. The granulometric analysis shows the bituminous sediments to be generally fine grained and moderate to well sorted, and the grains are angular to subangular. Porosity ranges from 15.5 to 33.6 ɸ with average value of 26.4 ɸ, while permeability ranges from 270 to 4800 mD, with an average value of 4800 mD (very high) recorded for the sandstones. Petrographic study, scanning electron microscopy and X-ray diffractometry showed quartz as the dominant mineral component, with subordinate feldspar and other accessory minerals. The predominance of quartz is probably due to its mechanical stability. The low frequency of feldspar is attributable to its susceptibility to chemical breakdown and alteration, respectively, during transport and after deposition, with latter accounting for the observed secondary porosity. Kaolinite is the common clay mineral present in the oil sands and may not have sufficiently reduced the reservoir quality to negatively impacting enhanced recovery operation by steam assisted gravity drainage.

Al-Otaibi, F.M., Zhou, X., Kokal, S.L., 2019. Laboratory evaluation of different modes of supercritical carbon dioxide miscible flooding for carbonate rocks. SPE Reservoir Evaluation & Engineering 22, 137-149.

https://doi.org/10.2118/177986-PA

Field application of supercritical carbon dioxide (sc-CO2) miscible flooding continues to grow. Optimization of sc-CO2 injection during miscible-flooding modes represents one of the dominant factors affecting its performance in carbonate oil reservoirs. The main objective of this study was to investigate the effect of different modes of sc-CO2 miscible injection on oil recovery and injectivity in carbonate rocks. Several modes of sc-CO2 injection were investigated, including continuous CO2 miscible flooding, water-alternating-gas (WAG), and tapered-WAG injection. Five coreflooding experiments were conducted to evaluate oil recovery for different modes of sc-CO2 injection under reservoir conditions. Composite cores of 25-cm length from a specific, producing carbonate reservoir were used in the study. Both horizontal- and vertical-coreflooding experiments of continuous-sc-CO2-injection mode were performed to compare oil recovery and injectivity during sc-CO2 flooding. Horizontal-coreflooding experiments under WAG mode were performed at pore pressures of 3,200 and 3,800 psi.

The experimental results indicate that tertiary oil recovery was influenced significantly by different sc-CO2-injection modes and the direction of displacement. Original oil in cores was recovered at 18.4 and 26.74% for horizontal and vertical experiments of continuous-sc-CO2-injection modes, respectively. In horizontal-WAG experiments with different pore pressures, higher oil recovery was observed at a pore pressure of 3,800 psi compared with 3,200 psi. The marginal increase in incremental oil recovery indicates that pressure increase beyond 3,200 psi will not have a significant effect. The injectivity of different sc-CO2-injection modes is reported in this paper.

Alden, C.B., Coburn, S.C., Wright, R.J., Baumann, E., Cossel, K., Perez, E., Hoenig, E., Prasad, K., Coddington, I., Rieker, G.B., 2019. Single-blind quantification of natural gas leaks from 1 km distance using frequency combs. Environmental Science & Technology 53, 2908–2917.

https://doi.org/10.1021/acs.est.8b06259

A new method is tested in a single-blind study for detection, attribution, and quantification of methane emissions from the natural gas supply chain, which contribute substantially to annual U.S. emissions. The monitoring approach couples atmospheric methane concentration measurements from an open-path dual frequency comb laser spectrometer with meteorological data in an inversion to characterize emissions. During single-blind testing, the spectrometer is placed >1 km from decommissioned natural gas equipment configured with intentional leaks of controllable rate. Single, steady emissions ranging from 0 to 10.7 g min–1 (0–34.7 scfh) are detected, located, and quantified at three gas pads of varying size and complexity. The system detects 100% of leaks, including leaks as small as 0.96 g min–1 (3.1 scfh). It attributes leaks to the correct pad or equipment group (tank battery, separator battery, wellhead battery) 100% of the time and to the correct equipment (specific separator, tank, or wellhead) 67% of the time. All leaks are quantified to within 3.7 g min–1 (12 scfh); 94% are quantified to within 2.8 g min–1 (9 scfh). These tests are an important initial demonstration of the methodology’s viability for continuous monitoring of large regions, with extension to other trace gases and industries



Petroleum-derived fuels are chronically spilled in urbanized areas, affecting the environment and the population’s health. Forensic investigations of oil spills aim to find the responsible source of the spills. Weathering processes (dissolution, evaporation, photo-oxidation and biodegradation) change the chemical composition of the spills and hamper the matching of spill-source pairs, especially for light diesel oils (i.e. n-C9 – n-C20) in which the source diesels can be very similar due to the refining process and only compounds resistant to short- or middle-term weathering are present. In this study, comprehensive two-dimensional gas chromatography – high resolution mass spectrometry (GC × GC – HRMS) and pixel-based analysis were combined for: i) improve the identification of very similar diesel oils, and ii) identify weathering-resistant compounds that can also distinguish samples from different sources. Diesel oils from two sources that have been exposed to different degrees of evaporation, photo-oxidation and biodegradation in a laboratory setup. The study revealed the tentatively identified octanoic acid methyl ester and n-nonaldehyde were more resistance to evaporation than hydrocarbons < n-C15. Furthermore, the hydrocarbons > n-C17 could be used for source-apportionment of all the diesel oils susceptible to evaporation and photo-oxidation, but only

pristane and phytane were also more resistant to biodegradation. Naphthenes, bicyclic sesquiterpanes and adamantanes were more resistant to only photo-oxidation and biodegradation. GC × GC – HRMS enhanced the separation of the highly similar naphthenes in the diesel oils; however, the diagnostic power for forensic spill investigations was still similar to 1D GC – HRMS.

Almenningen, S., Gauteplass, J., Hauge, L.P., Barth, T., Fernø, M.A., Ersland, G., 2019. Measurements of CH4 and CO2 relative permeability in hydrate-bearing sandstone. Journal of Petroleum Science and Engineering 177, 880-888.


This paper reports measurements of relative permeability to methane (CH4) and carbon dioxide (CO2) in hydrate-bearing sandstone core samples. The CH4 (or CO2) permeability was measured at reservoir conditions for different hydrate and brine saturations. The saturation span ranged from 0.18 to 0.60 (frac.) for CH4 gas and from 0.37 to 0.70 (frac.) for liquid CO2. The hydrate saturation ranged from 0.18 to 0.61 (frac.). The growth of hydrates within sandstone pores reduced the permeability for both the CH4 and CO2 system significantly, and the relative reduction was more pronounced for lower gas saturations. This effect is currently not included in numerical models of relative permeability in hydrate-bearing sediments and should be considered. The reported measurements are relevant to production-forecasting of methane gas from hydrate reservoirs and CO2 storage schemes where CO2 hydrates may provide self-sealing in cold aquifers.

Alqam, M.H., Abu-Khamsin, S.A., Sultan, A.S., Okasha, T.M., Yildiz, H.O., 2019. Effect of rock mineralogy and oil composition on wettability alteration and interfacial tension by brine and carbonated water. Energy & Fuels 33, 1983-1989.

https://doi.org/10.1021/acs.energyfuels.8b04143

Wettability has a significant impact on the flow of oil during enhanced oil recovery (EOR) and profound effect on fluid distribution in oil fields. Mechanisms that influence the interaction between the injected water and the components of crude oil in the presence of carbonate rock samples were investigated. The main objectives of this study were to investigate the role of both rock mineralogy and the compositions of various oils as a function of asphaltene content on the destabilization of the aqueous film separating the oil from the substrate rock surface of carbonates using aqueous phases such as brine and carbonated water. The contact angles as a function of time were measured using brine and carbonated water and two types of crude oil on four types of rock samples. Once the exact contact angle has been determined, the compositions of various oils, based on asphaltene contents, were characterized to investigate the role of oil composition on the destabilization of the aqueous film separating the oil from the rock surface. Interfacial tensions (IFTs) of brine and two types of crude oil were also measured. Four types of rock samples from carbonate reservoirs, with different compositions, selected based on X-ray diffraction results were as follows: (1) 100% dolomite D(100), (2) 100% calcite C(100), (3) 67% dolomite + 33% calcite (D67 + C33), and (4) 37% dolomite + 63% calcite (D37 + C63). Two types of crude oil were used based on the asphaltene content obtained using the saturate, aromatic, resin, and asphaltene analysis. The contents of asphaltenes for crude-1 and crude-2 were 11.6 and 6.4 wt % and represented as (I-11.6) and (II-6.4), respectively. In this study, crude oil/brine/carbonate systems showed that (D37 + C63) gave the lowest contact angle value of 67° with 6.4 wt % of asphaltene content (II-6.4) and that D(100) gave the highest contact angle of 136° with 11.6 wt % of asphaltene content (I-11.6). Brine was used as the external phase on both tests. On the other hand, using carbonated water as the external phase, the contact angle decreased from 97.6° (D67 + C33) to 75.5° (D37 + C63) for mixed dolomite/calcite systems. Decreasing the

dolomite content in mixed dolomite/calcite systems caused a shift in contact angle from the oil negative intermediate wet to weakly water wet regardless of the saturating fluid phase. Also, using the adhesion tension approach, in defining surface wettability, shows that with the decrease in the contact angle values, adhesion tension shifted to positive directions with an increase in the degree of water wetness. This behavior was mainly due to the effect of type-II crude oil. The novelty of this study stems from studying the effect of rock mineralogy based on dolomite and calcite distribution and oil composition based on the asphaltene content in wettability alteration using aqueous phases such as brine and carbonated water. The results of both contact angle and IFT were implemented in adhesion tension using the Thomas Young equation as an alternative approach in defining surface wettability. This study will provide a better understanding of mineralogy/fluid/interaction, which is very crucial in the optimization of water injection and wettability reversal during the EOR process.

Alwe, H.D., Millet, D.B., Chen, X., Raff, J.D., Payne, Z.C., Fledderman, K., 2019. Oxidation of volatile organic compounds as the major source of formic acid in a mixed forest canopy. Geophysical Research Letters 46, 2940-2948.

https://doi.org/10.1029/2018GL081526

Abstract: Formic acid (HCOOH) is among the most abundant carboxylic acids in the atmosphere, but its budget is poorly understood. We present eddy flux, vertical gradient, and soil chamber measurements from a mixed forest and apply the data to better constrain HCOOH source/sink pathways. While the cumulative above‐canopy flux was downward, HCOOH exchange was bidirectional, with extended periods of net upward and downward flux. Net above‐canopy fluxes were mostly upward during warmer/drier periods. The implied gross canopy HCOOH source corresponds to 3% and 38% of observed isoprene and monoterpene carbon emissions and is 15× underestimated in a state‐of‐science atmospheric model (GEOS‐Chem). Gradient and soil chamber measurements identify the canopy layer as the controlling source of HCOOH or its precursors to the forest environment; below‐canopy sources were minor. A correlation analysis using an ensemble of marker volatile organic compounds suggests that secondary formation, not direct emission, is the major source driving ambient HCOOH.

Plain Language Summary: Formic acid (HCOOH) is one of the most abundant acids in the atmosphere and affects the acidity of precipitation. A number of recent studies have shown that the atmospheric abundance of HCOOH is much higher than predicted, implying some unknown or underrepresented source. Here we present new measurements of HCOOH and related species above, within, and below a mixed forest canopy and use the results to investigate its sources and sinks in this ecosystem. We find that the forest is simultaneously a source and a sink of atmospheric HCOOH, and vertically resolved measurements identify the canopy layer as the major HCOOH source for this environment. Soils have been shown to be a source of HCOOH in some cases, but we show that their influence is unimportant for this ecosystem. The magnitude of the gross HCOOH source from this forest is 15 times higher than predicted in a current atmospheric model. A correlation analysis suggests that the main HCOOH source from this forest is oxidation of other compounds rather than direct emissions from vegetation.

Amend, A., Burgaud, G., Cunliffe, M., Edgcomb, V.P., Ettinger, C.L., Gutiérrez, M.H., Heitman, J., Hom, E.F.Y., Ianiri, G., Jones, A.C., Kagami, M., Picard, K.T., Quandt, C.A., Raghukumar, S., Riquelme, M., Stajich, J., Vargas-Muñiz, J., Walker, A.K., Yarden, O., Gladfelter, A.S., 2019. Fungi in the marine environment: Open questions and unsolved problems. mBio 10, Article e01189-01118.

http://mbio.asm.org/content/10/2/e01189-18.abstract

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Amir, M., Paul, D., Samal, R.N., 2019. Sources of organic matter in Chilika lagoon, India inferred from stable C and N isotopic compositions of particulates and sediments. Journal of Marine Systems 194, 81-90.


Stable isotopic compositions (δ13C and δ15N) and C/N ratios of suspended particulate organic matter (POM) and surface sediment organic matter (SOM) in the Asia's largest lagoon (Chilika, India) were analyzed to identify spatial and seasonal variabilities in sources of organic matter. The variability of POM composition (δ13C: −23.5‰ to −27.9‰, δ15N: 2.1‰ to 7.5‰, C/N: 9.5 ± 0.9) collected during monsoon, a period of highest river discharge, suggests dominant input of terrestrial organic matter, whereas wintertime POM (δ13C: −22.3‰ to −27.7‰, δ15N: −0.2‰ to 4.8‰, C/N: 9.1 ± 1.0) exhibits a mixed source of agricultural runoff, and lagoon phytoplankton and cyanobacteria. The composition of POM collected during summer/dry season (δ13C: −21.2‰ to −26.2‰, δ15N: 2.0‰ to 6.0‰, C/N: 8.9 ± 1.1) indicates enhanced lagoon phytoplankton and bacterial productivity. Spatial variability of POM isotopic composition clearly shows more contribution of terrestrial sources in the northern sector- influenced by perennial Mahanadi River distributaries- compared to the central and southern sectors. The isotopic compositions (δ13C: −20.9‰ to −22.9‰, δ15N: 1.9‰ to 6.6‰) and C/N ratios (10.1 ± 1.3) of SOM indicate major contribution from terrestrial and macrophyte sources and minor contribution from phytoplankton and/or cyanobacteria. The northern sector is also heavily influenced by urban/industrial wastewater input, whereas the outer channel with higher salinity remains dominated by marine organic matter. Western part of the central sector is significantly influenced by untreated domestic sewage discharged from nearby townships and villages, which endangers the lagoon ecosystem.

Amirhossein, F., Youse, A.N., 2018. A new method to classification of total organic carbon by petrophysical logs in Australia. Archives of Petroleum & Environmental Biotechnology 2018, Article APEB-141.

https://gavinpublishers.com/articles/Research-Article/Archives-of-Petroleum-Environmental-Biotechnology-ISSN-2574-7614/a-new-method-to-classification-of-total-organic-carbon-by-petrophysical-logs-in-australia

Total Organic Carbon (TOC) is an importance parameter in the assessment of rock sources. By evaluating this parameter, we can estimate the total amount of hydrocarbons in the rocks. The most

common method for measuring TOC is the use of cores obtained from drilled wells. This is a costly and time-consuming process and, in addition to the expenditure of coring, will cost a lot of maintenance. Over the past few years, extensive studies have been carried out to estimate TOC using less costly methods, which will be discussed in more details in the introduction. Modern and low-cost methods help to inspect reservoirs with high exploratory risk like gas shale reservoirs. In this paper, it was tried to make a correlation between conventional Petrophysical logs and TOC using the neural network in one well in western Australia. By encoding the initial data and categorizing them in the neural network, we finally conclude that it is possible to obtain a good accuracy of classification of hydrocarbon content.

An, B.A., Shen, Y., Voordouw, J., Voordouw, G., 2019. Halophilic methylotrophic methanogens may contribute to the high ammonium concentrations found in shale oil and shale gas reservoirs. Frontiers in Energy Research 7, 23. doi: 10.3389/fenrg.2019.00023.

https://www.frontiersin.org/article/10.3389/fenrg.2019.00023

Flow-back and produced waters from shale gas and shale oil fields contain high ammonium, which can be formed by methanogenic degradation of methylamines into methane and ammonium. Methylamines are added to fracturing fluid to prevent clay swelling or can originate from metabolism of the osmolyte triglycinebetaine (GB). We analyzed field samples from a shale gas reservoir in the Duvernay formation and from a shale oil reservoir in the Bakken formation in Canada to determine the origin of high ammonium. Fresh waters used to make fracturing fluid, early flow-back waters and late flow back waters from the shale gas reservoir had increasing salinity of 0.01, 0.58 and 2.66 Meq of NaCl, respectively. Microbial community analyses reflected this fresh water to saline transition with halophilic taxa including Halomonas, Halanaerobium and Methanohalophilus being increasingly present. Early and late flow-back waters had high ammonium concentrations of 32 and 15 mM, respectively. Such high concentrations had also been found in the Bakken produced waters. Enrichment cultures of Bakken produced waters in medium containing mono, di-, or trimethylamine or triglycinebetaine (GB) converted these substrates into ammonium (up to 20 mM) and methane. The methylotrophic methanogen Methanohalophilus, which uses methylamines for its energy metabolism and uses GB as an osmolyte, was a dominant community member in these enrichments. Halanaerobium was also a dominant community member that metabolizes GB into trimethylamine, which is then metabolized further by Methanohalophilus. However, the micromolar concentrations of GB measured in shale reservoirs make them an unlikely source for the 1000-fold higher ammonium concentrations in flow-back waters. This ammonium either originates directly from the reservoir or is formed from methylamines, which originate from the reservoir or are added during the hydraulic fracturing process. These methylamines are then converted into ammonium and methane by halophilic methylotrophic methanogens, such as Methanohalophilus, present in flow-back waters.

An, Y., Althaus, S.M., Liu, H.-H., Chen, J.-H., 2019. Nuclear magnetic resonance measurement of methane diffusion in organic-rich shales. Fuel 247, 160-163.


Organic-rich shales have pore size on nanometer scale and permeability on the order of nano-Darcy. These properties give rise to significant challenges in understanding and modeling flow processes during the hydrocarbon production from shale reservoirs. During production, light hydrocarbons move from nanopores in the rock matrix to fractures generated by hydraulic fracturing to the well. Diffusion becomes a key mechanism in controlling hydrocarbon transport within matrix and from matrix to fractures. However, reliable experimental data for hydrocarbon diffusion coefficients in

organic-rich shales are still lacking in the literature. This study presents experimental measurements of in situ methane diffusion coefficients in shales using a pulse-field-gradient nuclear magnetic resonance method. This method measures the diffusion coefficient at equilibrium state and thus eliminates the possibility of fluid flow effects in laboratory measurement generated from pressure or concentration gradient. The measured methane diffusion coefficients in shales are two orders of magnitude smaller than those in the bulk state in the pressure range from 75 to 6000 psi. The measured data can be used to more accurately evaluate and model the production from shale reservoirs.



Background Diagnostic delays are common for multiple sclerosis (MS) since diagnosis typically depends on the presentation of nonspecific clinical symptoms together with radiologically-determined central nervous system (CNS) lesions. It is important to reduce diagnostic delays as earlier initiation of disease modifying therapies mitigates long-term disability. Developing a metabolomic blood-based MS biomarker is attractive, but prior efforts have largely focused on specific subsets of metabolite classes or analytical platforms. Thus, there are opportunities to interrogate metabolite profiles using more expansive and comprehensive approaches for developing MS biomarkers and for advancing our understanding of MS pathogenesis. Methods To identify putative blood-based MS biomarkers, we comprehensively interrogated the metabolite profiles in 12 non-Hispanic white, non-smoking, male MS cases who were drug naïve for 3 months prior to biospecimen collection and 13 non-Hispanic white, non-smoking male controls who were frequency matched to cases by age and body mass index. We performed untargeted two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS) and targeted lipidomic and amino acid analysis on serum. 325 metabolites met quality control and supervised machine learning was used to identify metabolites most informative for MS status. The discrimination potential of these select metabolites were assessed using receiver operator characteristic curves based on logistic models; top candidate metabolites were defined as having area under the curves (AUC) >80%. The associations between whole-genome expression data and the top candidate metabolites were examined, followed by pathway enrichment analyses. Similar associations were examined for 175 putative MS risk variants and the top candidate metabolites. Results 12 metabolites were determined to be informative for MS status, of which 6 had AUCs >80%: pyroglutamate, laurate, acylcarnitine C14:1, N-methylmaleimide, and 2 phosphatidylcholines (PC ae 40:5, PC ae 42:5). These metabolites participate in glutathione metabolism, fatty acid metabolism/oxidation, cellular membrane composition, and transient receptor potential channel signaling. Pathway analyses based on the gene expression association for each metabolite suggested enrichment for pathways associated with apoptosis and mitochondrial dysfunction. Interestingly, the predominant MS genetic risk allele HLA-DRB1×15:01 was associated with one of the 6 top metabolites. Conclusion Our analysis represents the most comprehensive description of metabolic changes associated with MS in serum, to date, with the inclusion of genomic and genetic information. We identified atypical metabolic processes that differed between MS patients and controls, which may enable the development of biological targets for diagnosis and treatment.



In higher plants, leaf waxes provide a barrier to non-stomatal water loss, and their composition varies both between and within species. Characteristics of n-alkanes, a suite of ubiquitous compounds in these waxes, are thought to be influenced by the availability of water and the temperature in a plant’s growing environment. Longer n-alkane distributions with less variability in chain length are hypothesised to confer greater resistance to non-stomatal water loss and thus are expected in higher abundance in desiccating environments. Relationships between the distribution of n-alkanes and both precipitation and temperature have previously been observed. Despite this, it is unclear whether n-alkane chain length distributions vary plastically in response to climate, or whether they are fixed within populations in different climate settings. To better understand this, we examine the relationship between n-alkane characteristics of Melaleuca quinquenervia and both spatial and temporal climate variation. Across eastern Australia, we find that n-alkane homolog concentrations and distributions in leaves of M. quinquenervia do not vary with climate where samples are proximate, even when climate shows significant variability. However, the concentration and distribution of n-alkane homologs do differ considerably between geographically separated populations in very different climate regimes. These results suggest n-alkane characteristics are not a plastic response to climate variability, and instead are likely fixed and could be driven by genetic differences between populations. This has important implications for the use of n-alkane characteristics as palaeoenvironmental proxies.

Aponte, J.C., Whitaker, D., Powner, M.W., Elsila, J.E., Dworkin, J.P., 2019. Analyses of aliphatic aldehydes and ketones in carbonaceous chondrites. ACS Earth and Space Chemistry 3, 463-472.

https://doi.org/10.1021/acsearthspacechem.9b00006

Aliphatic aldehydes and ketones are essential building blocks for the synthesis of more complex organic compounds. Despite their potentially key role as precursors of astrobiologically important molecules, such as amino acids and carboxylic acids, this family of compounds has scarcely been evaluated in carbonaceous chondrites. The paucity of such analyses likely derives from the low concentration of aldehydes and ketones in the meteorites and from the currently used chromatographic methodologies that have not been optimized for meteorite analysis. In this work, we report the development of a novel analytical method to quantify the molecular distribution and compound-specific isotopic analysis of 29 aliphatic aldehydes and ketones. Using this method, we have investigated the molecular distribution and 13C-isotopic composition of aldehydes and ketones in 10 carbonaceous chondrites from the CI, CM, CR, and CV groups. The total concentration of carbonyl compounds ranged from 130 to 1000 nmol g–1 of meteorite with formaldehyde, acetaldehyde, and acetone being the most abundant species in all investigated samples. The 13C-isotopic values ranged from −67 to +64‰ and we did not observe clear relationships between 13C-content and molecular weight. Accurately measuring the relative abundances, determining the molecular distribution, and isotopic composition of chondritic organic compounds is central in assessing both their formation chemistry and synthetic relationships.

Arab, M., Bakour, S., Lalaoui, R., Aissaoui, N., Nas, F., Hoceini, A., Fournier, P.-E., Klouche-Khelil, N., 2019. Diversity of aerobic bacilli analysis using molecular and culture-based approaches in Debagh hot spring. Geomicrobiology Journal 36, 137-147.

https://doi.org/10.1080/01490451.2018.1520937

This study reports the first attempt to describe aerobic bacilli communities in Debagh hot spring, from which 41 aerobic, thermophile, and halotolerant bacilli were isolated and selected based on morphological, physiological, and biochemical tests. 16S rDNA sequence analysis revealed that the recovered isolates belonged to four bacterial genera dominated by the genus Bacillus represented with species B. mojavensis (16), B. licheniformis (11), B. subtilis (2), B. atrophaeus (1), B.amyloliquifaciens (1), and B .pimulus (1). The genus Aeribacillus represented by the species A. pallidus (3), the genus Geobacillus represented by the species G. toebii (2), and the genus Hydrogenophilus represented by the species H. hirschii (4). While, MALDI-TOF analysis determined that isolates belonged to the genus Bacillus that contained B. licheniformis (12), B. mojavensis (6), B. subtilis (2), B. atrophaeus (1), and B. pumilus (1). Furthermore, the isolates exhibited high hydrolytic activity to casein, lecithin, tween 80, olive oil, and starch with 53.65%, 83.33%, 70.73%, 92.68%, and 56.09%, respectively. Among these isolates, 26.82% were able to hydrolyze all the substrates tested.


https://doi.org/10.1029/2018GB005983

One pathway of the biological pump that remains largely unquantified in many export models is the active transport of carbon from the surface ocean to the mesopelagic by zooplankton diel vertical migration (DVM). Here, we develop a simple representation of zooplankton DVM and implement it in a global export model as a thought experiment to illustrate the effects of DVM on carbon export and mesopelagic biogeochemistry. The model is driven by diagnostic satellite measurements of net primary production, algal biomass, and phytoplankton size structure. Due to constraints on available satellite data, the results are restricted to the latitude range from 60°N to 60°S. The modeled global export flux from the base of the euphotic zone was 6.5 PgC/year, which represents a 14% increase over the export flux in model runs without DVM. The mean (± standard deviation, SD) proportional contribution of the DVM‐mediated export flux to total carbon export, averaged over the global domain and the climatological seasonal cycle, was 0.16 ± 0.04 and the proportional contribution of DVM activity to total respiration within the twilight zone was 0.16 ± 0.06. Adding DVM activity to the model also resulted in a deep local maximum in the oxygen utilization profile. The model results were most sensitive to the assumptions for the fraction of individuals participating in DVM, the fraction of fecal pellets produced in the euphotic zone, and the fraction of grazed carbon that is metabolized.

Ashok, A., Cusack, M., Saderne, V., Krishnakumar, P.K., Rabaoui, L., Qurban, M.A., Duarte, C.M., Agustí, S., 2019. Accelerated burial of petroleum hydrocarbons in Arabian Gulf blue carbon repositories. Science of The Total Environment 669, 205-212.


Massive consumption of petroleum since the past century has led to considerable emissions into marine ecosystems. Marine sediments may accumulate substantial quantities of petroleum and associated contaminants in oil-producing areas. Here, we report accelerated accumulation of total petroleum hydrocarbons (TPH) in ‘blue carbon’ vegetated ecosystems of the Arabian Gulf – the world's most important region for oil production. In addition to increased accumulation with the onset of oil exploitation, sediment records reflect a large depositional event associated with the 1991 Gulf War, with the magnitude of these maxima varying across habitats, depending on their elevation along the shoreline. Blue carbon ecosystems of the Arabian Gulf currently bury about 2300 megagrams

(Mg) of TPHs annually and have accumulated TPH stocks of 59,799 Mg over the past 25 years alone. Massive burial and sequestration of TPH by blue carbon ecosystems is an important, but thus far unrecognized, removal mechanism in the Arabian Gulf. Conserving these ecosystems is important to avoid possible remobilization of sequestered TPH into the surrounding environment.

Atalah, J., Cáceres-Moreno, P., Espina, G., Blamey, J.M., 2019. Thermophiles and the applications of their enzymes as new biocatalysts. Bioresource Technology 280, 478-488.


Ecological and efficient alternatives to industrial processes have sparked interest for using microorganisms and enzymes as biocatalysts. One of the difficulties is finding candidates capable of resisting the harsh conditions in which industrial processes usually take place.

Extremophiles, microorganisms naturally found in “extreme” ecological niches, produce robust enzymes for bioprocesses and product development. Thermophiles like Geobacillus, Alyciclobacillus, Anoxybacillus, Pyrococcus and Thermoccocus are some of the extremophiles containing enzymes showing special promise for biocatalysis.

Glutamate dehydrogenase used in food processes, laccases and xylanases in pulp and paper processes, nitrilases and transaminases for pharmaceutical drug synthesis and lipases present in detergents, are examples of the increasing use of enzymes for biocatalytic synthesis from thermophilic microorganisms. Some of these enzymes from thermophiles have been expressed as recombinant enzymes and are already in the market.

Here we will review recent discoveries of thermophilic enzymes and their current and potential applications in industry.

Atapattu, S.N., Rosenfeld, J.M., 2019. Micro scale analytical derivatizations on solid phase. TrAC Trends in Analytical Chemistry 113, 351-356.


Analytical derivatization (AD), a subset of functional group analysis, alters the structure of an analyte to a product more suitable for analysis. The reactions impart stability to the product and a functionality that enhances sensitivity and specificity to the determinations. By targeting the functional groups for labeling AD adds selectivity to the measurements. Associated with these advantages, however, is the additional step required in sample preparation. The issue of the extra step was resolved by solid phase analytical derivatization (SPAD) which combined the extraction and derivatization step or limited the process to a one-pot reaction in which extraction and derivatization occurred on the solid phase without intermediate isolation of the analyte. Within the broad class of organic acids, SPAD provides conditions that can: derivatize both functionalities; selectively derivatize carboxylic acids in the presence of phenols by reaction at neutral pH which does not ionize phenols; derivatize phenols in the presence of acids by selectively inhibiting derivatization of carboxylic acids at alkaline pH. These reaction characteristics hold whether carboxylic acids are on different compounds or on the same compounds. In the case of carbonyls, SPAD enhances the reaction rate over solution chemistry so that both aldehydes and the usually slower reacting ketones are rapidly extracted/derivatized in one step. The derivatization incorporates chromophores, fluorophores and electrophores for purpose of detection, as well lipophilicity for purpose of extraction. In the case of primary and secondary amines, SPAD functional groups that enhance

sensitivity and/or lipophilicity. Initially, SPAD was a batch process but transitioned into a microextraction/derivatization and an automated technique.

Ausín, B., Magill, C., Haghipour, N., Fernández, Á., Wacker, L., Hodell, D., Baumann, K.-H., Eglinton, T.I., 2019. (In)coherent multiproxy signals in marine sediments: Implications for high-resolution paleoclimate reconstruction. Earth and Planetary Science Letters 515, 38-46.

http://www.sciencedirect.com/science/article/pii/S0012821X1930144X

Accurate chronologies are the backbone of paleoclimate research, yet for marine sedimentary records the same age model is often applied to co-eval components that may have experienced different pre-depositional histories, leading to aliasing in corresponding proxy signals. Here we demonstrate 14C age discrepancies among several proxy carriers and use them to highlight spatio-temporal disparities among different components of the sediment. Total organic carbon (TOC), alkenones, and alkanoic (fatty) acids have older ages than co-occurring planktonic foraminifera in corresponding depth intervals of a sediment core retrieved from the so-called ‘Shackleton Sites’ on the southwest Iberian margin off Portugal. Temporal differences are explained by the addition of pre-aged material that is transported to the site by lateral advection, rivers or wind. We then modeled the age structure and relative abundance of the different pools that might have contributed to the older ages of TOC and alkenones. Results suggest the addition of a moderate (15-20%) proportion of very old allochthonous material (18,500-49,900 yr). This information was used to deconvolve the alkenone-derived sea surface temperature (SST) record and assess the impact of allochthonous inputs on paleoclimate signals.

Ayyıldız, T., Varol, B., Karakaş, Z., Sözeri, K., 2019. Basic geochemical characteristics of lacustrine rocks in the Neogene Kağızman–Tuzluca Basin, Northeastern Turkey. Journal of Petroleum Exploration and Production Technology 9, 141-157.

https://doi.org/10.1007/s13202-018-0512-x

The Neogene Kağızman–Tuzluca Basin is located in the NE Anatolia and extends eastward into Armenia Oktemberian Basin. The Halıkışlak (Late Oligocene), Turabi and Tuzluca formations (Lower–Middle Miocene) are time equivalents of the organic-rich Oligo-Miocene Maikop Series in the Caspian region. However, depositional conditions within the KBT are appreciably different and source rocks are not as richer as it. The Halıkışlak Formation has little source rock potentials, with very low values of TOC (0.04–0.25%), HI (14–90 mg HC/TOC) and genetic potential-GP (i.e. Rock–Eval S1 + S2 = 0.05 to 0.22 mg HC/g rock). Although a peat facies sample has a relatively high TOC (6.78%), Tmax of 428 °C, HI values are very low (45 mg HC/TOC). TOC and GP values for the Tuzluca Formation are between 0.06 and 0.39 wt%, and 0.16–1.51 mg HC/g rock, respectively. Some levels of the Turabi Formation have TOC contents up to 6.14 wt%; however, mainly Tmax values are low 435 °C, and HI range from 25 to 54 mg HC/TOC. The extract of one low-maturity Turabi sample possesses biomarker distributions of an immature rock. Low relative abundance of tricyclic terpane and dominant C29 ααα (20R) are in accordance with the immature source rock. Some samples collected from the outcrops nearby Pliocene/Pleistocene lava series show localized maturation stage. We suggest that the Oligocene to Middle Miocene units could be more studied beneath the volcanic plateau.

Azmy, K., 2019. Carbon-isotope stratigraphy of the uppermost Cambrian in eastern Laurentia: implications for global correlation. Geological Magazine 156, 759-771.

https://doi.org/10.1017/S001675681800002X

The δ13C profile from an interval of the Martin Point section in western Newfoundland (Canada) spans the upper Furongian (uppermost Cambrian). The interval (~90 m) is a part of the Green Point Formation of the Cow Head Group and consists of the Martin Point (lower) and the Broom Point (upper) members. It is formed of slope marine carbonates alternating with shales (rhythmites) and conglomeratic interbeds. The preservation of the investigated micritic carbonates was meticulously evaluated by multiple petrographic and geochemical screening tools. The δ13C and δ18O values (−0.5 ± 0.8 ‰VPDB and −7.1 ± 0.3 ‰VPDB, respectively) exhibit insignificant correlation (R2 = 0.002) and similarly the correlation of δ13C values with their Sr and Mn counterparts, which supports the preservation of at least near-primary δ13C signatures that can be utilized to construct a reliable high-resolution carbon-isotope profile for global correlations.

The δ13C profile exhibits two main negative excursions, a lower broad excursion (~3 ‰) that reaches its maximum at ~70 m below the Martin Point / Broom Point members boundary and an upper narrow excursion (~2.5 ‰) immediately below the same boundary. The lower excursion can be correlated with the global latest Furongian HERB event (TOCE), which is also recognized in the C-isotope profile of the GSSP boundary section at Green Point whereas the upper excursion matches with that of the Cambrian‒Ordovician boundary in the same section. The peak of the HERB δ13C excursion is correlated with positive shifts on the Th/U and Ni profiles (redox and productivity proxies).


https://www.karger.com/DOI/10.1159/000496797

In the last decades, biodegradation as an environmentally friendly approach has raised interest in connection with the removal of hydrocarbon pollutants. Its capacity for removing pollutants strongly depends on the type of living cell and environmental conditions. The degradative activity of a new sophorolipid-producing yeast, Candida catenulata KP324968, in the removal of high concentrations of diesel from effluents was statistically evaluated considering the initial pH, the agitation speed, and the initial diesel concentration. The optimal setting of the operational variables at an initial pH of 4.7, an agitation speed of 204 rpm, and an initial diesel concentration of 93.4 g L–1 resulted in the highest total petroleum hydrocarbon removal efficiency: about 82.1% after 6 days (biodegradation rate: 0.378 g gcell–1 h–1). During the cell growth phase, the emulsification index in the medium increased and reached its highest level at 64.6% after 48 h. Further tests indicated that the emulsification capacity was obtained by in situ production of two sophorolipid molecules with an m/z of 533 and 583. In summary, its effective diesel removal and high emulsification capacity makes C. catenulata KP324968 an attractive candidate yeast for the degradation of hydrocarbons from aqueous environments.



The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.IMPORTANCE Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

Badger, M.P.S., Chalk, T.B., Foster, G.L., Bown, P.R., Gibbs, S.J., Sexton, P.F., Schmidt, D.N., Pälike, H., Mackensen, A., Pancost, R.D., 2019. Insensitivity of alkenone carbon isotopes to atmospheric CO2 at low to moderate CO2 levels. Climate of the Past 15, 539-554.

https://www.clim-past.net/15/539/2019/

Atmospheric pCO2 is a critical component of the global carbon system and is considered to be the major control of Earth's past, present, and future climate. Accurate and precise reconstructions of its concentration through geological time are therefore crucial to our understanding of the Earth system. Ice core records document pCO2 for the past 800 kyr, but at no point during this interval were CO2 levels higher than today. Interpretation of older pCO2 has been hampered by discrepancies during some time intervals between two of the main ocean-based proxy methods used to reconstruct pCO2: the carbon isotope fractionation that occurs during photosynthesis as recorded by haptophyte biomarkers (alkenones) and the boron isotope composition (δ11B) of foraminifer shells. Here, we present alkenone and δ11B-based pCO2 reconstructions generated from the same samples from the Pliocene and across a Pleistocene glacial–interglacial cycle at Ocean Drilling Program (ODP) Site 999. We find a muted response to pCO2 in the alkenone record compared to contemporaneous ice core and δ11B records, suggesting caution in the interpretation of alkenone-based records at low pCO2 levels. This is possibly caused by the physiology of CO2 uptake in the haptophytes. Our new understanding resolves some of the inconsistencies between the proxies and highlights that caution may be required when interpreting alkenone-based reconstructions of pCO2.

Bahaghighat, H.D., Freye, C.E., Synovec, R.E., 2019. Recent advances in modulator technology for comprehensive two dimensional gas chromatography. TrAC Trends in Analytical Chemistry 113, 379-391.


One of the greatest advancements in the field of gas chromatography (GC) has been the development of comprehensive two-dimensional gas chromatography (GC × GC). As the field of GC evolved from one-dimensional gas chromatography (1D-GC) to heart cutting (GC–GC), followed by the advent of GC × GC, the critical component at the center of this evolution has been the interface between the separation columns. The interface, referred to as the modulator for GC × GC, links the primary and secondary columns. This review covers the evolution of modulator systems from the founding of GC × GC in 1991 by Liu and Phillips, while focusing on the last six years. Since its inception, modulators have evolved into two distinct categories: thermal, and valve-based. The advantages and shortcomings of each category will be covered. Recent developments in the research, development, and commercialization of these various modulators is provided, with a glimpse into future modulator designs.

Bai, F., Zhao, J., Liu, Y., 2019. An investigation into the characteristics and kinetics of oil shale oxy-fuel combustion by thermogravimetric analysis. Oil Shale 36, 1–18.

https://doi.org/10.3176/oil.2019.1.01

The characteristics of Huadian oil shale combustion in O2/CO2 atmospheres were compared to those in O2/N2 atmospheres by using non-isothermal methods. The combustion kinetics parameters were calculated using the Kissinger-Akahira-Sunose (KAS) and Friedman methods. Specifically, the effect of oxygen concentration (10, 20, 30, 50, 65 and 80% O2) and heating rate (2, 5, 10 and 20 °C min−1) on the combustion reactivity and kinetics of Huadian oil shale in CO2-based and N2-based atmospheres were investigated to identify the optimal gases mixture and oxygen concentration. Comparison of the combustion performances of oil shale in CO2/O2 and N2/O2 environments indicated that the organic matter combusted earlier in CO2-based atmospheres than in N2-based atmospheres when the oxygen concentration was 10% and 20%. Meanwhile, the average activation energies of organic matter combustion in CO2-based atmospheres was higher than those in N2-based atmospheres at an oxygen concentration of 10% and 20%. With an appropriate amount of O2 and CO2, the combustion performance of oil shale in 30% O2/70% CO2 was superior to that in 30% O2/70% N2, and the combustion activation energy in the 30% O2/70% CO2 atmosphere was also lower. The similar combustion processes and activation energies of oxy-fuel and conventional combustion with oxygen concentrations above 50% indicate that oxygen plays a leading role in organic matter combustion under high oxic conditions. The results reveal that the 30% O2/70% CO2 atmosphere is optimal for oil shale combustion.



Denitrifying anaerobic methane oxidation (DAMO) is the process of coupling the anaerobic oxidation of methane (AOM) with denitrification, which plays an important part in controlling the flow of methane in anoxic niches. In this study, we explored the feasibility of microbial selenite reduction

using methane by DAMO culture. Isotopic 13CH4 and long-term experiments showed that selenite reduction was coupled to methane oxidation, and selenite was ultimately reduced to Se (0) by the analyses of scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The introduction of nitrate, the original electron acceptor in the DAMO culture, inhibited selenite reduction. Meanwhile, the microbial community of DAMO culture was significantly changed when the electron acceptor was changed from nitrate to selenite after long-term selenite reduction. High-throughput 16S rRNA gene sequencing indicated that Methylococcus (26%) became the predominant microbe performing selenite reduction and methane oxidation and the possible pathways of AOM accompanied with selenite reduction were proposed. This study revealed more potential relation during the biogeochemical cycle of carbon, nitrogen, and selenium.

Bai, Y., Zhang, H., 2019. Organic geochemistry characterization of the Yan 9 crude oils and oil-source rock correlations in Jingbian Oil Field, Ordos Basin. Petroleum Science and Technology 37, 543-550.

https://doi.org/10.1080/10916466.2018.1552972

The geochemical characteristics of the Yan 9 reservoir were analyzed by means of the group composition and the biomarkers in order to clarify the oil source of the Yan 9 reservoir in Jingbian Oil Field. The results showed that the n-alkanes are distributed with a single mode with C21 as the main carbon peak, C30hopane as the dominant biomarker, followed by C29hopane. Regular steroids are mainly C29, while C27 and C28 are similar, showing an asymmetric ?V? distribution. The Yan 9 crude oil has similar geochemical characteristics and unified material source and evolution degree. It is a mature crude oil derived from a source deposited in a weak oxidation-reduction environment under freshwater conditions. Oil-source correlation showed that the reservoir of Yan 9 mainly comes from the contribution of Chang 7 hydrocarbon source rock in Jingbian Oil Field.

Baig, I., Faleide, J.I., Mondol, N.H., Jahren, J., 2019. Burial and exhumation history controls on shale compaction and thermal maturity along the Norwegian North Sea basin margin areas. Marine and Petroleum Geology 104, 61-85.

http://www.sciencedirect.com/science/article/pii/S026481721930100X

The North Sea area has been subjected to significant erosion and subsequent deposition of sediments in the basin margin and deeper basin areas, respectively, during the late Neogene. A large amount of Cretaceous-early Quaternary sediments have been removed below the angular unconformity along the west and southwest coast of Norway and deposited in the huge North Sea Fan at the mouth of the Norwegian Channel. At the same time, a considerable thickness of early Quaternary-Paleocene sediments was also eroded towards the east in the central North Sea and subsequently deposited in the deeper basin areas to the west. This study seeks to estimate exhumation from compaction and thermal maturity based techniques by using sonic velocities of shales/carbonates and vitrinite reflectance data in a large number of boreholes in the central, eastern and northern North Sea. The results indicate no or minor exhumation in the Central Graben and flanking high areas, whereas more than ∼1 km sediments are eroded in the basin margin areas towards the Norwegian coast. More than ∼500 m sediments are eroded in the Egersund Basin and Stord Basin areas. A similarity of exhumation estimates from the Early Cretaceous-Early Miocene shales and Late Cretaceous-Early Paleocene carbonates indicates maximum burial sometime after the Early Miocene in most of the central and northern North Sea areas. However, the maximum burial throughout the North Sea Basin may be diachronous. Seismostratigraphic analysis indicates maximum burial sometime during the Oligocene in the Sorgenfrei-Tornquist Zone area in the eastern North Sea. Maximum burial in the Norwegian-Danish Basin varies from Miocene-Pliocene in eastern parts to early Pleistocene in western parts,

whereas sediments are currently at their maximum burial in the Central Graben and southern Viking Graben areas. Restoration of surface elevations to their original position before the onset of erosion indicated large subaerially exposed areas in the Norwegian-Danish Basin and along the southwest coast of Norway. This is also supported by predominantly coastal and/or deltaic environments in the Norwegian-Danish Basin area during the late Neogene. These subaerially exposed areas may be linked to the regional tilting and erosion of the basin margin areas to the east and progressive basinward migration of deposition centres to the west since the Oligocene. The exhumation had significant effects on the petroleum system in the basin margin areas by cooling down the source rock. However, the deeper burial of sediments may also have changed the rheological properties of sediments from more ductile to brittle due to compaction and diagenetic processes which makes them more failure prone during exhumation leading to hydrocarbon leakage or seal failure in case of CO2 injection.


https://www.frontiersin.org/article/10.3389/fmicb.2019.00377

We analyzed the polar membrane lipids of thirteen strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2 and (d) novel cardiolipins contained a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the thirteen strains could be generally separated into groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glyc¬erol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the thirteen strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.



This study presents a 3D numerical model of a study area in the NW part of the Persian Gulf, offshore SW Iran. The purpose is to investigate the burial and thermal history of the region from the Cretaceous to the present day, and to investigate the location of hydrocarbon generating kitchens and the relative timing of hydrocarbon generation/migration versus trap formation. The study area covers about 20,000 km2 and incorporates part of the intra‐shelf Garau‐Gotnia Basin and the adjacent Surmeh‐Hith carbonate platform. A conceptual model was developed based on the interpretation of 2700 km of 2D seismic lines, and depth and thickness maps were created tied to data from 20 wells. The thermal model was calibrated using bottom‐hole temperature and vitrinite reflectance data from ten wells, taking into account the main phases of erosion/non‐deposition and the variable temporal and spatial heat flow histories. Estimates of eroded thicknesses and the determination of heat‐flow values were performed by burial and thermal history reconstruction at various well and pseudo‐well locations. Burial, temperature and maturation histories are presented for four of these locations. Detailed modelling results for Neocomian and Albian source rock successions are provided for six locations in the intra‐shelf basin and the adjacent carbonate platform. Changes in sediment supply and depocentre migration through time were analyzed based on isopach maps representing four stratigraphic intervals between the Tithonian and the Recent. Backstripping at various locations indicates variable tectonic subsidence and emergence at different time periods.

The modelling results suggest that the convergence between the Eurasian and Arabian Plates which resulted in the Zagros orogeny has significantly influenced the burial and thermal evolution of the region. Burial depths are greatest in the study area in the Binak Trough and Northern Depression. These depocentres host the main kitchen areas for hydrocarbon generation, and the organic‐rich Neocomian and Albian source rock successions have been buried sufficiently deeply to be thermally mature. Early oil window maturities for these successions were reached between the Late Cretaceous (90 Ma) and the early Miocene (18 Ma) at different locations, and hydrocarbon generation may continue at the present‐day.

Bar-On, Y.M., Milo, R., 2019. Towards a quantitative view of the global ubiquity of biofilms. Nature Reviews Microbiology 17, 199-200.

https://doi.org/10.1038/s41579-019-0162-0

Biofilms are a fundamental form of microbial life and occur in diverse environments, ranging from the mammalian gut to deep subsurface rocks. It is often claimed that most bacteria and archaea live in biofilms, but this claim awaits quantification. Recent updates on global microbial cell numbers prompt a revisiting of this question.

Barabasch, J., Ducros, M., Hawie, N., Bou Daher, S., Nader, F.H., Littke, R., 2019. Integrated 3D forward stratigraphic and petroleum system modeling of the Levant Basin, Eastern Mediterranean. Basin Research 31, 228-252.

https://doi.org/10.1111/bre.12318

The Eastern Mediterranean Levant Basin is a proven hydrocarbon province with recent major gas discoveries. To date, no exploration wells targeted its northern part, in particular the Lebanese

offshore. The present study assesses the tectono-stratigraphic evolution and related petroleum systems of the northern Levant Basin via an integrated approach that combines stratigraphic forward modeling and petroleum systems/basin modeling based on the previous published work. Stratigraphic modeling results provide a best-fit realisation of the basin-scale sedimentary filling, from the post-rift Upper Jurassic until the Pliocene. Simulation results suggest dominant eastern marginal and Arabian Plate sources for Cenozoic siliciclastic sediments and a significant contribution from the southern Nilotic source mostly from Lower Oligocene to Lower Miocene. Basin modeling results suggest the presence of a working thermogenic petroleum system with mature source rocks localised in the deeper offshore. The generated hydrocarbons migrated through the deep basin within Jurassic and Cretaceous permeable layers towards the Latakia Ridge in the north and the Levant margin and offshore topographic highs. Furthermore, the basin model indicates a possibly significant influence of salt deposition during Messinian salinity crisis on formation fluids. Ultimately, the proposed integrated workflow provides a powerful tool for the assessment of petroleum systems in underexplored areas.

Barakat, A.O., Mostafa, A.R., El-Gayar, M.S., Omar, M.F., 2019. Organic geochemical characterization of crude oils based on alkanes and acyclic isoprenoids distribution. Petroleum Science and Technology 37, 243-254.

https://doi.org/10.1080/10916466.2018.1539747

A variety of biomarker and non-biomarker parameters has been used to geochemical characterization of seven crude oils from the Gulf of Suez region of Egypt. The carbon number distribution and the identities of specific compounds were determined by GC and GC?MS analysis of the saturated fraction obtained by liquid chromatography. n-Alkanes ranging from C10 to C35 were the major constituent series, while acyclic isoprenoids from C13 to C20 except C17, iso- and anteiso-alkanes and cyclic alkanes were the minor constituent series. The close range of bulk property values and biomarker distribution indicated that the investigated oils are belong to only one type. Correlation plots between biomarker and non-biomarker parameters revealed that the oil samples are typical of crude oils generated from marine sediments deposited in suboxic conditions.

Barakat, M.A., Abd El-Gawad, E.A., Gaber, M.A.W., Lotfy, M.A., Abd El Ghany, A.A., 2019. Mineralogical and geochemical studies of oil shale deposits in the Cretaceous/Paleogene succession at Quseir area, Egypt. Egyptian Journal of Petroleum 28, 11-19.


Cretaceous/Paleogene succession in Quseir area represents one of the most important economic sedimentary rocks, which contain phosphate and oil shale beds. Oil shale samples selected from nine mines around Quseir area were subjected to mineralogical, petrographical and geochemical analyses. As raveled by X-ray diffraction analysis, the oil shale samples are composed of calcite, quartz, dolomite, smectite, kaolinite, gypsum and pyrite. The petrographical investigation of the studied oil shales indicates the dominance of two microfacies: calcareous foraminiferal claystone and Calci-mudstone. The EDX results of oil shale samples show that the pyrite found as framboidal-disseminated particles in smectite. The high ratio of the sulfur and organic carbon contents in the selected mines indicate highly reducing environment. Five mines (El-Nakheil, Abu Tundub, Abu Tundub Bahree, El Beida and Hammadat) are markedly rich in organic content and can be considered as good to excellent source rock.

Barge, L.M., Flores, E., Baum, M.M., VanderVelde, D.G., Russell, M.J., 2019. Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems. Proceedings of the National Academy of Sciences 116, 4828-4833.

https://doi.org/10.1073/pnas.1812098116

Significance: Amino acids are formed from simple organic precursors in iron oxyhydroxide mineral systems that contain geochemical gradients. Redox and pH gradients significantly impact reaction pathways: Amino acids only form when the mineral contains both oxidized and reduced iron, and when the surrounding solution is alkaline. This shows that aqueous, partially reducing iron mineral systems (which would have been common in early-Earth seafloor/vent environments) could have facilitated synthesis and concentration of prebiotic organic molecules relevant for the emergence of life. It also suggests that geochemical gradients in vent environments can drive product selectivity for prebiotic chemistry, perhaps leading to more complex organic reaction systems as these molecules continue to diffuse and react under different conditions within the gradients.

Abstract: Iron oxyhydroxide minerals, known to be chemically reactive and significant for elemental cycling, are thought to have been abundant in early-Earth seawater, sediments, and hydrothermal systems. In the anoxic Fe2+-rich early oceans, these minerals would have been only partially oxidized and thus redox-active, perhaps able to promote prebiotic chemical reactions. We show that pyruvate, a simple organic molecule that can form in hydrothermal systems, can undergo reductive amination in the presence of mixed-valence iron oxyhydroxides to form the amino acid alanine, as well as the reduced product lactate. Furthermore, geochemical gradients of pH, redox, and temperature in iron oxyhydroxide systems affect product selectivity. The maximum yield of alanine was observed when the iron oxyhydroxide mineral contained 1:1 Fe(II):Fe(III), under alkaline conditions, and at moderately warm temperatures. These represent conditions that may be found, for example, in iron-containing sediments near an alkaline hydrothermal vent system. The partially oxidized state of the precipitate was significant in promoting amino acid formation: Purely ferrous hydroxides did not drive reductive amination but instead promoted pyruvate reduction to lactate, and ferric hydroxides did not result in any reaction. Prebiotic chemistry driven by redox-active iron hydroxide minerals on the early Earth would therefore be strongly affected by geochemical gradients of Eh, pH, and temperature, and liquid-phase products would be able to diffuse to other conditions within the sediment column to participate in further reactions.

Barik, S.S., Singh, R.K., Jena, P.S., Tripathy, S., Sharma, K., Prusty, P., 2019. Spatio-temporal variations in ecosystem and CO2 sequestration in coastal lagoon: A foraminiferal perspective. Marine Micropaleontology 147, 43-56.


Seasonal variability in fresh water influx and ingression of sea water establish a unique transition zone in Asia's largest coastal lagoon – the Chilika lake. The seasonal variability in water and sediment input has significant impacts on the ecosystem influencing the rate of CO2 sequestration. We have assessed the impact of seasonal variability on CO2 sequestration using foraminiferal analysis and grain size data end member modeling. Lake floor sediment samples were collected seasonally, besides in situ measurements of physicochemical parameters of the lake bottom water at fixed stations influenced by seasonally variable fresh and saline water influx. Low electrical conductivity, pH of bottom water and absence of calcareous foraminifera suggest that the region proximal to the river mouth has fresh water ecosystem and has very limited role in CO2 sequestration. The region near to the sea mouth experiences high energy condition and seasonally changes from brackish to marine water ecosystem are ideal for diversification and opportunistic populations of foraminifera,

but not ideal for flourishing (high population) of calcareous foraminifera. Inter-mixing of fresh and saline sea water develops fresh to brackish water conditions with medium energy condition in the interior region. These locations are away from the river and sea mouths and have high calcareous foraminifera abundances, but low diversity along with high bottom water pH suggesting seasonal variations in the sinking of CO2. Like other shallow coastal areas, Ammonia beccarii and Ammonia tepida are the dominant calcareous species, but their smaller size suggests a seasonal stressed condition. The opening of new and artificial sea mouth has increased the inflow of sea water into the lagoon that maintains its brackish water conditions, suggested by significant increase in calcareous foraminifera abundance. The sinking of these calcareous foraminifera may enhance the rate of CO2 sequestration and reduce degassing of dissolved carbon carried by the fresh water to the atmosphere.

Barreteau, H., Vandervennet, M., Guédon, L., Point, V., Canaan, S., Rebuffat, S., Peduzzi, J., Carré-Mlouka, A., 2019. Haloarcula sebkhae sp. nov., an extremely halophilic archaeon from Algerian hypersaline environment. International Journal of Systematic and Evolutionary Microbiology 69, 732-738.

https://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.003211

A halophilic organism, SWO25T, was isolated from water sampled in Algeria at the salt lake (sebkha) of Ouargla. The novel strain stained Gram-negative, and cells were pleomorphic with a red pigmentation. Strain SWO25T grew optimally at 35–45 °C, at pH 6.0–8.0 and 0.05–0.25 M MgCl2 concentrations. Cells were extremely halophilic, with optimal growth at 4.3–5.1 M NaCl. The predominant membrane polar lipids were C20C20 glycerol diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate, phosphatidylglycerol sulfate, triglycosyl diether and diglycosyl diether. The major respiratory menaquinone component was MK-8. Cells were highly tolerant to the presence of decane and isooctane in the growth medium. Chemotaxonomic properties supported the assignment of strain SWO25T to the genus Haloarcula . The DNA G+C content was 61.1mol%. DNA–DNA hybridization and phylogenetic analyses of the 16S rRNA and rpoB′ genes showed that strain SWO25T is distinct from known Haloarcula species. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic data, we describe a novel species of the genus Haloarcula , for which the name Haloarcula sebkhae sp. nov. is proposed. The type strain is SWO25T (=CIP 110583T=JCM 19018T).

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, rrnA and rpoB' gene sequences of strain SWO25 T are HQ844527 and KJ644779, respectively.

Bartl, B., Zapletal, M., Urbánek, Š., Slavíková, M.K., Trejbal, J., Hrdlička, Z., 2019. Why do historical beeswax seals become brittle over time? Studies in Conservation 64, 138-145.

https://doi.org/10.1080/00393630.2018.1544430

Mechanical properties of aged beeswax were studied by an indirect measurement, using hydrogenated beeswax as a model material. The adequacy of the model was evaluated by comparison of its chemical composition and thermal properties with those of samples of historical beeswax. It was found that the gradual decrease in content of unsaturated compounds in beeswax contributes significantly to changes of its mechanical properties. As a consequence, beeswax artefacts become increasingly prone to mechanical damage during natural ageing. Understanding the difference between mechanical properties of recent and historical beeswax is primarily important from the point of view of safe handling and storage of such artefacts. Besides, this knowledge could help conservation scientists, e. g. when preparing model samples for testing new conservation methods.



The surface mining of oil sands north of Fort McMurray, Alberta produces considerable tailings waste that is stored in large tailings ponds on industrial lease sites. Viable strategies for the detoxification of oil sands process affected water (OSPW) are under investigation. In order to assess the toxic potential of the suite of dissolved organics in OSPW, a method for their extraction and fractionation was developed using solid phase extraction. The method successfully isolated organic compounds from 180 L of an aged OSPW source. Using acidic- or alkaline-conditioned non-polar ENV+ resin and soxhlet extraction with ethyl acetate and methanol, three fractions (F1–F3) were generated. Chemical characterization of the generated fractions included infusion to electrospray ionization ultrahigh-resolution mass spectrometry (ESI-UHRMS), liquid chromatography quadrupole time-of-flight mass spectrometry, gas chromatography triple quadrupole time-of-flight mass spectrometry, and synchronous fluorescence spectroscopy (SFS). Additionally, ESI-UHRMS class distribution data and SFS identified an increased degree of oxygenation and aromaticity, associated with increased polarity. Method validation, which included method and matrix spikes with surrogate and labelled organic mono carboxylic acid standards, confirmed separation according to acidity and polarity with generally good recoveries (average 76%). Because this method is capable of extracting large sample volumes, it is amenable to thorough chemical characterization and toxicological assessments with a suite of bioassays. As such, this protocol will facilitate effects-directed analysis of toxic components within bitumen-influenced waters from a variety of sources.



The process of surface mining and extracting bitumen from oil sand produces large quantities of tailings and oil sands process-affected water (OSPW). The industry is currently storing OSPW on-site while investigating strategies for their detoxification. One such strategy relies on the biodegradation of organic compounds by indigenous microbes, resulting in aged tailings waters with reduced toxicity. This study assessed the toxicity of OSPW aged statically for approximately 18 years. Dissolved organics in aged OSPW were fractionated using a preparative solid-phase extraction method that generated three organic fractions (F1–F3) of increasing polarity. Eight aquatic species from different trophic levels were exposed to whole OSPW (WW) and the derived OSPW organic fractions to assess toxicity: Pimephales promelas, Oryzias latipes, Vibrio fischeri, Daphnia magna, Lampsilis cardium, Hyalella azteca, Ceriodaphnia dubia, and Hexagenia spp. Broad comparisons revealed that P. promelas and H. azteca were most sensitive to dissolved organics within aged OSPW, while WW was most toxic to L. cardium and H. azteca. Three cases of possible contaminant interactions occurred within whole OSPW treatments, as toxicity was higher than organic fractions for H. azteca and L. cardium, and lower for P. promelas. As such, the drivers of toxicity appeared to be dependent on the species exposed. Of the organic fractions assessed, F3 (most polar) was the most toxic overall while F2 (intermediate polarity) displayed little toxicity to all species evaluated. This presents strong evidence that classical mono-carboxylic naphthenic acids, mostly present in F1 (least

polar), are not primarily responsible for the toxicity in aged tailings. The current study indicates that although the aged tailings source (≥18 years) did not display acute toxicity to the majority of organisms assessed, inorganic components and polyoxygenated organics may pose a persistent concern to some aquatic organisms.

Baveye, P.C., Wander, M., 2019. The (bio)chemistry of soil humus and humic substances: Why is the “new view” still considered novel after more than 80 years? Frontiers in Environmental Science 7, 27. doi: 10.3389/fenvs.2019.00027.

https://www.frontiersin.org/article/10.3389/fenvs.2019.00027

Three years ago, a novel “soil continuum model” was proposed, in which soil organic matter was suggested to be of heterogeneous composition and to consist of a continuum of organic fragments of all sizes. A search of the literature reveals that this model is identical to several similar conceptualizations proposed about 15 years ago, and that it corresponds closely with the description of humic substances given in Waksman’s (1936) remarkably thorough book on the topic, that also emphasized the intimate connections existing between humic substances and soil microorganisms. Several historical reasons, reviewed in this Perspective article, may explain why Waksman’s viewpoint might still be considered novel more than 80 years later. Here we argue that the key reason for the agonizingly slow rate of progress in the field is linked to the extreme compartmentalization of research and education in soil science, which has been organized along distinct subdisciplines, with the result that interdisciplinary efforts that are desperately needed to understand the dynamics of soil humic substances are very hard to launch. To meet growing demands on soils we need to understand the mechanisms that underpin their many functions. To gain this understanding and finally make badly needed progress, we must reorganize funding and educational efforts to support exploration of “Waksman’s frontier”, which includes the microscale where the microbial, physical and biochemical processes governing organic matter turnover occur.

Bayestehparvin, B., Farouq Ali, S.M., Abedi, J., 2019. Solvent-based and solvent-assisted recovery processes: State of the art. SPE Reservoir Evaluation & Engineering 22, 29-49.

https://doi.org/10.2118/179829-PA

Steam injection is a widely used oil-recovery method that has been commercially successful in many types of heavy-oil reservoirs, including the oil sands of Alberta, Canada. Steam is very effective in delivering heat that is the key to heavy-oil mobilization. In the distant past in California, and also recently in Alberta, solvents were/are being used as additives to steam for additional viscosity reduction. The current applications are in field projects involving steam-assisted gravity drainage (SAGD) and cyclic steam stimulation (CSS).

The past and present projects using solvents alone or in combination with steam are reviewed and evaluated, including enhanced solvent SAGD (ES-SAGD) and liquid addition to steam for enhancing recovery (LASER). The use of solvent in other processes, such as effective solvent extraction incorporating electromagnetic heating (ESEIEH) and after cold-heavy-oil production with sand (CHOPS), are also reviewed. The theories behind the use of solvents with steam are outlined. These postulate additional heavy-oil/bitumen mobilization; oil mobilization ahead of the steam front; and oil mobilization by solvent dispersion caused by frontal instability. The plausibility of the different approaches and solvent availability and economics are also discussed.

Beaton, K.H., Chappell, S.P., Abercromby, A.F.J., Miller, M.J., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Payler, S.J., Hughes, S.S., Lim, D.S.S., 2019. Assessing the acceptability of science operations concepts and the level of mission enhancement of capabilities for human Mars exploration extravehicular activity. Astrobiology 19, 321-346.

https://doi.org/10.1089/ast.2018.1912

The Biologic Analog Science Associated with Lava Terrains (BASALT) research project is investigating tools, techniques, and strategies for conducting Mars scientific exploration extravehicular activity (EVA). This has been accomplished through three science-driven terrestrial field tests (BASALT-1, BASALT-2, and BASALT-3) during which the iterative development, testing, assessment, and refinement of concepts of operations (ConOps) and capabilities were conducted. ConOps are the instantiation of operational design elements that guide the organization and flow of personnel, communication, hardware, software, and data products to enable a mission concept. Capabilities include the hardware, software, data products, and protocols that comprise and enable the ConOps. This paper describes the simulation quality and acceptability of the Mars-forward ConOps evaluated during BASALT-2. It also presents the level of mission enhancement and acceptability of the associated Mars-forward capabilities. Together, these results inform science operations for human planetary exploration.

Beaton, K.H., Chappell, S.P., Abercromby, A.F.J., Miller, M.J., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Payler, S.J., Hughes, S.S., Lim, D.S.S., 2019. Using science-driven analog research to investigate extravehicular activity science operations concepts and capabilities for human planetary exploration. Astrobiology 19, 300-320.

https://doi.org/10.1089/ast.2018.1861

Biologic Analog Science Associated with Lava Terrains (BASALT) is a science-driven exploration program seeking to determine the best tools, techniques, training requirements, and execution strategies for conducting Mars-relevant field science under spaceflight mission conditions. BASALT encompasses Science, Science Operations, and Technology objectives. This article outlines the BASALT Science Operations background, strategic research questions, study design, and a portion of the results from the second field test. BASALT field tests are used to iteratively develop, integrate, test, evaluate, and refine new concepts of operations (ConOps) and capabilities that enable efficient and productive science. This article highlights the ConOps investigated during BASALT in light of future planetary extravehicular activity (EVA), which will focus on scientific exploration and discovery, and serves as an introduction to integrating exploration flexibility with operational rigor, the value of tactical and strategic science planning and execution, and capabilities that enable and enhance future science EVA operations.



Understanding formation mechanisms of modern microbialites enables interpretation of biosignatures associated with fossilized stromatolites. Photosynthetic influences on carbonate precipitation are one proposed mechanism. Photosynthetic isotope biosignatures (13C) associated with freshwater microbialites in Pavilion Lake, British Columbia were widespread through the lake but less prevalent

with increasing depth. Importantly, they were variably detectable on the exterior surface of individual microbialites. At depths ≤18 m, microbialite surface carbonates, associated with either nodular microbial communities or surface biofilms, had δ13Ccarb values up to +3.7‰ that were 13C-enriched above the predicted range of δ13Ccarb values for equilibrium precipitation from bulk ambient lake water dissolved inorganic carbon (DIC) (predicted mean δ13Ccarb = −0.2 ± 1.3‰). Vertical profiles of exterior, non-nodular biofilm present on microbialites collected from depths of 21 m and below showed instances of 13C-enrichment near the apex, consistent with hypothesized maximum light exposure. With increased distance from the apex toward the structure base, δ13Ccarb values typically decreased into the predicted range of equilibrium δ13C values. Surface biosignatures persisted internally for distances of 0.5 to 2 cm below the exterior of the structures, beyond which they fell within the predicted isotopic equilibrium range. This shift in δ13Ccarb values may be due to secondary carbonate precipitation masking of the 13C-enriched signature. The contribution of secondary carbonate precipitation was estimated to be 14–59% of total carbonate mass if derived from heterotroph-influenced or bulk lake DIC, respectively. Growth rate estimates suggested these accretion processes can mask photosynthetic signatures in 20–400 years.

Belcher, A., Henson, S.A., Manno, C., Hill, S.L., Atkinson, A., Thorpe, S.E., Fretwell, P., Ireland, L., Tarling, G.A., 2019. Krill faecal pellets drive hidden pulses of particulate organic carbon in the marginal ice zone. Nature Communications 10, Article 889.

https://doi.org/10.1038/s41467-019-08847-1

The biological carbon pump drives a flux of particulate organic carbon (POC) through the ocean and affects atmospheric levels of carbon dioxide. Short term, episodic flux events are hard to capture with current observational techniques and may thus be underrepresented in POC flux estimates. We model the potential hidden flux of POC originating from Antarctic krill, whose swarming behaviour could result in a major conduit of carbon to depth through their rapid exploitation of phytoplankton blooms and bulk egestion of rapidly sinking faecal pellets (FPs). Our model results suggest a seasonal krill FP export flux of 0.039 GT C across the Southern Ocean marginal ice zone, corresponding to 17–61% (mean 35%) of current satellite-derived export estimates for this zone. The magnitude of our conservatively estimated flux highlights the important role of large, swarming macrozooplankton in POC export and, the need to incorporate such processes more mechanistically to improve model projections.

Bellenberg, S., Huynh, D., Poetsch, A., Sand, W., Vera, M., 2019. Proteomics reveal enhanced oxidative stress responses and metabolic adaptation in Acidithiobacillus ferrooxidans biofilm cells on pyrite. Frontiers in Microbiology 10, 592. doi: 510.3389/fmicb.2019.00592.


Reactive oxygen species (ROS) cause oxidative stress and growth inhibition by inactivation of essential enzymes, DNA and lipid damage in microbial cells. Acid mine drainage (AMD) ecosystems are characterized by low pH values, enhanced levels of metal ions and low species abundance. Furthermore, metal sulfides, such as pyrite and chalcopyrite, generate extracellular ROS upon exposure to acidic water. Consequently, oxidative stress management is especially important in acidophilic leaching microorganisms present in industrial biomining operations, especially when forming biofilms on metal sulfides. Several adaptive mechanisms have been described, but the molecular repertoire of responses upon exposure to pyrite and the presence of ROS are not thoroughly understood in acidophiles. In this study the impact of the addition of H2O2 on iron oxidation activity in Acidithiobacillus ferrooxidans DSM 14882T was investigated. Iron(II)- or

sulfur-grown cells showed a higher sensitivity towards H2O2 than pyrite-grown ones. In order to elucidate which molecular responses may be involved, we used shot-gun proteomics and compared proteomes of cells grown with iron(II)-ions against biofilm cells, grown for five days in presence of pyrite as sole energy source. In total 1157 proteins were identified. 213 and 207 ones were found to have increased levels in iron(II)-grown or pyrite-biofilm cells, respectively. Proteins associated with inorganic sulfur compound (ISC) oxidation were among the latter. In total, 80 proteins involved in ROS degradation, thiol redox regulation, macromolecule repair mechanisms, biosynthesis of antioxidants, as well as metal and oxygen homeostasis were found. 42 of these proteins had no significant changes in abundance, while 30 proteins had increased levels in pyrite-biofilm cells. New insights in ROS mitigation strategies, such as importance of globins for oxygen homeostasis and prevention of unspecific reactions of free oxygen that generate ROS are presented for A. ferrooxidans biofilm cells. Furthermore, proteomic analyses provide insights in adaptations of carbon fixation and oxidative phosphorylation pathways under these two growth conditions.

Benally, C., Messele, S.A., Gamal El-Din, M., 2019. Adsorption of organic matter in oil sands process water (OSPW) by carbon xerogel. Water Research 154, 402-411.


This study illustrated the preparation, characterization and the use of carbon xerogel materials for the adsorption of acid-extractable fractions (AEF) and naphthenic acids (NAs) from oil sands process water (OSPW). Adsorption results demonstrated that the mesoporous carbonaceous material can successfully be used to adsorb persistent and toxic organic contaminants from OSPW. Carbon xerogel (CX) made at pH 5.5 showed high surface area (573 m2/g) and removed a larger amount of AEF than CX made at pH 6.9 (391 m2/g). The adsorption equilibrium was reached by 24 h for both AEF and classical NAs. 74.6% of AEF and 88.8% of classical NAs were removed by CX5.5 during 24-h adsorption. With respect to classical NAs, a larger the carbon number resulted in higher NA removal. Carbon number had more influence on NA removal when compared with hydrogen deficiency resulting from rings or unsaturated bonding formation (–Z number). The equilibrium adsorption capacity was found to be 15 mg AEF/g and 7.8 mg NAs/g for CX5.5. Adsorption of AEF and classical NAs onto CX5.5 followed pseudo-second order kinetics. With respect to diffusion of AEF and NAs, there were three distinct diffusion regions: bulk, film and pore. Pore diffusion had the lowest rate constant in all cases analyzed and was thus the rate limiting step. The results of this study showed that a mesoporous carbonaceous material such as CX may have the potential to be utilized in a fixed bed adsorption/filtration systems for continuous treatment of OSPW or as a semi-passive treatment method in pit lakes for the removal of organic constituents from OSPW.


http://science.sciencemag.org/content/363/6433/eaau0323.abstract

Editor's Summary: Automating geoscience analysis. Solid Earth geoscience is a field that has very large set of observations, which are ideal for analysis with machine-learning methods. Bergen et al. review how these methods can be applied to solid Earth datasets. Adopting machine-learning techniques is important for extracting information and for understanding the increasing amount of complex data collected in the geosciences.

Structured Abstract

Background: The solid Earth, oceans, and atmosphere together form a complex interacting geosystem. Processes relevant to understanding Earth’s geosystem behavior range in spatial scale from the atomic to the planetary, and in temporal scale from milliseconds to billions of years. Physical, chemical, and biological processes interact and have substantial influence on this complex geosystem, and humans interact with it in ways that are increasingly consequential to the future of both the natural world and civilization as the finiteness of Earth becomes increasingly apparent and limits on available energy, mineral resources, and fresh water increasingly affect the human condition. Earth is subject to a variety of geohazards that are poorly understood, yet increasingly impactful as our exposure grows through increasing urbanization, particularly in hazard-prone areas. We have a fundamental need to develop the best possible predictive understanding of how the geosystem works, and that understanding must be informed by both the present and the deep past. This understanding will come through the analysis of increasingly large geo-datasets and from computationally intensive simulations, often connected through inverse problems. Geoscientists are faced with the challenge of extracting as much useful information as possible and gaining new insights from these data, simulations, and the interplay between the two. Techniques from the rapidly evolving field of machine learning (ML) will play a key role in this effort.

Advances: The confluence of ultrafast computers with large memory, rapid progress in ML algorithms, and the ready availability of large datasets place geoscience at the threshold of dramatic progress. We anticipate that this progress will come from the application of ML across three categories of research effort: (i) automation to perform a complex prediction task that cannot easily be described by a set of explicit commands; (ii) modeling and inverse problems to create a representation that approximates numerical simulations or captures relationships; and (iii) discovery to reveal new and often unanticipated patterns, structures, or relationships. Examples of automation include geologic mapping using remote-sensing data, characterizing the topology of fracture systems to model subsurface transport, and classifying volcanic ash particles to infer eruptive mechanism. Examples of modeling include approximating the viscoelastic response for complex rheology, determining wave speed models directly from tomographic data, and classifying diverse seismic events. Examples of discovery include predicting laboratory slip events using observations of acoustic emissions, detecting weak earthquake signals using similarity search, and determining the connectivity of subsurface reservoirs using groundwater tracer observations.

Outlook: The use of ML in solid Earth geosciences is growing rapidly, but is still in its early stages and making uneven progress. Much remains to be done with existing datasets from long-standing data sources, which in many cases are largely unexplored. Newer, unconventional data sources such as light detection and ranging (LiDAR), fiber-optic sensing, and crowd-sourced measurements may demand new approaches through both the volume and the character of information that they present.

Practical steps could accelerate and broaden the use of ML in the geosciences. Wider adoption of open-science principles such as open source code, open data, and open access will better position the solid Earth community to take advantage of rapid developments in ML and artificial intelligence. Benchmark datasets and challenge problems have played an important role in driving progress in artificial intelligence research by enabling rigorous performance comparison and could play a similar role in the geosciences. Testing on high-quality datasets produces better models, and benchmark datasets make these data widely available to the research community. They also help recruit expertise from allied disciplines. Close collaboration between geoscientists and ML researchers will aid in making quick progress in ML geoscience applications. Extracting maximum value from geoscientific data will require new approaches for combining data-driven methods, physical modeling, and algorithms capable of learning with limited, weak, or biased labels. Funding opportunities that target the intersection of these disciplines, as well as a greater component of data science and ML education in the geosciences, could help bring this effort to fruition.

Abstract: Understanding the behavior of Earth through the diverse fields of the solid Earth geosciences is an increasingly important task. It is made challenging by the complex, interacting, and multiscale processes needed to understand Earth’s behavior and by the inaccessibility of nearly all of Earth’s subsurface to direct observation. Substantial increases in data availability and in the increasingly realistic character of computer simulations hold promise for accelerating progress, but developing a deeper understanding based on these capabilities is itself challenging. Machine learning will play a key role in this effort. We review the state of the field and make recommendations for how progress might be broadened and accelerated.

Berghuis, B.A., Yu, F.B., Schulz, F., Blainey, P.C., Woyke, T., Quake, S.R., 2019. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proceedings of the National Academy of Sciences 116, 5037-5044.


Significance: Methane-producing microorganisms are thought to be among the earliest cellular life forms colonizing our planet, and are major contributors to the past and present global carbon cycle. Currently, all methanogens belong to the archaeal domain of life, and there is compounding evidence for a variety of methanogenic metabolisms among a wide distribution of archaeal phyla. However, the predominantly hydrogenotrophic (CO2-fixing) Euryarchaeota are distinct from the recently discovered methylotrophic (biomass-degrading) noneuryarchaea, making the shared ancestry and origins of all methanogens unclear. We discovered hydrogenotrophic methanogenesis in a thermophilic order of the Verstraetearchaeota, a noneuryarchaeote. The Verstraetearchaeota, hitherto known as methylotrophs, unify the origins of methanogenesis and shed light on how organisms can evolve to adapt from hydrogenotrophic to methylotrophic methane metabolism.

Abstract: Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

Berndt, C., Chi, W.C., Jegen, M., Lebas, E., Crutchley, G., Muff, S., Hölz, S., Sommer, M., Lin, S., Liu, C.S., Lin, A.T., Klaeschen, D., Klaucke, I., Chen, L., Hsu, H.H., Kunath, P., Elger, J., McIntosh, K.D., Feseker, T., 2019. Tectonic controls on gas hydrate distribution off SW Taiwan. Journal of Geophysical Research: Solid Earth 124, 1164-1184.

https://doi.org/10.1029/2018JB016213

Abstract: The northern part of the South China Sea is characterized by widespread occurrence of bottom simulating reflectors indicating the presence of marine gas hydrate. Because the area covers both a tectonically inactive passive margin and the termination of a subduction zone, the influence of tectonism on the dynamics of gas hydrate systems can be studied in this region. Geophysical data show that there are multiple thrust faults on the active margin while much fewer and smaller faults exist in the passive margin. This tectonic difference matches with a difference in the geophysical characteristics of the gas hydrate systems. High hydrate saturation derived from ocean bottom seismometer data and controlled source electromagnetic data and conspicuous high‐amplitude reflections in P‐Cable 3‐D seismic data above the bottom simulating reflector are found in the anticlinal ridges of the active margin. In contrast, all geophysical evidence for the passive margin points to normal to low hydrate saturations. Geochemical analyses of gas samples collected at seep sites on the active margin show methane with heavy δ13C isotope composition, while gas collected at the passive margin shows light carbon isotope composition. Thus, we interpret the passive margin as a typical gas hydrate province fueled by biogenic production of methane and the active margin gas hydrate system as a system that is fueled not only by biogenic gas production but also by additional advection of thermogenic methane from the subduction system.

Plain Language Summary: Gas hydrates are ice‐like crystals in marine sediments. They store an enormous amount of carbon and may be used as a future energy source. So far, little is known about the geological processes that control the distribution of gas hydrates. In this study we have combined a very wide range of geophysical and geochemical data to find out if the movements in the Earth crusts matter for the amount of gas hydrate in the surface rocks. We found out that there is much more hydrate in areas where there is a lot of movement than in those that are stable. This contradicts the previously held believes. It seems a good idea to focus hydrate exploration close to subduction zones rather than on old continental margins.



Integrated petrophysical analysis is used in conventional and unconventional reservoirs to visualize the distribution pattern of different lithofacies and interpret depositional environments. In this study, core data from 17 wells and well logs from 517 wells are used to construct 3D data-driven lithofacies models for the upper and lower shale members in the Bakken Formation of the Williston basin in North Dakota, United States. The principal objective of this multi-scale (core, well log, and regional) study is to use the petrophysical response of lithofacies defined in core from a very limited number of wells to identify different shale lithofacies in the Bakken Formation in the numerous and geographically extensive wells with wireline log suites.

Shale lithofacies are defined in the core using quantitative mineralogy, Total Organic Carbon content, and petrophysical properties. These lithofacies are calibrated to advanced geochemical spectroscopy logs and conventional well logs at well scales. A machine learning algorithm, Support Vector Machine, is used to recognize the pattern of different shale lithofacies, associated with basic petrophysical parameters from ubiquitous conventional well log suites. Sequential Indicator Simulation is used to populate all lithofacies in a 3D grid, covering a large portion of the Williston basin in North Dakota. The results show that the Bakken shale members are vertically and laterally heterogeneous, but are successfully classified into five different lithofacies. Organic-rich shale lithofacies outweigh the proportion of organic-lean shale lithofacies. It appears several factors influenced the pattern of shale lithofacies distribution of the Bakken Formation.

Biedermann, M., Grob, K., 2019. Advantages of comprehensive two-dimensional gas chromatography for comprehensive analysis of potential migrants from food contact materials. Analytica Chimica Acta 1057, 11-17.


All substances migrating from food contact materials (FCMs), such as packagings, into food must be safe. This presupposes comprehensive analysis of all constituents potentially reaching a concentration in food that may be of toxicological concern. There is no single technique meeting this task and usually several need to be combined. In many cases, comprehensive two-dimensional gas chromatography (GCxGC) is the best technique available to start with. It provides high resolution and an overview in well-structured plots, grouping similar substances in a manner facilitating identifications. Further, flame ionization detection (FID) enables approximate quantitation without standards, and electron impact (EI) fragmentation in mass spectrometry (MS) provides access to large libraries for identification. GC is limited in amenable molecular mass, but the characterization of the lower mass constituents is usually helpful also for the identification of higher mass ones by techniques like HPLC-MS. The scope of this paper is to advocate the use of GCxGC for comprehensive migrate analysis, based on advantages illustrated by examples.

Bikkina, P., Kawamura, K., Bikkina, S., Kunwar, B., Tanaka, K., Suzuki, K., 2019. Hydroxy fatty acids in remote marine aerosols over the Pacific Ocean: Impact of biological activity and wind speed. ACS Earth and Space Chemistry 3, 366-379.


Current parametrization of cloud–aerosol interactions of nascent sea-spray aerosols (SSA) in the climate models is hampered by our limited understanding of the constituents of organic aerosols. We investigated here the mass concentrations, molecular distributions, and relative abundances of hydroxy fatty acids (FAs), ubiquitous lipid compounds in the SSA collected over the western Pacific Ocean (35°N–40°S). Detectable levels of methanesulfonic acid (an oxidation product of dimethyl sulfide) and high enrichment factors of Mg2+ and Ca2+ relative to Na+ emphasize the impact of the marine biological activity on the organic fraction of SSA. The molecular distributions of β-hydroxy FAs with characteristic “odd-C” predominance (C9 > C10 and C11 > C12) among short-chain homologues (<C14) reveal their formation from the photochemical oxidation of marine-derived organic matter. Molecular distributions and the carbon preference index of n-fatty acids and n-alkanes in the SSA also indicate their oceanic origin. A rapid decrease in the mass ratio of low molecular weight FAs to sea-salts with wind speed indicates the significant variability of organic compounds with production pathways of SSA (fine film-drops versus coarse jet-droplets). On the basis of the multitracer approach, this study underscores the background oceanic influence on the abundances of microbial lipids over the remote Pacific Ocean.

Bloetscher, F., 2019. Using predictive Bayesian Monte Carlo- Markov Chain methods to provide a probablistic solution for the Drake equation. Acta Astronautica 155, 118-130.


Are we alone in the universe? It is an age-old question that continues to encourage interest and controversy among the public as well as academics. Development of explanations for life elsewhere ranges widely, but few mathematical models have been developed to measure the likelihood of

concurrent, intelligent life, and those that exist are widely speculative due to the lack of information. However, with the addition of information from Kepler explorations for new solar systems within our galaxy, and calculation of the potential number of stars in the expanse of the universe, data for a useful probabilistic model to determine the likelihood of life beyond Earth may be possible with the use of predictive Bayesian statistics. Predictive Bayesian statistical methods are designed to use limited, uncertain data, to develop results. The result provides a probability curve of the likelihood of life in the universe that includes both uncertainty and potential variability within the result to provide a means to define the probability of life in the galaxy as well as life within proximity to earth. That said, the results indicate that the probability we are alone (<1) in the galaxy is significant, while the maximum number of contemporary civilizations might be as few as a thousand. With so few concurrent civilizations, and such large distances, it is little surprise that the SETI project has not found that alien signal. Our nearest neighbor is 4 light years away, and there are under 100 stars within 50 light years, the total of the project's existence.

Bogard, M.J., Kuhn, C.D., Johnston, S.E., Striegl, R.G., Holtgrieve, G.W., Dornblaser, M.M., Spencer, R.G.M., Wickland, K.P., Butman, D.E., 2019. Negligible cycling of terrestrial carbon in many lakes of the arid circumpolar landscape. Nature Geoscience 12, 180-185.

https://doi.org/10.1038/s41561-019-0299-5

High-latitude environments store nearly half of the planet’s below-ground organic carbon (OC), mostly in perennially frozen permafrost soils. Climatic changes drive increased export of terrestrial OC into many aquatic networks, yet the role that circumpolar lakes play in mineralizing this carbon is unclear. Here we directly evaluate ecosystem-scale OC cycling for lakes of interior Alaska. This arid, low-relief lake landscape is representative of over a quarter of total northern circumpolar lake area, but is greatly under-represented in current studies. Contrary to projections based on work in other regions, the studied lakes had a negligible role in mineralizing terrestrial carbon; they received little OC from ancient permafrost soils, and had small net contribution to the watershed carbon balance. Instead, most lakes recycled large quantities of internally derived carbon fixed from atmospheric CO2, underscoring their importance as critical sites for material and energy provision to regional food webs. Our findings deviate from the prevailing paradigm that northern lakes are hotspots of terrestrial OC processing. The shallow and hydrologically disconnected nature of lakes in many arid circumpolar landscapes isolates them from terrestrial carbon processing under current climatic conditions.

Bomberg, M., Mäkinen, J., Salo, M., Kinnunen, P., 2019. High diversity in iron cycling microbial communities in acidic, iron-rich water of the Pyhäsalmi Mine, Finland. Geofluids 2019, Article 7401304.

https://doi.org/10.1155/2019/7401304

Microbial communities of iron-rich water in the Pyhäsalmi mine, Finland, were investigated with high-throughput amplicon sequencing and qPCR targeting bacteria, archaea, and fungi. In addition, the abundance of Leptospirillum and Acidithiobacillus was assessed with genus-specific qPCR assays, and enrichment cultures targeting aerobic ferrous iron oxidizers and ferric iron reducers were established. The acidic (pH 1.4–2.3) mine water collected from 240 m, 500 m, and 600 m depth from within the mine had a high microbial diversity consisting of 63-114 bacterial, 10-13 archaeal, and 104-117 fungal genera. The most abundant microorganisms in the mine water were typical acid mine drainage (AMD) taxa, such as acidophilic, iron-oxidizing Leptospirillum, Acidiphilum, Acidithiobacillus, Ferrovum, and Thermoplasma. The fungi belonged mostly to the phylum

Ascomycetes, although a great part of the fungal sequences remained unclassified. The number of archaeal 16S rRNA genes in the mine water was between 0.3 and 1.2 × 107 copies mL−1 in the samples from 500 m and 600 m, but only 3.9 × 103 at 240 m and archaea were in general not enriched in cultures. The number of fungal 5.8S rRNA genes was high only in the mine water from 500 m and 600 m, where 0.2–3.4 × 104 spore equivalents mL−1 were detected. A high number of Leptospirillum 16S rRNA genes, 0.6–1.6 × 1010 copies mL−1, were detected at 500 m and 600 m depth and in cultures containing ferrous iron, showing the importance of iron oxidizers in this environment. The abundance of bacteria in general was between 103 and 106 16S rRNA gene copies mL−1. Our results showed a high microbial diversity in the acid- and iron-impacted waters of the Pyhäsalmi mine, where Leptospirillum bacteria were especially prominent. These iron oxidizers are also the main nitrogen-fixing microorganisms in this ecosystem.


https://doi.org/10.1007/s10533-019-00558-5

Psychrotolerant microbes are crucial for carbon cycling and biotechnological applications. Nonetheless, the mechanisms enabling their survival and functioning in frozen environments remain unclear. To elucidate adaptations of microbial cell membranes to freezing, we incubated soils with position-specific 13C labeled glucose at + 5 (control), − 5 and − 20 °C and quantified 13C in CO2 and phospholipid fatty acids. High oxidation of glucose C-1 at + 5 °C revealed a transformation via the pentose phosphate pathway. At subzero temperatures, however, the preferential oxidation of C-4 position suggested a switch to glycolysis. The threefold increase of Gram-negative phospholipid fatty acids in soil incubated at − 5 °C was accompanied by a twofold increase in 13C incorporation. This unequal increase of phospholipid fatty acids and incorporated 13C can be explained by simultaneous desaturation of existing fatty acid chains and the de novo synthesis of monounsaturated fatty acids, which indicates microbial growth. In contrast, Gram-positive bacteria incorporated 2 times higher 13C into their phospholipid fatty acids at − 20 °C than at − 5 and + 5 °C without a significant increase in their fatty acid contents. This reflects intensive repair of membranes damaged at − 20 °C without microbial growth. The fungal/bacterial ratio was 1.5 times lower at subzero temperatures than at + 5 °C, reflecting a shift in microbial community structure towards bacteria. Accordingly, soil microorganisms adapted to freezing by (1) switching their metabolic pathway from the pentose phosphate pathway to glycolysis, (2) modifying phospholipid fatty acids by desaturation and, (3) shifting microbial community structure towards Gram-negative bacteria by reducing the fungal population.

Borrel, G., Adam, P.S., McKay, L.J., Chen, L.-X., Sierra-García, I.N., Sieber, C.M.K., Letourneur, Q., Ghozlane, A., Andersen, G.L., Li, W.-J., Hallam, S.J., Muyzer, G., de Oliveira, V.M., Inskeep, W.P., Banfield, J.F., Gribaldo, S., 2019. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology 4, 603-613.

https://doi.org/10.1038/s41564-019-0363-3

Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic,

anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘Candidatus Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.

Botsyun, S., Sepulchre, P., Donnadieu, Y., Risi, C., Licht, A., Caves Rugenstein, J.K., 2019. Revised paleoaltimetry data show low Tibetan Plateau elevation during the Eocene. Science 363, Article eaaq1436.

http://science.sciencemag.org/content/363/6430/eaaq1436.abstract

Editor's summary: Ancient height of the Tibetan Plateau. The elevation of the Tibetan Plateau has a major impact on climate, affecting the monsoons and regional weather patterns. Although some isotope proxies have suggested a roughly equivalent height for the plateau as far back as the Eocene (∼40 million years ago), other lines of evidence suggest a lower elevation in the distant past. Botsyun et al. used a model to show that several previously overlooked factors contribute to the isotopic record from the Eocene (see the Perspective by van Hinsbergen and Boschman). The results harmonize the isotopic record with other proxies and argue for a Tibetan Plateau that was about 1000 meters lower than it is today.

Structured Abstract

introduction: The uplift history of the Tibetan Plateau (TP) is critical for understanding the evolution of the Asian monsoons and the geodynamic forces involved in collisional orogens. The early topographic history of the TP is uncertain, and the timing of the initiation of uplift remains controversial. The majority of studies that find evidence for an old plateau (as early as the Eocene, ~40 million years ago) rely on stable isotope paleoaltimetry. This method is based on observations and models that show depletion in heavy oxygen isotopes in rainfall during orographic ascent. Ancient carbonates of the TP record past rainfall isotopes; when available, their isotopic signature can be compared with isotopic lapse rates in order to estimate at what elevation they grew in the past, but the use of this method in deep time has many uncertainties.

Rationale: Applying stable-isotope paleoaltimetry in greenhouse climates makes the implicit assumption that the factors that control atmospheric distillation and rainfall oxygen isotopic composition (δ18Ow) have remained constant over millions of years. However, the impact of past climate change on δ18Ow values is unclear. In particular, for the Eocene, higher atmospheric CO2 concentration (Pco2) and markedly different Asian paleogeography, including a wide and shallow Paratethys Sea in central China and a latitudinal shift of the southern Tibet margin ~10° to the south, have been hypothesized to modify the Asian climate and regional δ18Ow values. In addition, the carbonate formation temperature is often unknown, increasing the uncertainty in the reconstructed δ18Ow.

Results: We ran climate simulations with Eocene boundary conditions and varying TP elevation. We accounted for changing Pco2, land surface albedo, orbital variation, and sea-surface temperatures,

which potentially cause shifts in δ18Ow, by changing the relative contribution of different air masses and the local hydrological cycle—the evaporation-to-precipitation ratio and the fractioning between convective and large-scale rainfalls. In our simulations, the south-shifted location of the entire Indian foreland induces strong convection over the southern flank of the TP and a radically different pattern of water recycling compared with that of present day. Our simulations reproduce monsoonlike seasonal precipitation over the Indian foreland, with summer convective rainfall reaching the TP. An intense anticyclonic circulation during summer months induces widespread aridity on the northern part of the Plateau. This peculiar atmospheric circulation, together with intensified water recycling and multiple moisture sources, results in a reversed isotopic lapse rate across the southern flank of the TP, with the most negative δ18Ow over northern India and increased δ18Ow northward. On the basis of Eocene experiments with varied boundary conditions, we argue that this is a robust feature of Eocene climate over the region. Furthermore, this pattern is the opposite of the present-day δ18Ow over the Himalayas, which decreases with elevation, driven by orographic rainout following a Rayleigh distillation process. Last, using our simulated temperatures and δ18Ow, we derived virtual carbonates for different elevation scenarios and compared them with the geological record. Statistical analysis shows that a low TP topography during the Eocene is the scenario that provides the best match between model and data.

Conclusion: Our simulations indicate that standard stable isotope paleoaltimetry methods are not applicable in Eocene Asia because of a combination of increased convective precipitation, mixture of air masses of different origin, and widespread aridity. In the Eocene, the presence of a reversed isotopic lapse rate precludes use of any of the previously developed δ18Ow-elevation relationships for estimating the Eocene elevation of the TP. Rather, a model-data comparison on the carbonates δ18O suggests that the TP reached only low to moderate (<3000 m) elevations during the Eocene, reconciling oxygen isotope data with other proxies of elevation and with geodynamic models that propose a recent (Neogene) uplift. More generally, we suggest that using climate models in conjunction with stable isotope data from the geological archives provides a powerful tool to incorporate climatic changes into the analysis of paleoelevations.

Bowers, G.M., Schaef, H.T., Miller, Q.R.S., Walter, E.D., Burton, S.D., Hoyt, D.W., Horner, J.A., Loring, J.S., McGrail, B.P., Kirkpatrick, R.J., 2019. 13C nuclear magnetic resonance spectroscopy of methane and carbon dioxide in a natural shale. ACS Earth and Space Chemistry 3, 324-328.


13C nuclear magnetic resonance (NMR) spectroscopy shows that high-resolution spectra of isotopically enriched CH4 and CO2 can be obtained for a millimeter-sized natural shale sample under in situ conditions relevant to petroleum reservoirs (T = 323 K, and Pfluid = 90 bar) using magic angle spinning. These results show for the first time that this technique has the potential to provide otherwise unobtainable, species-specific structural and dynamical insight into the pore systems of shales and other tight reservoir and source rocks and can thus help guide the design of the methods used in enhanced petroleum production. The NMR results show that CH4 and CO2 readily displace each other in the nanoporosity (<10 nm) and mesoporosity (>10 nm) pore spaces of the shale studied here, that CH4 in nanopores, mesopores, and bulk fluid can be distinguished by NMR, and that the partitioning of CH4 between nano- and mesopores depends upon the CH4/CO2 ratio and, thus, partial pressures of the individual fluid species.

Brady, A.L., Kobs Nawotniak, S.E., Hughes, S.S., Payler, S.J., Stevens, A.H., Cockell, C.S., Elphic, R.C., Sehlke, A., Haberle, C.W., Slater, G.F., Lim, D.S.S., 2019. Strategic planning insights for future science-driven extravehicular activity on Mars. Astrobiology 19, 347-368.

https://doi.org/10.1089/ast.2018.1850

Short-term and long-term science plans were developed as part of the strategic planning process used by the Biologic Analog Science Associated with Lava Terrains (BASALT) science team to conduct two Mars-simulation missions investigating basalt habitability at terrestrial volcanic analog sites in 2016. A multidisciplinary team of scientists generated and codified a range of scientific hypotheses distilled into a Science Traceability Matrix (STM) that defined the set of objectives pursued in a series of extravehicular activity (EVA) campaigns performed across multiple field deployments. This STM was used to guide the pre-deployment selection of sampling stations within the selected Mars analog sites on the Earth based on precursor site information such as multispectral imagery. It also informed selection of hand-held instruments and observational data to collect during EVA to aid sample selection through latency-impacted interaction with an Earth-based Science Support Team. A significant portion of the pre-deployment strategic planning activities were devoted to station selection, ultimately the locations used for sample collection and EVA planning. During development of the EVAs, the BASALT science team identified lessons learned that could be used to inform future missions and analog activities, including the critical need for high-resolution precursor imagery that would enable the selection of stations that could meet the scientific objectives outlined in the STM.



The main objective of this research was to develop an algorithm that would be able to relate ultraviolet absorbing moieties in potable water to trihalomethanes (THMs) and other water quality parameters. The characterization was carried out using high performance size exclusion chromatography (HPSEC) to separate water samples based on apparent molecule weight (AMW); while the developed algorithm utilized multi-spectral information extracted from 7 Manitoba source waters, and from samples treated with strong base ion-exchange (IX). AMW components between 2.2-4 k Da were strongly associated with the formation of THMs, and more strongly with chlorinated byproducts, determined using Spearman and Pearson coefficients. associations were not improved upon removal of the raw samples from the dataset, indicating that the applied methodology is not specific to IX treatment. Strong associations were also found between initial wavelengths of 226–239 nm and final wavelengths of 257–273 nm, which suggests that absorbing moieties in these ranges are prime precursors in the reaction mechanism to form THMs. A closer look noted that chlorinated THMs were more strongly associated than THMs in general; with brominated byproducts following closely to profiles of UV254 - indicating these parameters are closely related.


https://doi.org/10.1080/01490451.2018.1506528

Carbon-bearing compounds (glucose, sodium acetate, methanol, yeast extract, and nutrient broth) were added in different proportions to cultures to stimulate methanogenesis in a lignite incubation experiment. Their addition significantly influenced the isotopic composition of methane generated during the fermentation of lignite. Glucose was degraded mainly in the first 2 weeks of incubation, when the atmospheric air was present in the headspace and used for biomass growth. Sodium acetate,

methanol, and, presumably, lignite were decomposed in the next phase, in which anaerobic conditions occurred. The simultaneous decomposition of sodium acetate and methanol (as single substrates or as a mixture) with lignite resulted in the formation of methane with δ13C(CH4) values typical for methyl-type fermentation. The identification of decomposed compounds in the mixture of sodium acetate and methanol was accomplished via isotopic analysis of carbon and hydrogen in the methane. The δ2H(CH4)

values in the case of methanol biodegradation were characterized by a negative trend over time, in contrast to a positive trend observed when sodium acetate decomposed. This observation may help to identify a very good tracer for the determination of methane precursors during methyl-type fermentation.



Orange filamentous Beggiatoaceae form massive microbial mats on hydrothermal sediments in Guaymas Basin; these bacteria are considered to oxidize sulfide with nitrate and nitrite as electron acceptors. From a previously analyzed genome of an orange Beggiatoaceae filament, three candidate genes for enzymes with nitrite-reducing function – an orange octaheme cytochrome, a nirS nitrite reductase, and a nitrite/tetrathionate-reducing octaheme cytochrome - were cloned and expressed in E.coli. The expressed and purified orange cytochrome showed reduced nitrite-reducing activity compared to the multifunctional native protein obtained from microbial mats. The nirS gene product showed in vitro but no in-gel nitrite-reducing activity; and the nitrite/tetrathionate-reducing octaheme cytochrome was capable of reducing both nitrite and tetrathionate in vitro. Phylogenetic analysis shows that the orange Beggiatoaceae nirS, in contrast to the other candidate nitrite reductases, does not form monophyletic lineages with its counterparts in other large sulfur-oxidizing bacteria, and most likely represents a recent acquisition by lateral gene transfer. The nitrite/tetrathionate-reducing enzyme of the orange Beggiatoaceae is related to nitrite- and tetrathionate reductases harbored predominantly by Gammaproteobacteria, including obligate endosymbionts of hydrothermal vent tubeworms. Thus, the orange Guaymas Basin Beggiatoaceae have a repertoire of at least three different functional enzymes for nitrite reduction. By demonstrating the unusual diversity of enzymes with a potential role in nitrite reduction, we show that bacteria in highly dynamic, sulfide-rich hydrothermal vent habitats adapt to these conditions that usually prohibit nitrate and nitrite reduction. In the case of the orange Guaymas Beggiatoaceae, classical denitrification appears to be replaced by different multifunctional enzymes for nitrite and tetrathionate reduction; the resulting ecophysiological flexibility provides a new key to the dominance of these Beggiatoaceae in hydrothermal hot spots.

Burkert, A., Douglas, T.A., Waldrop, M.P., Mackelprang, R., 2019. Changes in the active, dead, and dormant microbial community structure across a Pleistocene permafrost chronosequence. Applied and Environmental Microbiology 85, Article e02646-02618.

http://aem.asm.org/content/85/7/e02646-18.abstract

Abstract: Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in

ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.

Importance: Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

Caesar, L.K., Kellogg, J.J., Kvalheim, O.M., Cech, N.B., 2019. Opportunities and limitations for untargeted mass spectrometry metabolomics to identify biologically active constituents in complex natural product mixtures. Journal of Natural Products 82, 469-484.

https://doi.org/10.1021/acs.jnatprod.9b00176

Compounds derived from natural sources represent the majority of small-molecule drugs utilized today. Plants, owing to their complex biosynthetic pathways, are poised to synthesize diverse secondary metabolites that selectively target biological macromolecules. Despite the vast chemical landscape of botanicals, drug discovery programs from these sources have diminished due to the costly and time-consuming nature of standard practices and high rates of compound rediscovery. Untargeted metabolomics approaches that integrate biological and chemical data sets potentially enable the prediction of active constituents early in the fractionation process. However, data acquisition and data processing parameters may have major impacts on the success of models produced. Using an inactive botanical mixture spiked with known antimicrobial compounds, untargeted mass spectrometry-based metabolomics data were combined with bioactivity data to produce selectivity ratio models subjected to a variety of data acquisition and data processing parameters. Selectivity ratio models were used to identify active constituents that were intentionally added to the mixture, along with an additional antimicrobial compound, randainal (5), which was masked by the presence of antagonists in the mixture. These studies found that data-processing approaches, particularly data transformation and model simplification tools using a variance cutoff, had significant impacts on the models produced, either masking or enhancing the ability to detect

active constituents in samples. The current study highlights the importance of the data processing step for obtaining reliable information from metabolomics models and demonstrates the strengths and limitations of selectivity ratio analysis to comprehensively assess complex botanical mixtures.

Callaway, E., 2019. Siberia’s ancient ghost clan starts to surrender its secrets. Nature 566, 444-446.

https://www.nature.com/articles/d41586-019-00672-2

A mysterious group of extinct humans known as Denisovans is helping to rewrite our understanding of human evolution. Who were they?

Samantha Brown didn’t have high hopes when she opened the ziplock bag containing some 700 shards of bone. It would be a lot of work to analyse them and none was likely to be human, she had been warned.

The fossils were from Denisova Cave — an archaeological site in southern Siberia where, in 2010, scientists had discovered a previously unknown group of ancient humans1. Researchers had identified them, whom they named Denisovans, on the basis of DNA preserved in a finger bone, and that finding had made the remote shelter one of the most important archaeological sites in the world.

Brown went through her bag of bones, testing each for proteins that are distinctly hominin. She found bears, bison, hyenas and even mammoths and rhinoceroses, but no trace of any hominins. So she flew to Siberia to collect more bone samples that had been excavated from Denisova Cave, knowing that her chances of success were slim.

Her luck turned in June 2015, when a 2-centimetre sliver of long bone tested positive for hominin collagen. “It was such an insane moment to find out that one of them was a hominin,” she says. Yet nothing would prepare her for a subsequent discovery by colleagues in Germany, who had sequenced the complete genome of DNA in the bone. Last year, a team that included Brown reported that the bone belonged to a woman who had lived around 100,000 years ago, and whose mother was a Neanderthal and father a Denisovan2. They gave the remarkable young woman a name: Denny.

“It was such a one-in-a-million find in the first place — and then for it to be a first-generation offspring. It’s magic, it’s amazing,” Brown says. “It’s a real testament to what we can still find.”

Brown and her colleagues have since discovered other hominin bone fragments in Denisova Cave, and the team is embarking on a project to analyse tens of thousands of bone shards from the cave and further sites in Asia. The effort is one of several that are extending the search for Denisovans across the continent, where traces of their DNA are found in many modern human populations. Researchers hope to determine the range of this enigmatic group — which might have stretched from Siberia to Oceania — and to chart its encounters with other hominins, including Homo sapiens and Neanderthals. Many scientists dream of finding more complete Denisovan remains and artefacts, so that they can work out what Denisovans looked like and begin to understand how they might have behaved.

Almost one decade after their discovery, Denisovans are finally coming into focus. Scientists are gaining confidence that they will soon uncover more remains of this ancient population from sites other than Denisova cave — if they haven’t already. Researchers have raised the possibility that some unusual fossils in China might be Denisovan.

“It’s really a hunt to find Denisovans,” says Andrey Krivoshapkin, an archaeologist at the Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences in Novosibirsk, who is excavating caves near Denisova and sites in central Asia for clues.

A hermit’s cave: Denisova Cave lies at the foot of the Altai Mountains, near Russia’s borders with Mongolia, China and Kazakhstan. Located in a verdant river valley that reminds some visitors of Switzerland, the site gets its name, according to legends, from a local herder or an eighteenth-century hermit who found seclusion in its high-ceilinged chambers. The cave remains remote, even for the researchers who flock there during the six-month excavation season that spans the spring and summer. “You are completely cut off from the world,” says Katerina Douka, an archaeological scientist and Brown’s supervisor at the Max Planck Institute for the Science of Human History in Jena, Germany, who first visited the cave in 2013. “It was a paradise,” she says.

Soviet archaeologists began to excavate the cave in the 1970s and early 1980s, discovering tens of thousands of stone tools and fragments of animal bone, many gnawed and digested by hyenas or other carnivores that had lived in the cave. In 2009, Svante Pääbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, received a bone from the finger of a hominin, small and broken in half, that Russian archaeologists had pulled from the cave the previous year. He wondered whether it belonged to a Neanderthal, because his team had found the group’s DNA in fragmentary remains from a cave nearby. But Pääbo’s expectations were low because the bone was so small and therefore unlikely to contain much DNA. “It was actually lying around for half a year,” he says, before his team analysed it.

Denisova 3, as the bone is now known, raised questions that scientists are still grappling with. As well as revealing the existence of the mysterious new hominins1, the DNA found in it suggested that Denisovans and Neanderthals are both descended from an ancestral population that, further research has shown, diverged from that of modern humans in the past 800,000 years, and probably lived throughout Asia3. Humans across the continent still carry Denisovan ancestry in varying proportions.

Denisova Cave is still the only place where Denisovans have been found, and discoveries such as Denny suggest that the site was once a nexus for various groups of human. When it comes to understanding such interactions, Pääbo adds: “It’s one of the most — if not the most — important sites in the world.”

In the years that followed the discovery of Denisovans, scientists used DNA sequencing to attribute a few molar teeth from the cave to the same group4. They have also found other remains that harboured Neanderthal DNA. The analysis of Denny fills in some important details about the two groups. “We knew that Denisovans and Neanderthals had been there. We just didn’t think they interacted this intimately,” says Pääbo. “It was so amazing to find direct proof — to find these people in the act, almost, of mixing.”

Denny’s discovery has also convinced Pääbo and other scientists that the remains of similar individuals, with recent ancestry from two groups of hominin, will be found — perhaps also in Denisova Cave. Researchers who analysed Denny’s genome found signs that the chromosome set that was contributed by her father, although clearly Denisovan, harboured some Neanderthal ancestry, which hints at earlier encounters between the groups2. “We should be able to pick up these individuals,” says Douka.

“It’s still a head scratcher,” adds Tom Higham, an archaeological scientist at the University of Oxford, UK, who works with Douka and Brown. “It’s either an incredible piece of luck, or interbreeding happens so frequently that we might expect to find these types of occurrence in the archaeological record.”

Busy crossroads: Although some researchers hope to stumble on another Denny, others are trying to identify periods when different groups of hominin overlapped — and perhaps interbred — in the cave. Geochronologists Zenobia Jacobs and Richard Roberts at the University of Wollongong, Australia, led a team that dated sediment from Denisova Cave by analysing hundreds of thousands of grains of quartz and feldspar5.

Judging by the oldest stone tools found there, the cave’s first residents moved in around 300,000 years ago and were, presumably, Denisovans or Neanderthals. Denisovans occupied the cave from at least 200,000 years ago to about 55,000 years ago — when the sediments in which Denisova 3 was found were laid down, Jacobs and Roberts reported in January5. The team also dated Neanderthal remains and sediment to between about 100,000 and 190,000 years ago.

This could imply that the two groups overlapped for long stretches, but Jacobs cautions that the team cannot yet pinpoint such periods, in part, because of the scarcity of hominin remains. Pääbo’s team is scouring the hundreds of sediment samples from Jacobs and Roberts’ study for hominin DNA, which could help to nail down when Denisovans and Neanderthals occupied the cave and whether they overlapped.

There are also clues that modern humans inhabited the cave and perhaps encountered these other groups. In the cave’s younger deposits, archaeologists have uncovered tools and jewellery sculpted from the bones and teeth of deer and other animals that resemble artefacts associated with the first H. sapiens to reach Europe, during a period known as the Initial Upper Palaeolithic, which began roughly 50,000 years ago. In another paper published in January6, a team led by Douka and Higham calculated that these artefacts were 43,000–49,000 years old. However, a hominin bone fragment that was 46,000–50,000 years old lacked the DNA needed to pin it to a specific group.

The Russian archaeologists who led the cave’s excavation have proposed that the tools and jewellery were made by Denisovans and suggest that the group had the capacity for symbolic thinking. But archaeologists in the West tend to favour the idea that the artefacts were made by early modern humans, whose remains have been found at another Siberian site, Ust’-Ishim7, and date to the Initial Upper Palaeolithic.

Researchers are now searching the younger sediments of Denisova Cave for more hominin remains and DNA that could help to uncover who made the artefacts. Similar work at other archaeological sites in Siberia, including several in the vicinity of Denisova Cave, could also yield answers, says Higham. “There’s a lot of really exciting stuff happening. Things are moving quite fast.”

Search for bones: Researchers have been held back by a lack of fossil evidence of Denisovans. Bence Viola has studied the lot, including Denisova 3 — which was ground up for DNA analysis — and several unusually large molars that do not resemble those of Neanderthals or modern humans8. “All the Denisovan material fits in a very, very small box,” says Viola, a palaeoanthropologist at the University of Toronto, Canada. “I’ve spent a lot of time staring at these very small fragments and teeth. I am probably the only one who’s seen it all.”

But more material is emerging slowly. Archaeologists excavating Denisova Cave in 2016 discovered a freshly broken chunk of parietal bone — part of the skull — that contains mitochondrial DNA from a Denisovan. The bone is shaped a bit like that of Homo erectus, a species of hominin that most researchers consider to be a close ancestor of humans, Neanderthals and, presumably, Denisovans (see ‘Tangled tree’). “Sadly, it’s not very informative. I expected more of it,” says Viola, who will describe his analysis in March at the annual meeting of the American Association of Physical Anthropologists. He hopes that the other pieces of the parietal bone, or even a complete skull, might soon be found. “It would be nice to have somewhat more,” he adds.

There seems to be no shortage of fragmentary remains. Earlier this month, Higham tweeted a picture of a long-bone fragment in a small plastic bag. “Good luck little Denisovan bone,” he wrote, although he doesn’t yet know to which hominin group it belongs. It was the fifth bone from the cave, including Denny’s remains, to be identified as hominin by the team. The researcher used a method called zooarchaeology by mass spectrometry (ZooMS), which was developed to quickly identify the animal bones that often litter archaeological sites. ZooMS breaks collagen, the most abundant protein in bone, into smaller peptides, and then uses a mass spectrometer to identify differences between animal species. Hominins have identical collagen peptide sequences, so DNA is needed to pin remains to specific groups.

On the back of early successes, Douka and her colleagues won €2 million (US$2.3 million) in European Research Council funding in 2017 to expand the search for Denisovans to some 20 sites across Europe and Asia by sifting through another 30,000–40,000 bones. “There are days I’m very hopeful, and there are days where you go through a thousand bones and find a thousand hyenas,” says Douka. “I have a feeling China is the place to look.”

Other scientists share Douka’s hunch, largely owing to the distribution of Denisovan DNA in modern humans —it is common in many Chinese populations. Some scientists wonder whether there might even be a Denisovan skeleton already knocking around a museum collection in China. In 2017, for instance, palaeoanthropologists described the unusually large skulls of hominins that lived 105,000–125,000 years ago, excavated from a site near the city of Xuchang in central China9. On the basis of their age, location and distinct anatomy, the remains have got some researchers, including Chris Stringer, a palaeoanthropologist at the Natural History Museum in London, wondering whether they might belong to Denisovans. “Who are the Denisovans outside of Denisova Cave?” Stringer says. “They’ve got to be there in China.”

Viola says that the Xuchang skulls don’t resemble his parietal bone fragment. He’s more interested in the roughly 300,000-year-old remains from a site in northern China called Xujiayao, which contain molars that look similar to those from Denisova Cave. “I would be very surprised if it turns out that some of the material from China, especially Xujiayao, is not Denisovan,” says Viola.

A team led by geneticist Qiaomei Fu, who has established an ancient-DNA lab at the Chinese Academy of Sciences’ Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, has analysed the Xuchang skulls and those from other potential Denisovans, but says that none of the remains, so far, has contained any hominin DNA.

Proteins might offer researchers a better shot at finding a Denisovan in China or elsewhere in Asia, because they tend to persist longer than DNA. Douka has just recruited a PhD student in China to comb through samples there, and she also hopes to analyse remains from southeast Asia and Papua New Guinea.

Because the form of collagen that ZooMS looks at does not differ between Denisovans and other hominins, researchers will need to sequence bone proteins that show more variation to find a Denisovan. Frido Welker, a molecular anthropologist at the Natural History Museum of Denmark in Copenhagen, has just begun a project to see whether hominin remains, including those of potential Denisovans, from the early and middle Pleistocene epoch — a period that spanned 2.6 million to 126,000 years ago — harbour proteins that indicate evolutionary relationships. “That’s a time period when ancient DNA does not survive necessarily, but where proteins do,” says Welker.

Many scientists now presume that Denisova Cave was a northern outpost that Denisovans and other hominins called home when the climate allowed. Yet even long after those ancient populations disappeared from the site, it remains a magnet for disparate groups. In July 2018, anthropologists,

archaeologists and geneticists who have become obsessed with the cave gathered there to share their latest finds. The conference was called ‘The Origins of the Upper Palaeolithic in Eurasia and the evolution of the genus Homo’ but it might as well have been dubbed Denisovastock.

It was Brown’s first visit, and she knew that she would be wowed by the cave that has yielded so many discoveries. She says that the surrounding landscape, lush and green, gave her a glimpse at what drew in Denny and her relatives. “You can just imagine people wanting to be there.”

References

1. Krause, J. et al. Nature 464, 894–897 (2010).2. Slon, V. et al. Nature 561, 113–116 (2018).3. Meyer, M. et al. Nature 531, 504–507 (2016).4. Slon, V. et al. Sci. Adv. 3, e1700186 (2017).5. Jacobs, Z. et al. Nature 565, 594–599 (2019).6. Douka, K. et al. Nature 565, 640–644 (2019).7. Fu, Q. et al. Nature 514, 445–449 (2014).8. Sawyer, S. et al. Proc. Natl Acad. Sci. USA 112, 15696–15700 (2015).9. Li, Z. Y. et al. Science 355, 969–972 (2017).

Cao, Y., Song, H., Algeo, T.J., Chu, D., Du, Y., Tian, L., Wang, Y., Tong, J., 2019. Intensified chemical weathering during the Permian-Triassic transition recorded in terrestrial and marine successions. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 166-177.


Global warming is inferred to have been one of the main causes of the Permian-Triassic (P-Tr) boundary mass extinction. Although a strong temperature rise in tropical sea-surface temperatures during the latest Permian has been documented, coeval climate changes in terrestrial sections are less well-known. Here, we analyzed multiple weathering indexes (including CIA, CIW, and PIA) for two terrestrial sections in North China (Shichuanhe and Yima), all of which show a major excursion toward higher values (greater weathering intensity) around the end-Permian plant extinction (EPPE). At Shichuanhe, the CIA (chemical index of alteration) increases from 70 to 75 over the interval of 11–36 m, which straddles the EPPE at 33 m, and then decreases from 75 to 71 in the overlying strata. At Yima, CIA increases from 63 to 79 over the interval of 57–68 m, extending up to the EPPE at 68 m, and then gradually decreases from 78 to 72 in the overlying strata. These results imply a strong warming event coupled with intense chemical weathering in soil environments leading up to the end-Permian plant extinction. The decline in CIA values following the EPPE may reflect loss of weathered soils through physical erosion rather than climatic cooling. Estimation of atmospheric temperatures from the CIA data indicate rapid rises at Shichuanhe (from ~11.6 °C to 16.5 °C) and Yima (from 9.3 °C to 18.4 °C) during the end-Permian crisis. The findings in this study are consistent with the hypothesis that a sharp temperature rise caused the extinction of terrestrial organisms during the end-Permian crisis.

Carlson, H.K., Price, M.N., Callaghan, M., Aaring, A., Chakraborty, R., Liu, H., Kuehl, J.V., Arkin, A.P., Deutschbauer, A.M., 2019. The selective pressures on the microbial community in a metal-contaminated aquifer. The ISME Journal 13, 937-949.

https://doi.org/10.1038/s41396-018-0328-1

In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO2

2+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.

Carroll-Nellenback, J., Frank, A., Wright, J., Scharf, C., 2019. The Fermi Paradox and the aurora effect: Exo-civilization settlement, expansion and steady states. arXiv:1902.04450 [physics.pop-ph].

https://arxiv.org/abs/1902.04450

We model the settlement of the galaxy by space-faring civilizations in order to address issues related to the Fermi Paradox. We explore the problem in a way that avoids assumptions about the intent and motivation of any exo-civilization seeking to settle other planetary systems. We first consider the speed of an advancing settlement via probes of finite velocity and range to determine if the galaxy can become inhabited with space-faring civilizations on timescales shorter than its age. We also include the effect of stellar motions on the long term behavior of the settlement front which adds a diffusive component to its advance. The results of these models demonstrate that the Milky Way can be readily 'filled-in' with settled stellar systems under conservative assumptions about interstellar spacecraft velocities and launch rates. We then consider the question of the galactic steady-state achieved in terms of the fraction of settled planets. We do this by considering the effect of finite settlement civilization lifetimes on the steady states. We find a range of parameters for which the galaxy supports a population of interstellar space-faring civilizations even though some settleable systems are uninhabited. Both results point to ways in which Earth might remain unvisited in the midst of an inhabited galaxy. Finally we consider how our results can be combined with the finite horizon for evidence of previous settlements in Earth's geologic record. Our steady-state model can constrain the probabilities for an Earth visit by a settling civilization before a given time horizon. These results break the link between Hart's famous "Fact A" (no interstellar visitors on Earth now) and the conclusion that humans must, therefore, be the only technological civilization in the galaxy.

Castillo-Rogez, J.C., Hesse, M.A., Formisano, M., Sizemore, H., Bland, M., Ermakov, A.I., Fu, R.R., 2019. Conditions for the long-term preservation of a deep brine reservoir in Ceres. Geophysical Research Letters 46, 1963-1972.

https://doi.org/10.1029/2018GL081473

Abstract: We propose a new internal evolution model for the dwarf planet Ceres matching the constraints on Ceres' present internal state from the Dawn mission observations. We assume an

interior differentiated into a volatile‐dominated crust and rocky mantle, and with remnant brines in the mantle, all consistent with inferences from the Dawn geophysical observations. Simulations indicate Ceres should preserve a warm crust until present if the crust is rich in clathrate hydrates. The temperature computed at the base of the crust exceeds 220 K for a broad range of conditions, allowing for the preservation of a small amount of brines at the base of the crust. However, a temperature ≥250 K, for which at least 1 wt.% sodium carbonate gets in solution requires a crustal abundance of clathrate hydrates greater than 55 vol.%, a situation possible for a narrow set of evolutionary scenarios.

Plain Language Summary: We search internal evolution models of dwarf planet Ceres that match the observations returned by the Dawn mission. A key feature to be reproduced is the long‐term persistence of liquid below the crust, at about 40 km depth, as suggested by the observed topography. The possibility for the occurrence of liquid in Ceres at present depends on the presence of insulating material in the crust, for example, in the form of gas hydrates. The latter are also suggested from geophysical and geological observations and geochemical modeling. Our modeling shows in these conditions that liquid can be preserved for a wide range of evolutionary scenarios.



Analyses of both type II organic-rich low-mature mudstones from the Kimmeridge Clay Formation (Yorkshire, England) and gas-mature mudstones from the Vaca Muerta formation (Argentina) were performed using petrographic and SEM observations to characterize the organic and inorganic components of the rocks and their relationship with porosity. The porosity analyses using nitrogen adsorption measurements and mercury intrusion porosimetry were then evaluated as a function of both composition and thermal maturity. Despite the absence of variation in the pore size distribution and the total pore volume with maturity, which is controlled by total organic carbon content (TOC), this study demonstrates that the pore network of these marine mudstones varies considerably with thermal maturity. Contrary to low-mature samples, whose porosity depends essentially on mineral interparticle pores, the porosity of thermally-mature rocks is mainly influenced by organic-matter-hosted pores located within secondary solid bitumen. Organic matter (OM) porosity, which is rare in the low-mature stage, appears to increase during thermal maturation in response to the thermal cracking of kerogen and oil, to become predominant in gas-mature rocks. It can therefore be considered that thermal maturation is a major process for the development of the OM porosity. However, the OM of high-TOC (>5.5 wt%) gas-mature samples contains smaller pores than gas-mature low-TOC mudstones probably due to a difference in the original OM composition between these high- and low-TOC samples. By analogy with the Kimmeridge Clay formation, which is often considered as time equivalent in terms of OM composition (Uliana et al., 1999), the high-TOC Vaca Muerta samples appear to have originally contained greater proportions of oil-prone amorphous OM and thus a better OM intrinsic quality for oil generation. This difference of OM composition and petroleum potential between Vaca Muerta marine mudstones appears to have dramatically influenced the OM-hosted pore genesis during maturation. Consistent with other studies, these results show that thermal maturity is not the only process that can explain OM-hosted pore genesis in gas shale systems. The OM composition can greatly influence the evolution of this porosity during maturation. Organic composition and OM thermal maturity may therefore have a complementary effect, explaining the diversity of trends observed on porosity in natural formations.

Chaichana, S., Jickells, T., Johnson, M., 2019. Interannual variability in the summer dissolved organic matter inventory of the North Sea: implications for the continental shelf pump. Biogeosciences 16, 1073-1096.

https://www.biogeosciences.net/16/1073/2019/

We present the distribution and C:N stoichiometry of dissolved organic matter (DOM) in the North Sea in two summers (August 2011 and August 2012), with supporting data from the intervening winter (January 2012). These data demonstrate local variability superimposed on a general pattern of decreasing DOM with increasing distance from land, suggesting concentrations of DOM are controlled on large spatial scales by mixing between the open North Atlantic and either riverine sources or high DOM productivity in nearshore coastal waters driven by riverine nutrient discharge. Given the large size and long residence time of water in the North Sea, we find concentrations are commonly modified from simple conservative mixing between two endmembers. We observe differences in dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) concentrations and land–ocean gradients between the two summers, leading to an estimated 10–20 Tg difference in the DOC inventory between the two years, which is of the same order of magnitude as the annual uptake of atmospheric CO2 by the North Sea system, and thus significant for the carbon budget of the North Sea. This difference is not consistent with additional terrestrial loading and is more likely to be due to balancing of mixing and in situ production and loss processes across the North Sea. Differences were particularly pronounced in the bottom layer of the seasonally stratifying northern North Sea, with higher DOC and C:N ratio in 2011 than in 2012. Using other data, we consider the extent to which these differences in the concentrations and C:N ratio of DOM could be due to changes in the biogeochemistry or physical circulation in the two years, or a combination of both. The evidence we have is consistent with a flushing event in winter 2011/12 exchanging DOM-rich, high C:N shelf waters, which may have accumulated over more than 1 year, with deep North Atlantic waters with lower DOC and marginally higher DON. We discuss the implications of these observations for the shelf sea carbon pump and the export of carbon-rich organic matter off the shelf and hypothesise that intermittent flushing of temperate shelf systems may be a key mechanism in the maintenance of the continental shelf pump, via the accumulation and subsequent export of carbon-rich DOM.

Chan, M.A., Bowen, B.B., Corsetti, F.A., Farrand, W.H., Law, E.S., Newsom, H.E., Spear, J.R., Thompson, D.R., 2019. Exploring, mapping, and data management integration of habitable environments in astrobiology. Frontiers in Microbiology 10, 147. doi: 110.3389/fmicb.2019.00147.


New approaches to blending geoscience, planetary science, microbiology-geobiology/ecology, geoinformatics and cyberinfrastructure technology disciplines in a holistic effort can be transformative to astrobiology explorations. Over the last two decades, overwhelming orbital evidence has confirmed the abundance of authigenic (in situ, formed in place) minerals on Mars. On Earth, environments where authigenic minerals form provide a substrate for the preservation of microbial life. Similarly, extraterrestrial life is likely to be preserved where crustal minerals can record and preserve the biochemical mechanisms (i.e., biosignatures). The search for astrobiological evidence on Mars has focused on identifying past or present habitable environments-- places that could support some semblance of life. Thus, authigenic minerals represent a promising habitable environment where extraterrestrial life could be recorded and potentially preserved over geologic time scales. Astrobiology research necessarily takes place over vastly different scales; from molecules to viruses and microbes to those of satellites and solar system exploration, but the differing scales of analyses are rarely connected quantitatively. The mismatch between the scales of these

observations— from the macro- satellite mineralogical observations to the micro- microbial observations— limits the applicability of our astrobiological understanding as we search for records of life beyond Earth. Each-scale observation requires knowledge of the geologic context and the environmental parameters important for assessing habitability. Exploration efforts to search for extraterrestrial life should attempt to quantify both the geospatial context and the temporal/spatial relationships between microbial abundance and diversity within authigenic minerals at multiple scales, while assimilating resolutions from satellite observations to field measurements to microscopic analyses. Statistical measures, computer vision, and the geospatial synergy of Geographic Information Systems (GIS), can allow analyses of objective data-driven methods to locate, map, and predict where the “sweet spots” of habitable environments occur at multiple scales. This approach of science information architecture or an “Astrobiology Information System” can provide the necessary maps to guide researchers to discoveries via testing, visualizing, documenting, and collaborating on significant data relationships that will advance explorations for evidence of life in our solar system and beyond.

Chang, Z., Chu, M., 2019. The chemical composition and pyrolysis characteristics of thermal bitumen derived from pyrolyzing Huadian oil shale, China. Oil Shale 36, 62–75.

https://doi.org/10.3176/oil.2019.1.05

Thermal bitumen is an important intermediate derived from kerogen decomposition during oil shale pyrolysis. In this study, thermal bitumen was obtained by extracting oil shale char generated from pyrolysis of Huadian oil shale at 360‒530 °C. The chemical composition and pyrolysis characteristics of bitumen were investigated by ultimate analysis, liquid chromatography fractionation, Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). The decomposition of oxygen-containing structures at 420‒450 °C decreased the oxygen content from 4.66 to 0.75 wt%. The intense cracking of aliphatic compounds or alkyl chains at 450‒480 °C resulted in the selective concentration of aromatic compounds and the decrease of H/C ratio from 1.350 to 1.262. The pyrolysis of thermal bitumen could be tentatively divided into two stages – the evaporation of light components (150‒410 °C) and the cracking of heavy components (410‒550 °C), which corresponded respectively to a shoulder and an obvious peak in differential thermal gravimetry (DTG) curves. For pyrolysis of oil shale, the evaporation process dominated the pyrolysis of thermal bitumen at 420‒450 °C, which decreased the content of light components. In a higher temperature range, 450‒480 °C, the cracking of large molecules became more intense and, as a result, increased the content of light components and decreased that of heavy components.

Chen, D., Wang, A., Li, Y., Hou, Y., Wang, Z., 2019. Biosurfactant-modified palygorskite clay as solid-stabilizers for effective oil spill dispersion. Chemosphere 226, 1-7.


An effective and conventional remediation technique in marine oil spills is to apply chemical dispersants to emulsify oil slicks into small oil droplets. Still, the potential hazards of chemical dispersants onto the marine ecosystem have motivated the research for environmentally friendly alternative while keeping exceptional dispersion ability. Here, we showed that the mixture of palygorskite (PAL) and rhamnolipid (Rha) formed a biocompatible alternative to synthetic surfactants used for oil spill dispersion. The oil droplets dispersed by R-PAL presented a small average size and long-term stability, which illustrated the synergistic interactions between Rha and PAL acting as an efficient dispersant in artificial sea water (ASW). Due to the strong flocculation caused by high salinity, PAL alone was not effective emulsifiers in ASW. A small amount of Rha could played a

major role in modifying the surface characteristics of PAL and decreasing oil-water interfacial tension. Therefore, PAL particles irreversibly adsorbed onto the oil-ASW interface and formed a rigid interfacial film around oil droplets in the presence of Rha, which offered an efficient barrier to droplet coalescence. The synergistic interactions between PAL and Rha could enable the dispersion of tetradecane in ASW. Such a functionality was further tested in dispersing crude oil in ASW. The study presents a new strategy of using a mixture of PAL and Rha for oil dispersion, thus providing an ecofriendly alternative to conventional dispersants.


https://doi.org/10.1007/s00253-018-09574-1

Branched alkanes are important constituents of crude oil and are usually regarded as resistant to microbial degradation, resulting in little knowledge of biochemical processes involved in anaerobic branched alkanes biodegradation. Here, we initiated an incubation study by amendment of iso-C9 (2-methyl, 3-methyl, and 4-methyloctane) as substrates for methanogenic degradation in production water from a high-temperature petroleum reservoir. Over an incubation period of 367 days, significant methanogenesis was observed in samples amended with these branched alkanes. The strong methanogenic activity only observed in iso-C9 amendments suggested the presence of microbial transformation from iso-alkanes into methane. GC-MS-based examination of the original production water identified an intermediate tentatively to be iso-C9-like alkylsuccinate, but was not detected in the enrichment cultures, combined with the successful amplification of assA functional gene in inoculating samples, revealing the ability of anaerobic biodegradation of iso-C9 via fumarate addition pathway. Microorganisms affiliated with members of the Firmicutes, Synergistetes, and methanogens of genus Methanothermobacter spp. were highly enriched in samples amended with iso-C9. The co-occurrence of known syntrophic acetate oxidizers Thermoacetogenium spp. and Methanothermobacter spp. (known hydrogenotrophic methanogens) indicates a potential syntrophic acetate oxidation associated with the methanogenic biodegradation of iso-C9. These results provide some useful information on the potential biodegradation of branched alkanes via methanogenesis and also suggest that branched alkanes are likely activated via fumarate addition in high-temperature petroleum reservoirs.

Chen, J., Song, H., He, W., Tong, J., Wang, F., Wu, S., 2019. Size variation of brachiopods from the Late Permian through the Middle Triassic in South China: Evidence for the Lilliput Effect following the Permian-Triassic extinction. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 248-257.


Whether body size reduction (the Lilliput Effect) occurred in the Early Triassic invertebrates remains a matter of debate. Here, we investigate the size evolution of brachiopods spanning the Late Permian through the Early to Middle Triassic based on 3316 brachiopod specimens from South China. Our results show that the maximum and median size among species decreased dramatically from the latest Permian (Changhsingian) to the earliest Triassic (Griesbachian), and then increased during the Olenekian and Anisian. Our data support the Lilliput Effect on brachiopods during the Permian-Triassic mass extinction and its immediate aftermath. Size plots at species, genus, and family levels suggest that the earliest Triassic size reduction resulted from two factors: the preferential extinction of large brachiopod taxa (size-selective extinction), and the size reductions in the survivors. Persistent

increases in brachiopod size in the Olenekian and Anisian are likely the result of the extinction of small survivors, the appearance of large-sized species and the Cope's rule that the new lineages tend to increase in body size over the early evolutionary time. The cause of the earliest Triassic size reduction of brachiopods might be environmental pressures such as global warming, oceanic anoxia, and increased water turbidity.

Chen, J., Zhao, L., Algeo, T.J., Zhou, L., Zhang, L., Qiu, H., 2019. Evaluation of paleomarine redox conditions using Mo-isotope data in low-[Mo] sediments: A case study from the Lower Triassic of South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 178-193.


Molybdenum isotopes are considered to be a promising paleoredox proxy in reducing facies for evaluating either global-ocean redox conditions (given quantitative Mo uptake) or local redox conditions (given non-quantitative Mo uptake). Here, we examine the Mo-isotopic composition of black to gray shales from the Permian-Triassic boundary (PTB) section at Chaohu, eastern China, in order to assess the utility of this proxy under a range of paleoredox conditions. We evaluated local redox conditions using a combination of redox-sensitive trace-element concentrations (Mo, U) and FeT/Al ratios, recognizing six intervals of more reducing conditions at the PTB and Induan-Olenekian boundary (IOB), in the mid-Smithian, at the Smithian-Spathian boundary (SSB), and in the mid- and upper Spathian. These six intervals are associated with variably weak to moderate enrichments of Mo, and they show variable shifts away from background δ98Mo values of ca. −0.4 to +0.1‰ (recording detrital Mo-isotopic compositions) toward δ98Mo values as high as +2.3 ± 0.2‰. Based on an analysis of local redox proxies versus δ98Mo as well as of sample-to-sample variance in δ98Mo values, we conclude that only one of the six reducing intervals in the study section is likely to record contemporaneous seawater δ98Mo (as a result of quasi-quantitative Mo uptake), i.e., the interval from the Hindeodus typicalis conodont Zone close to the PTB, for which δ98Mo values of +2.3 ± 0.2‰ suggest average global-ocean redox conditions similar to those of the modern ocean. For the remaining five reducing intervals, non-quantitative Mo uptake led to Mo-isotope signatures reflecting local, mostly suboxic redox conditions. The highest Mo concentrations (17–23 ppm) were yielded by the mid- and upper Spathian intervals, and the lack of concurrent U enrichment in the mid-Spathian interval suggests the local operation of a Mn-Fe particulate shuttle, an inference that is consistent with its relatively low δ98Mo values (0 ± 0.3‰). The lack of evidence for strong oceanic anoxia in the South China Craton following the PTB crisis may have been a factor in the relatively rapid recovery of marine ecosystems in this region during the Early Triassic. The present contribution serves as a case study of the application of Mo-isotopes as a paleoredox proxy in low-[Mo] sediments, which requires a careful assessment of the relative importance of global versus local redox influences based on additional proxies and evaluation criteria.


https://doi.org/10.1080/10916466.2018.1558244

This study investigated the property and composition of crude oils from in-situ combustion (ISC) and steam assisted gravity drainage (SAGD). We made comparison of the elemental composition and molecular weight distribution of the two crude oils. It was overserved that ISC crude oil has significant higher oxygen content. The ultra-high resolution mass spectrometry was applied to investigate the molecular composition of acidic compounds in two crude oils. The acidic compounds in ISC crude oil have higher carbon numbers than that of SAGD crude oils.

Chen, Z.-Q., Algeo, T.J., Schoepfer, S.D., 2019. The Permian–Triassic transition in the eastern Paleo-Tethys and adjacent regions: Environmental and biotic changes in ocean and on land. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 1-7.


Introduction: The 20-million-year interval from the late Middle Permian to early Middle Triassic (~260–240 Ma) was a critical period for the evolution of life on Earth. It witnessed two major biocrises: the first at the Guadalupian/Lopingian (Middle/Late Permian) boundary, and the second–the most severe and most protracted biocrisis of the Phanerozoic–at the Permian/Triassic (P–Tr) boundary (Stanley and Yang, 1994; Yin et al., 2007). The P–Tr boundary (PTB) event was followed by multiple secondary episodes of faunal mortality and recovery during the ~5-Myr-long Early Triassic (Bottjer et al., 2008; Chen and Benton, 2012; Song et al., 2013) that were probably linked to episodic global environmental perturbations (Algeo et al., 2011; Retallack et al., 2011; Song et al., 2014). This extended P–Tr transition interval has attracted increasing attention from paleontologists and geologists worldwide. The South China Craton preserves many near-complete and little-altered Upper Permian to Middle Triassic successions representing a range of deep-marine, shallow-marine, and terrestrial facies, which have been intensively studied since the 1980s (Chen and Benton, 2012).

The pace of new findings related to the P–Tr transition coming from studies of South China successions continues to accelerate. Accordingly, we organized a special issue of Palaeogeography Palaeoclimatology Palaeoecology, in two volumes, focused on the Paleozoic–Mesozoic transition in South China. The first volume of the special issue (v. 486), which was published in 2017, consisted of 12 papers covering various aspects of the biostratigraphy, paleoecology, sedimentology, geochemistry, and paleoceanography of the transition interval (Chen et al., 2017). The present (second) volume contains a further 18 papers covering the same general topics while advancing our knowledge of these fields with fresh studies from the past two years. The 18 studies of the present volume span the Upper Permian to Triassic of the eastern Paleo-Tethys region (mainly the South China Block) and adjacent areas (Fig. 1; below, blue text indicates studies in this volume). These contributions enhance our understanding of extreme events and organism-environment interactions during this critical period of Earth history.

Chen, Z.-Q., Hu, X., Montañez, I.P., Ogg, J.G., 2019. Sedimentology as a key to understanding Earth and life processes. Earth-Science Reviews 189, 1-5.


China Association of Sedimentologists (CAS) organized successfully one international Sedimentology Summit Meeting and International Workshop on “Building the Future of Sedimentology” on 22nd to 28th of September, 2016 in Beijing. This workshop invited all bureau members of The International Association of Sedimentology (IAS) and several world-leading experts in various fields of sedimentology discipline as well as almost all senior and active sedimentologists from China to give keynote lectures to summarize recent achievements in sedimentology studies. These presentations focus on nine themes, namely Precambrian sedimentology, biological process and sedimentology, energy sedimentology, basin dynamics and sequence stratigraphy, paleogeography reconstruction, modern sedimentological process, depositional environments and facies, sedimentary geochemistry, and deep-time paleoclimate. Each theme group finished one formal report for development strategy of various disciplines within sedimentology in short future. These comprehensive reviews of all fields of sedimentology therefore will provide strategy advice for the future funds in sedimentology researches, at least, in China and also may re-shape the future

development direction of sedimentology worldwide. To better understand sedimentology as the key to unravel Earth and life processes, this special issue assembles 12 papers directly from this workshop or invited from other world-leading experts outside the workshop to address integrated global stratigraphy, biosedimentology, sedimentologic implications in reconstructing paleoclimate and paleogeographic configurations, and implications on P-Tr mass extinction and recovery in ocean and on land, with emphasis on sedimentary records from China.

Chen, Z.-Q., Tu, C., Pei, Y., Ogg, J., Fang, Y., Wu, S., Feng, X., Huang, Y., Guo, Z., Yang, H., 2019. Biosedimentological features of major microbe-metazoan transitions (MMTs) from Precambrian to Cenozoic. Earth-Science Reviews 189, 21-50.


Biotic activities are involved in almost all sedimentation processes throughout the evolutionary history of life on our planet. However, deep-time organism-induced sedimentation and biosedimentary records remain unclear in terms of lithologic types, strata stacking patterns and possible controlling factors. We document biosedimentary features of major transitions from microbe-dominated switching to metazoan-dominated biosedimentary systems based on the global distributions of both microbial and metazoan carbonates through Precambrian to Phanerozoic times, with emphasis on sedimentary records from China. The compilation of 150 and 180 well-documented metazoan and microbial reefs, respectively, from China, reveals that metazoan reefs proliferated during the Middle Ordovician, Middle Devonian and Middle Permian, whereas microbial reefs were well developed during the Cambrian, Late Devonian and Early–Middle Triassic, plus a moderate development during the early Silurian. These stratigraphic abundances of metazoan and microbial carbonates of China generally match the global patterns. The updated variation trends of microbial and metazoan carbonates throughout the late Precambrian and Phanerozoic reveal that there were five major microbe-metazoan transitions (MMTs): the late Ediacaran, the Cambrian, and the aftermaths of the mass extinctions of the end-Ordovician, Late Devonian, and end-Permian. The late Ediacaran MMT began with microbe-dominated oceans with occasional occurrences of metazoans. The presence of Cloudina-dominated reefs in the latest Ediacaran marks the completion of the switching of this microbe-dominated depositional system into a metazoan-dominated system. The Cambrian saw the expansion of skeletal microbes (i.e., Epiphyton, Renalcis) in the oceans; and the stratigraphic successions yield the most diverse biosedimentary deposits and/or structures of the entire Phanerozoic. The Cambrian MMT was the longest microbial-metazoan alternation period and is marked by two metazoan occurrence peaks marked by dominance of abundant archaeocyath buildups during its Epoch 2 and by maceriate and lithistid sponge reefs during the late Furongian Epoch. The early Silurian in China saw the deposition of a thick suite of organic-rich black shales followed by alternations of microbe-rich sediments (oil shales) and metazoan-bearing deposits, which are replaced by microbial and metazoan reefs during the late early Silurian. The Late Devonian MMT started during the late Frasnian and persisted into the early Mississippian, and thus extended slightly longer than the aftermath of the Frasnian–Famennian extinction interval. Alternating occurrences of microbial and metazoan reefs characterize this Late Devonian MMT. Almost all microbe-mediated sediments/structures observed in the Cambrian MMT reoccurred in the aftermath of the end-Permian mass extinction during the Early–Middle Triassic MMT, suggesting high similarities between those two MMTs. Cambrian and Early–Middle Triassic MMTs also share comparable carbon and sulfur isotopic perturbations, warming regimes, and generally oxygen-deficient seawaters. Some of these environmental and climatic extremes may also occur during other MMTs, but they usually did not occur synchronously.

Most MMTs seem to have undergone four developmental stages. They initiated as microbe-dominated successions (Stage A), and then were characterized by alternations of microbe-dominated

and of metazoan-bearing or bioturbated successions (Stage B). Both microbial and metazoan reefs co-occurred during Stage C; and a dominance of metazoan reefs marks the development of Stage D. Ediacaran and Cambrian MMTs seem to have undergone the first three development stages, whereas the three post-extinction MMTs experienced the full set of Stages A−D, corresponding to metazoan survival, initial recovery and full recovery.

The majority of volatile-rich Large Igneous Provinces (LIPs), coupled with intensive acidification events, anoxia and global warming regimes, took place during the Mesozoic–Cenozoic. However, microbe-dominated sediments were only widely deposited during the Early Triassic, and greatly declined after that time. Therefore, it seems that microbial abundance in MMTs may not be directly related to these extreme LIP events. This is probably because a primary source of food for the metazoans might have shifted to phytoplankton (e.g., coccoliths, dinoflagellates, and radiolarians) in the marine waters since the Triassic. Certainly, the pre-Mesozoic oceans were not dominated by phytoplankton. Perturbations in the carbon isotope record characterize all MMTs, and thus may be reliable proxies indicating MMT biosedimentary systems.

Cheng, X., Hou, D., Zhao, Z., Chen, X., Diao, H., 2019. Sources of natural gases in the Xihu sag, East China Sea Basin: Insights from stable carbon isotopes and confined system pyrolysis. Energy & Fuels 33, 2166-2175.


The Xihu Sag is the most gas-rich area in the East China Sea Basin. However, the origin of the natural gases is still controversial. Twenty-seven natural gas samples collected from the Xihu Sag were analyzed for chemical and stable carbon isotopic compositions. In addition, three source rock samples (a coal, a carbonaceous mudstone, and a mudstone) from the Middle–Upper Eocene Pinghu Formation were pyrolyzed in a closed system using a gold tube. The stable carbon isotopes of pyrolysis gaseous hydrocarbons were analyzed for gas-source correlation. Five distinct gas families (A to E) were classified based on stable carbon isotopic compositions of methane (δ13C1), ethane (δ13C2), and propane (δ13C3) using the natural gas plot and δ13C2-δ13C1 versus δ13C3-δ13C2. Family A contains 10 samples that are widespread in the Pinghu Slope; family B consists of 12 samples mainly from southern parts of the Central Inverse Anticline Belt; family C consists of three samples and occurs in the Pinghu Slope; families D and E both contain only one gas and occur in the Pinghu Slope. Families A, B, C, and D are thermogenic gas derived from type III kerogens. Family D may have been subjected to alteration by diffused 12C-rich methane. C2+ of family E were mainly generated by oil-prone kerogen, while the C1 is associated with type III kerogen. Thermal maturity of the gases was reassessed based on newly proposed empirical isotope-maturity models for the Xihu Sag. Results suggest that the gases were generated during the late oil window to late wet gas window. The δ13C values of C1–C3 from the pyrolysis experiments are useful in direct correlations with natural gas accumulations. Gas-source correlation suggests that families A and B were derived from coal and mudstone of the Middle–Upper Eocene Pinghu Formation, respectively. Family C could be an admixture of gases generated by mudstone and carbonaceous mudstone of the Pinghu Formation. The C2+ in family D were mainly derived from the more mature Lower–Middle Eocene Baoshi Formation, while the 12C-rich C1 might be diffused upward from greater depth. Family E is mixture of sapropelic gas probably from the Paleocene source rock and high-maturity humic gas probably from the Baoshi Formation. Gas-source rock correlation indicates that the Pinghu Formation is the main gas source rock unit in the Xihu Sag and that gas distribution is source controlled. Confirmation of the Lower–Middle Eocene Baoshi Formation and Paleocene as additional effective source rocks in the Xihu Sag suggests that new exploration plays targeting these alternative hydrocarbon source rocks are possible and worth exploring.

Chiarenza, A.A., Mannion, P.D., Lunt, D.J., Farnsworth, A., Jones, L.A., Kelland, S.-J., Allison, P.A., 2019. Ecological niche modelling does not support climatically-driven dinosaur diversity decline before the Cretaceous/Paleogene mass extinction. Nature Communications 10, Article 1091.

https://doi.org/10.1038/s41467-019-08997-2

In the lead-up to the Cretaceous/Paleogene mass extinction, dinosaur diversity is argued to have been either in long-term decline, or thriving until their sudden demise. The latest Cretaceous (Campanian–Maastrichtian [83–66 Ma]) of North America provides the best record to address this debate, but even here diversity reconstructions are biased by uneven sampling. Here we combine fossil occurrences with climatic and environmental modelling to quantify latest Cretaceous North American dinosaur habitat. Ecological niche modelling shows a Campanian-to-Maastrichtian habitability decrease in areas with present-day rock-outcrop. However, a continent-wide projection demonstrates habitat stability, or even a Campanian-to-Maastrichtian increase, that is not preserved. This reduction of the spatial sampling window resulted from formation of the proto-Rocky Mountains and sea-level regression. We suggest that Maastrichtian North American dinosaur diversity is therefore likely to be underestimated, with the apparent decline a product of sampling bias, and not due to a climatically-driven decrease in habitability as previously hypothesised.



Polycyclic aromatic compounds (PACs) can have multiple sources in the Athabasca Oil Sands Region (AOSR). The current study was designed to identify and explore the potential of nitrogen heterocyclic PACs (NPACs) as source indicators in snowpack, lake sediment and passive air samples from the AOSR during 2014–2015. Source samples including petroleum coke (petcoke), haul road dust, and unprocessed oil sands were also analyzed. Samples were analyzed using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry, and liquid chromatography-high resolution Orbitrap mass spectrometry. Over 200 NPACs were identified and classified into at least 24 isomer groups, including alkylated carbazoles, benzocarbazoles, and indenoquinolines. Levels of NPACs in environmental samples decreased with distance from the main developments and with increasing depth in lake sediments but were detected within 50 km from the major developments. The composition profiles of several NPAC isomer classes, such as dimethylcarbazoles, showed that petcoke had a distinct distribution of NPACs compared to the haul road dust and unprocessed oil sands ores and was the most similar source material to near-field environmental samples. These results suggest that petcoke is a major contributing source for the identified NPACs and that these compounds have the potential to be used as source indicators for future research in the AOSR.



In this study, molecular-level chemical compositions of soils contaminated by oil spilled during the Gulf War were studied. Two soil samples, respectively collected at 0.1 m and between 0.5 and 1 m below the surface from an oil spill site, were extracted with organic solvents and water. The extracts were analyzed via ultrahigh resolution FT-ICR and two-dimensional gas chromatography/high resolution mass spectrometry. The data showed that the spilled oil was significantly affected by vaporization due to high surface temperatures in the desert. The data obtained with (+) atmospheric pressure photo ionization (APPI) and (-) electrospray ionization (ESI) coupled with ultrahigh resolution–mass spectrometry (UHR-MS) indicated that the degradation of aromatic compounds and increase in oxygen-containing classes occurred in the following order: surface soil > below surface soil > crude oil. The oxygenated compounds were confirmed by principal component analysis. The score and loading plots of Ox and SOx showed that they were the major contributors to differentiate the samples. However, a comparison with previously reported oceanic oil spills showed that less significant degradation occurred even after almost 30 years. Our data can provide an information basis for designing a strategy for clean-up and restoration efforts of Gulf War oil spills.

Chu, D., Tong, J., Benton, M.J., Yu, J., Huang, Y., 2019. Mixed continental-marine biotas following the Permian-Triassic mass extinction in South and North China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 95-107.


Correlation between marine and continental Permian-Triassic (P-Tr) strata is crucial for full understanding of the nature of this global extinction event, but it has proved difficult to achieve. Here, we show that two sections in South China and North China record similar mixed continental-marine biota in the post-extinction stratigraphic interval, including conchostracans, plants, insects, marine bivalves and lingulid brachiopods. In addition, the continental P-Tr mass extinction was represented by a sharp decrease in the diversity and abundance of the Gigantopteris flora in South China, but eliminated the Palaeozoic-type conifer flora and herbivorous pareiasaurs in North China. These mixed continental-marine biota provide the biological evidence for stratigraphic correlation between marine and continental P-Tr transitional beds in South China and North China, especially the co-occurrence of the Pteria-Towapteria-Eumorphotis bivalve assemblage and the Euestheria gutta-bearing conchostracan fauna or Euestheria gutta-Magniestheria mangaliensis-Palaeolimnadiopsis vilujensis conchostracan assemblage. We propose that these specific marine bivalve and continental conchostracan assemblages could be considered as markers of P-Tr transitional beds in marine-continental siliciclastic settings.

Cisternas-Novoa, C., Le Moigne, F.A.C., Engel, A., 2019. Composition and vertical flux of particulate organic matter to the oxygen minimum zone of the central Baltic Sea: impact of a sporadic North Sea inflow. Biogeosciences 16, 927-947.


Particle sinking is a major form of transport for photosynthetically fixed carbon to below the euphotic zone via the biological carbon pump (BCP). Oxygen (O2) depletion may improve the efficiency of the BCP. However, the mechanisms by which O2 deficiency can enhance particulate organic matter (POM) vertical fluxes are not well understood. Here, we investigate the composition and vertical fluxes of POM in two deep basins of the Baltic Sea (GB: Gotland Basin and LD: Landsort Deep). The two basins showed different O2 regimes resulting from the intrusion of oxygen-rich water from the North Sea that ventilated the water column below 140 m in GB, but not in LD, during the time of sampling. In June 2015, we deployed surface-tethered drifting sediment traps in oxic surface waters

(GB: 40 and 60 m; LD: 40 and 55 m), within the oxygen minimum zone (OMZ; GB: 110 m and LD: 110 and 180 m) and at recently oxygenated waters by the North Sea inflow in GB (180 m). The primary objective of this study was to test the hypothesis that the different O2 conditions in the water column of GB and LD affected the composition and vertical flux of sinking particles and caused differences in export efficiency between those two basins.

The composition and vertical flux of sinking particles were different in GB and LD. In GB, particulate organic carbon (POC) flux was 18 % lower in the shallowest trap (40 m) than in the deepest sediment trap (at 180 m). Particulate nitrogen (PN) and Coomassie stainable particle (CSP) fluxes decreased with depth, while particulate organic phosphorus (POP), biogenic silicate (BSi), chlorophyll a (Chl a) and transparent exopolymeric particle (TEP) fluxes peaked within the core of the OMZ (110 m); this coincided with the presence of manganese oxide-like (MnOx-like) particles aggregated with organic matter. In LD, vertical fluxes of POC, PN and CSPs decreased by 28 %, 42 % and 56 %, respectively, from the surface to deep waters. POP, BSi and TEP fluxes did not decrease continuously with depth, but they were higher at 110 m. Although we observe a higher vertical flux of POP, BSi and TEPs coinciding with abundant MnOx-like particles at 110 m in both basins, the peak in the vertical flux of POM and MnOx-like particles was much higher in GB than in LD. Sinking particles were remarkably enriched in BSi, indicating that diatoms were preferentially included in sinking aggregates and/or there was an inclusion of lithogenic Si (scavenged into sinking particles) in our analysis. During this study, the POC transfer efficiency (POC flux at 180 m over 40 m) was higher in GB (115 %) than in LD (69 %), suggesting that under anoxic conditions a smaller portion of the POC exported below the euphotic zone was transferred to 180 m than under reoxygenated conditions present in GB. In addition, the vertical fluxes of MnOx-like particles were 2 orders of magnitude higher in GB than LD. Our results suggest that POM aggregates with MnOx-like particles formed after the inflow of oxygen-rich water into GB, and the formation of those MnOx–OM-rich particles may alter the composition and vertical flux of POM, potentially contributing to a higher transfer efficiency of POC in GB. This idea is consistent with observations of fresher and less degraded organic matter in deep waters of GB than LD.

Coble, A.A., Koenig, L.E., Potter, J.D., Parham, L.M., McDowell, W.H., 2019. Homogenization of dissolved organic matter within a river network occurs in the smallest headwaters. Biogeochemistry 143, 85-104.

https://doi.org/10.1007/s10533-019-00551-y

Understanding the drivers of variability in the concentration and composition of dissolved organic matter (DOM) in running waters is a fundamental challenge for aquatic biogeochemistry. Although multiple conceptual frameworks have been proposed to quantify expected changes in DOM within a river network, few studies have collected data to document the variability of DOM within such a network. We examine spatial and temporal variability in the concentration, optical properties, and biodegradability of DOM within a river network in New Hampshire, U.S.A. We examined dissolved organic carbon (DOC) concentration and DOM optical properties across 21 locations within the Lamprey River network (548 km2) with weekly to monthly sampling for 4 years, and biodegradable DOC (BDOC) at 7 mainstem locations for 1 year. DOC concentration and DOM character were highly heterogeneous at the scale of the smallest streams, where variability in land cover and nutrient concentrations were also greatest. At the landscape scale, DOC concentrations and DOM aromaticity increased with wetland cover and decreased with developed land cover and nitrate concentrations. Despite this heterogeneity across streams, we observed similar synchronous seasonal variation in DOC concentration and DOM character regardless of position within the river network, suggesting that broad environmental factors shape the sources and transport of DOM in river networks. In contrast, variation in BDOC over time or across sites was not strongly related to DOM quality or

other predictors. Spatiotemporal patterns in DOM provide insight into the complex processes that influence terrestrial carbon export, in-stream processes, and DOM delivery to downstream ecosystems.

Cockell, C.S., Harrison, J.P., Stevens, A.H., Payler, S.J., Hughes, S.S., Kobs Nawotniak, S.E., Brady, A.L., Elphic, R.C., Haberle, C.W., Sehlke, A., Beaton, K.H., Abercromby, A.F.J., Schwendner, P., Wadsworth, J., Landenmark, H., Cane, R., Dickinson, A.W., Nicholson, N., Perera, L., Lim, D.S.S., 2019. A low-diversity microbiota inhabits extreme terrestrial basaltic terrains and their fumaroles: Implications for the exploration of Mars. Astrobiology 19, 284-299.

https://doi.org/10.1089/ast.2018.1870

A major objective in the exploration of Mars is to test the hypothesis that the planet hosted life. Even in the absence of life, the mapping of habitable and uninhabitable environments is an essential task in developing a complete understanding of the geological and aqueous history of Mars and, as a consequence, understanding what factors caused Earth to take a different trajectory of biological potential. We carried out the aseptic collection of samples and comparison of the bacterial and archaeal communities associated with basaltic fumaroles and rocks of varying weathering states in Hawai‘i to test four hypotheses concerning the diversity of life in these environments. Using high-throughput sequencing, we found that all these materials are inhabited by a low-diversity biota. Multivariate analyses of bacterial community data showed a clear separation between sites that have active fumaroles and other sites that comprised relict fumaroles, unaltered, and syn-emplacement basalts. Contrary to our hypothesis that high water flow environments, such as fumaroles with active mineral leaching, would be sites of high biological diversity, alpha diversity was lower in active fumaroles compared to relict or nonfumarolic sites, potentially due to high-temperature constraints on microbial diversity in fumarolic sites. A comparison of these data with communities inhabiting unaltered and weathered basaltic rocks in Idaho suggests that bacterial taxon composition of basaltic materials varies between sites, although the archaeal communities were similar in Hawai‘i and Idaho. The taxa present in both sites suggest that most of them obtain organic carbon compounds from the atmosphere and from phototrophs and that some of them, including archaeal taxa, cycle fixed nitrogen. The low diversity shows that, on Earth, extreme basaltic terrains are environments on the edge of sustaining life with implications for the biological potential of similar environments on Mars and their exploration by robots and humans.

Coldwell, B.C., Pankhurst, M.J., 2019. Evaluating the influence of meteorite impact events on global potassium feldspar availability to the atmosphere since 600 Ma. Journal of the Geological Society 176, 209-224.

http://jgs.lyellcollection.org/content/176/2/209.abstract

Potassium feldspar present in global mineral aerosol (<5%) plays a disproportionate role in modulating the microphysics of mixed-phase cloud. Via exceptional ice nucleation properties, it is capable of changing cloud properties and behaviour. Here we identify times of substantial and abrupt change in the global availability of potassium feldspar since 600 Ma. Normally, weathering and vegetation cover contribute to low availability, with clay dominating mineral aerosol. Periods of maximum availability are reasoned to follow the emplacement and remobilization of ejecta blankets from major meteorite impact events, before returning to background after some hundreds to thousands of years. We review the 44 largest confirmed craters and evaluate the potassium feldspar content of their target rocks, which range from c. 0 to >30%. By combining crater size and tectonic reconstructions, we are able to provide a quantitative and self-consistent assessment of changes to

global potassium feldspar availability. Considerable differences in potassium feldspar availability following meteorite impact events are revealed. Different impact events generated dust containing different amounts of potassium feldspar. Differing levels of influence upon climate are hypothesized, and should now be tested by looking at stratigraphic records of these events to reveal the sensitivity of climate to different dust mineralogy.

Supplementary material: Figures showing palaeolatitude determinations using various methods and reconstruction models, and estimates of alkali feldspar abundance and distribution across contemporary continental landmasses for meteorite impact events are available at: https://doi.org/10.6084/m9.figshare.c.4253312

Cordero, C., Kiefl, J., Reichenbach, S.E., Bicchi, C., 2019. Characterization of odorant patterns by comprehensive two-dimensional gas chromatography: A challenge in omic studies. TrAC Trends in Analytical Chemistry 113, 364-378.


Sensomics, like other “omics” fields, cuts across chemistry and biology and so requires holistic strategies capable of comprehensively mapping the set of all potential ligands (e.g., sensometabolome) that trigger the multimodal perception of food flavor. These complex mixtures when directed to odor receptors in the nose, define the so-called Chemical Odor Code. Analytical chemistry is challenged to comprehensively map the complex volatile fractions of real samples, including odorants and interferents, and define univocal odor patterns for correlative studies. This review critically discusses state-of-the-art research in the field of odorants and volatiles characterization in food by comprehensive two-dimensional gas chromatography, illustrating how hyphenation with mass spectrometry and olfactometry, accurate quantitation, suitable sample preparation, and dedicated data mining can capture essential information on odor patterns exploiting the higher level of information on sample sensory features.



The metal excretion and metal sorption are two important microbial processes in the regulation of intracellular metal concentration. However, the contribution of freshwater phototrophic biofilm to metal efflux in the environment and its related isotopic fractionation remain poorly known. In this study, Cu efflux from a mature phototrophic biofilm and related Cu isotopic fractionation between the biofilm and aqueous solution were studied over 4 days in closed batch and open drip-flow reactors (BR and DFR, respectively). The impact of a 48-h drying event on Cu efflux from the biofilm and its isotopic signature was quantified in the BR. Cu excretion from the biofilm depended on Cu concentration in the biomass and did not show a latent phase. For the wet biofilm, in DFR, the Cu efflux rate decreased over time whereas in BR, Cu efflux exhibited fluctuations with a net re-sorption phase.

During short-term early excretion over the first 4 h (BR) and 24 h (DFR), the enrichment of solution in heavy isotopes with a Δ65Cu(sol–biofilm) of +0.7 ± 0.2‰ could be explained by a combination of i) desorption via competition between H+ and Cu2+ for surface sites and ii) release of isotopically heavy Cu(II)-organic complexes. In addition, there was a retention of isotopically light Cu (I) within the cells which is consistent with the biofilm ability to reduce Cu. With further exposure of the wet

biofilm to the solution, a progressive decrease of Δ65Cu(sol–biofilm), down to 0 and −0.36‰ respectively in BR and DFR after 96 h, could be explained by an active efflux of Cu(I) and by a passive diffusion of Cu2+, both of these processes favoring light isotopes. The re-hydrated and wet biofilms showed distinctly different behavior during excretion, in terms of magnitude of the flux and direction of the fractionation for long term exposure. Indeed, the efflux from the re-hydrated biofilm was ten times higher than the one from the wet biofilm and the re-hydrated biofilm did not exhibit a decrease of Δ65Cu(sol–biofilm) after 24 h of reaction. This could be related to partial devitalization of the biofilm during drying, producing a release of isotopically heavy Cu and decreasing the intensity of Cu(I) active efflux of light isotopes. Taken together, the Cu isotopic signature in natural aquatic environments containing phototrophic biofilms varies up to 1‰ on a daily scale.

Crosby, J.R., Laemthong, T., Lewis, A.M., Straub, C.T., Adams, M.W.W., Kelly, R.M., 2019. Extreme thermophiles as emerging metabolic engineering platforms. Current Opinion in Biotechnology 59, 55-64.


Going forward, industrial biotechnology must consider non-model metabolic engineering platforms if it is to have maximal impact. This will include microorganisms that natively possess strategic physiological and metabolic features but lack either molecular genetic tools or such tools are rudimentary, requiring further development. If non-model platforms are successfully deployed, new avenues for production of fuels and chemicals from renewable feedstocks or waste materials will emerge. Here, the challenges and opportunities for extreme thermophiles as metabolic engineering platforms are discussed.

Cyr, F., Tedetti, M., Besson, F., Bhairy, N., Goutx, M., 2019. A glider-compatible optical sensor for the detection of polycyclic aromatic hydrocarbons in the marine environment. Frontiers in Marine Science 6, 110. doi: 110.3389/fmars.2019.00110.

https://www.frontiersin.org/article/10.3389/fmars.2019.00110

This study presents the MiniFluo-UV, an ocean glider-compatible fluorescence sensor that targets the detection of polycyclic aromatic hydrocarbons (PAHs) in the marine environment. Two MiniFluos can be installed on a glider, each equipped with two optical channels (one PAH is measured per channel). This setup allows the measurement of up to 4 different fluorescent PAHs: Naphthalene, Phenanthrene, Fluorene and Pyrene. Laboratory tests on oil products (Maya crude oil and Diesel fuel) as well as on marine samples near industrial areas (urban harbor and offshore installations) revealed that the concentration of the four PAHs targeted accounted for 62–97% of the total PAH concentration found in samples (∑16 PAHs determined by standard international protocols). Laboratory tests also revealed that for marine applications, the calibration on Water Accommodated Fraction (WAF) of crude oil is more appropriate than the one on pure standards (STD). This is because PAH fluorescence is constituted in large part of alkylated compounds that are not considered with STD calibration. Results from three glider deployments with increasing levels of complexity (a laboratory trial, a field mission in non-autonomous mode and a fully autonomous mission) are also presented. During field deployments, the MiniFluo-glider package was able to detect concentration gradients from offshore marine waters toward the head of a Mediterranean harbor (< 80 ng L−1) as well as hydrocarbon patches at the surface waters of an oil and gas exploitation field in the North Sea (< 200 ng L−1, mainly Naphthalene). It is suggested that using only the WAF calibration, the concentration derived with the MiniFluo agrees within one order of magnitude with the concentration determined by Gas Chromatography coupled with Mass Spectrometry (overestimation by a factor 7

on average). These performances can be improved if the calibration is made with a WAF with PAH proportions similar to the one find in the environment. Finally, it is shown that the use of in situ calibration on water samples collected during the glider deployment, when possible, gives the best results.

Dąbrowski, K.M., Kuczyński, S., Barbacki, J., Włodek, T., Smulski, R., Nagy, S., 2019. Downhole measurements and determination of natural gas composition using Raman spectroscopy. Journal of Natural Gas Science and Engineering 65, 25-31.


This paper analysis the measurements of the natural gas composition in a wellbore in real time in situ conditions using the RS785 nm spectrometer. The measuring system was interchangeably equipped with a fiber optic system with a length of 105 and 1605 m enabling transmission of a signal to and from the wellbore. The comparison of the Raman signal transmitted for both lengths of the optical fiber is presented. Raman signal from the probe in the borehole converted to the molar composition of natural gas using regression methods and using the artificial neural network. The natural gas composition was estimated at the wellhead at the depth 271 m in the gas well using a 1605 m long fiber optic. The acquired Raman signal from well are compared with the composition measured in the case of gas taken from the well in laboratory conditions using gas chromatography, as well as measurements from a Raman system equipped with a 105-m optical fiber.

Dai, G., Zhu, Y., Yang, J., Pan, Y., Wang, G., Reubroycharoen, P., Wang, S., 2019. Mechanism study on the pyrolysis of the typical ether linkages in biomass. Fuel 249, 146-153.


The in-depth study of the cleavage behaviors of linkages in biomass is important for the better understanding of biomass pyrolysis mechanism. This study aimed to clarify the pyrolysis mechanism of the typical ether linkages in biomass including β-1,4-glycosidic bond, α-O-4 bond and methoxyl using cellobiose, benzylphenyl ether and guaiacol as the model compounds. Combining the detection of the key intermediates, especially radicals by SVUV-PIMS and the evaluation of the reaction pathways by density functional theory (DFT) quantum chemical calculations, it was found that the concerted cleavage of β-1,4-glycosidic bond was more kinetically favorable than homolytic cleavage and heterolytic cleavage, and the ring opening of cellobiose via the breakage of C1′-O was likely to occur before the cleavage of glycosidic bond. The α-O-4 bond in benzylphenyl ether was mainly cleaved by Cα-O homolysis, and it was easy for the formed radicals to recombine with each other to yield phenolic dimers. In the initial evolution process of methoxyl in guaiacol, homolytic demethylation was the most important unimolecular reaction, while demethoxylation and radical-induced rearrangement reactions were difficult to occur due to their high energy barriers. In the presence of the formed methyl radicals from homolytic demethylation reaction, these two reactions would occur since their energy barriers were significantly reduced at this condition.

Dalai, P., Sahai, N., 2019. Mineral–lipid interactions in the origins of life. Trends in Biochemical Sciences 44, 331-341.


Protocells, the first life-like entities, likely contained three molecular components: a membrane, an information-carrying molecule, and catalytic molecules. Minerals have a wide range of properties that

might have contributed to the synthesis and self-assembly of these molecular components. Minerals could have mediated the formation and concentration of prebiotic organic monomers, catalyzed their polymerization into biomolecules, and catalyzed protometabolic pathways, leading to protocell self-assembly. This review considers the following major aspects of protocell membrane-mineral interactions: (i) the effect of dissolved cations on the stability of mixed fatty acid and phospholipid vesicles; (ii) the rate of lipid self-assembly to vesicles; and (iii) the role of photocatalytic minerals in harvesting light energy to drive electron transfer reactions across membranes in the development of protometabolism.

Dale, A.W., Flury, S., Fossing, H., Regnier, P., Røy, H., Scholze, C., Jørgensen, B.B., 2019. Kinetics of organic carbon mineralization and methane formation in marine sediments (Aarhus Bay, Denmark). Geochimica et Cosmochimica Acta 252, 159-178.


Sediments were sampled at nine stations on a transect across a 7–10 m thick Holocene mud layer in Aarhus Bay, Denmark, to investigate the linkages between CH4 dynamics and the rate and depth distribution of organic matter degradation. High-resolution sulfate reduction rates determined by tracer experiments (35S-SRR) decreased by several orders of magnitude down through the mud layer. The rates showed a power law dependency on sediment age: SRR (nmol cm−3 d−1) = 106.18 × Age−2.17. The rate data were used to independently quantify enhanced SO4

2− transport by bioirrigation. Field data (SO4

2−, TCO2, T13CO2, NH4+ and CH4 concentrations) could be simulated with a reaction-

transport model using the derived bioirrigation rates and assuming that the power law was continuous into the methanogenic sediments below the sulfate-methane transition zone (SMTZ). The model predicted an increase in anaerobic organic carbon mineralization rates across the transect from 2410 to 3540 nmol C cm−2 d−1 caused by an increase in the sediment accumulation rate. Although methanogenesis accounted for only ∼1% of carbon mineralization, a large relative increase in methanogenesis along the transect led to a considerable shallowing of the SMTZ from 428 to 257 cm. Methane gas bubbles appeared once a threshold in the sedimentation accumulation rate was surpassed.

The 35S-measured SRR data indicated active sulfate reduction throughout the SO42− zone whereas

quasi-linear SO42− gradients over the same zone indicated insignificant sulfate reduction. This

apparent inconsistency, observed at all stations, was reconciled by considering the transport of SO42−

into the sediment by bioirrigation, which accounted for 94 ± 2% of the total SO42− flux across the

sediment-water interface. The SRR determined from the quasi-linear SO42− gradients were two orders

of magnitude lower than measured rates. We conclude that models solely based on SO42−

concentration gradients will not capture high SRRs at the top of the sulfate reduction zone if they do not properly account for (i) SO4

2− influx by bioirrigation, and/or (ii) the continuity of organic matter reactivity with sediment depth or age.

Daley, A.C., 2019. A treasure trove of Cambrian fossils. Science 363, 1284-1285.

http://science.sciencemag.org/content/363/6433/1284.abstract

One of the most important discoveries in paleontological history was the Burgess Shale in the Canadian Rocky Mountains, discovered in 1909 by Charles Walcott. At this 508 million–year-old fossil locality, soft-bodied fossils are exquisitely preserved, showing skin, eyes, and internal organs such as guts and brains. The Burgess Shale and similar localities found since—including the equally diverse and important Chengjiang biota of China (1), numerous other sites in China (2), and the Emu

Bay Shale in Australia (3)—record the sudden appearance of a huge diversity of animals in a geologically short period of time, an event called the Cambrian Explosion (4). On page 1338 of this issue, Fu et al. (5) reveal a stunning new locality, the Qingjiang biota, which is slightly older (518 million years) than the Burgess Shale. The fossils from the site fill gaps in our knowledge and raise questions about the earliest animal ecosystems.

Dandare, S.U., Young, J.M., Kelleher, B.P., Allen, C.C.R., 2019. The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy. Science of The Total Environment 671, 19-27.


Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential ‘public good’ proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.

Dangelmayr, M.A., Figueroa, L.A., Williams, K.H., Long, P.E., 2019. Characterizing organic carbon dynamics during biostimulation of a uranium contaminated field site. Biogeochemistry 143, 117-132.

https://doi.org/10.1007/s10533-019-00553-w

Uranium contamination of groundwater remains a pressing problem at many former uranium mining and milling operations, such as the Rifle, Integrated Field Research Challenge (IFRC) site. Biostimulation of the subsurface with an organic carbon source such as acetate, followed by the microbially-induced reductive precipitation of uranium has been proposed as an effective remediation strategy. While uranium bioreduction has been studied in several field experiments, the transformation and fate of injected carbon remains poorly understood. This study evaluated the impact of added organic carbon on the long-term biogeochemical attenuation of uranium in the subsurface of a former mill tailings site. Fluorescence and ultraviolet–visible absorbance analyses were used together with dissolved organic carbon (DOC) measurements to track organic carbon dynamics during and post-biostimulation of the 2011 Rifle IFRC experiment. An electron mass balance was performed on well CD01 to account for any unidentified carbon sinks. Measured DOC values increased to 1.76 mM-C during biostimulation, and to 3.18 mM-C post-biostimulation over background DOC values of 0.3–0.4 mM-C. Elevated DOC levels persisted for 90 days after acetate injections ceased. The electron mass balance revealed that assumed electron acceptors would not account for the total amount of acetate consumed. Excitation–emission matrices showed an increase

in signals associated with soluble microbial products, during biostimulation, which disappeared post-biostimulation despite an increase in total DOC. Specific ultraviolet absorbance analyses, indicated that DOC present post-biostimulation is less aromatic in nature, compared to background DOC. Our results suggest that microbes convert injected acetate into a form of solid phase organic matter that may be available to sustain iron reduction post-stimulation.


https://doi.org/10.1002/mbo3.630

Abstract To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms.

de Bar, M.W., Dorhout, D.J.C., Hopmans, E.C., Rampen, S.W., Sinninghe Damsté, J.S., Schouten, S., 2019. Corrigendum to “Constraints on the application of long chain diol proxies in the Iberian Atlantic margin” [Org. Geochem. 101 (2016) 184–195]. Organic Geochemistry 130, 51-52.


Table 1 in de Bar et al. (2016) was found to contain a few incorrect values; the corrected Table is shown below. The data archived in PANGAEA were also corrected. Since the differences are relatively small these corrections do not change the overall interpretation of the data presented in the paper. The authors would like to apologize for any inconvenience caused.

de Carvalho, L.M., Borelli, G., Camargo, A.P., de Assis, M.A., de Ferraz, S.M.F., Fiamenghi, M.B., José, J., Mofatto, L.S., Nagamatsu, S.T., Persinoti, G.F., Silva, N.V., Vasconcelos, A.A., Pereira, G.A.G., Carazzolle, M.F., 2019. Bioinformatics applied to biotechnology: A review towards bioenergy research. Biomass and Bioenergy 123, 195-224.


The ever-increasing demand for energy, along with worldwide policies aiming sustainability, resulted in an escalation of research projects focusing on alternative routes for energy production. Among the

available options, microorganism fermentation using lignocellulosic biomass as a carbon source to generate bioproducts is considered a promising technology for industrial applications, with potential to replace several sources of non-renewable origin that are widely used today. In this context, various new industrial processes have been developed, such as the second-generation ethanol technology, which allows bioethanol production from lignocellulosic biomass by genetically modified microorganisms.

In recent years, fields in biotechnology were mainly driven by advances in molecular biology and genetic engineering tools, which culminated in the ‘omics’ revolution. Recent developments in DNA sequencing and liquid/mass spectrometry technologies, supported by research in bioinformatics and high-performance computing, allowed the identification of new organisms and metabolic processes, expanding the human knowledge about biological systems. The result of this newly gained understanding is the ability to perform genetic modifications focusing on the obtention of interesting phenotypes with increased productivity and resistance or the synthesis of new compounds that were previously produced using non-renewable routes.

In this context, this review presents the bioinformatics workflows and applications of ‘omics’ approaches in biotechnological research, focusing on genomics, metagenomics, phylogenomics, transcriptomics, proteomics, metabolomics and their integration to enable a holistic overview of biological systems.

Dean, J.F., Garnett, M.H., Spyrakos, E., Billett, M.F., 2019. The potential hidden age of dissolved organic carbon exported by peatland streams. Journal of Geophysical Research: Biogeosciences 124, 328-341.

https://doi.org/10.1029/2018JG004650

Abstract: Radiocarbon (14C) is a key tracer for detecting the mobilization of previously stored terrestrial organic carbon (C) into aquatic systems. Old C (>1,000 years BP) may be ?masked? by postbomb C (fixed from the atmosphere post-1950 CE), potentially rendering bulk aquatic dissolved organic C (DOC) 14C measurements insensitive to old C. We collected DOC with a modern 14C signature from a temperate Scottish peatland stream and decomposed it to produce CO2 under simulated natural conditions over 140 days. We measured the 14C of both DOC and CO2 at seven time points and found that while DOC remained close to modern in age, the resultant CO2 progressively increased in age up to 2,356 ± 767 years BP. The results of this experiment demonstrate that the bulk DO14C pool can hide the presence of old C within peatland stream DOC export, demonstrating that bulk DO14C measurements can be an insensitive indicator of peatland disturbance. Our experiment also demonstrates that this old C component is biologically and photochemically available for conversion to the greenhouse gas CO2, and as such, bulk DO14C measurements do not reflect the 14C signature of the labile organic C pool exported by inland water systems more broadly. Moreover, our experiment suggests that old C may be an important component of CO2 emissions to the atmosphere from peatland aquatic systems, with implications for tracing and modeling interactions between the hydrological and terrestrial C cycles.

Plain Language Summary: The introduction of old carbon previously stored in soils for thousands of years into rivers can increase the net flux of greenhouse gases to the atmosphere, impacting global climate. This is because rivers transport the equivalent of one third of human carbon emissions annually from land to the oceans. Much river‐borne carbon is plant and soil (organic) matter that can decompose during transport, releasing greenhouse gases to the atmosphere. Radiocarbon dating can

reveal the age of river‐borne carbon, but previous measurements may have underestimated the age of carbon released into rivers by not considering the potential for old carbon hidden within individual bulk water samples. Using an incubation experiment, we demonstrate that dissolved organic carbon from a Scottish peatland stream that would be considered modern in age using traditional bulk radiocarbon dating can readily decompose to produce carbon dioxide with an old radiocarbon signature up to ~2,500 years old. This demonstrates that radiocarbon dating of bulk riverine dissolved organic carbon can hide the presence of old carbon. Furthermore, these results indicate that old carbon may be more common in the global carbon cycle than previously thought, with important implications for our understanding and modeling of peatland ecosystems.

Degli Esposti, M., Mentel, M., Martin, W., Sousa, F.L., 2019. Oxygen reductases in alphaproteobacterial genomes: Physiological evolution from low to high oxygen environments. Frontiers in Microbiology 10, 499. doi: 410.3389/fmicb.2019.00499.


Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 µM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 µM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well.

Dehwah, A.H.A., Anderson, D.M., Li, S., Mallon, F.L., Batang, Z., Alshahri, A.H., Hegy, M., Missimer, T.M., 2019. Transparent exopolymer particle binding of organic and inorganic particles in the Red Sea: Implications for downward transport of biogenic materials. Biogeosciences Discussions 2019, 1-40.

https://www.biogeosciences-discuss.net/bg-2019-59/

Binding of particulate and dissolved organic matter in the water column by marine gels allows sinking and cycling of organic matter into deeper water of the Red Sea and other marine water bodies. A series of four offshore profiles were made at which concentrations of bacteria, algae, particulate transparent exopolymer particles (p-TEP), colloidal transparent exopolymer particles (c-TEP), and the fractions of natural organic matter (NOM), including biopolymers, humic substances, low molecular weight neutrals, and low molecular weight acids were measured to depths ranging from 90 to 300 m. It was found that a statistically-significant relationship occurs between the concentrations of p-TEP and bacteria while a minimal, non-significant relationship between p-TEP and algae occurs. This

likely reflects the low abundance of larger algal species in the study region. Variation in the biopolymer fraction of NOM in relationship to TEP and bacteria suggests that extracellular discharges of polysaccharides and proteins from the bacteria and algae are occurring without immediate abiotic assembly into p-TEP. In the water column below the photic zone, TOC, bacteria, and biopolymers show a generally common rate of reduction in concentration, but p-TEP decreases at a diminished rate, showing that it persists in moving organic carbon deeper into the water column despite consumption by bacteria.

Deng, K., Zhang, F., Tan, Q., Huang, Y., Song, W., Rong, Z., Zhu, Z.-J., Li, Z., Li, K., 2019. WaveICA: a novel algorithm to remove batch effects for large-scale untargeted metabolomics data based on wavelet analysis. Analytica Chimica Acta 1061, 60-69.


Metabolomics provides new insights into disease pathogenesis and biomarker discovery. Samples from large-scale untargeted metabolomics studies are typically analyzed using a liquid chromatography-mass spectrometry platform in several batches. Batch effects that are caused by non-biological systematic biases are unavoidable in large-scale metabolomics studies, even with properly designed experiments. The statistical analysis of large-scale metabolomics data without managing batch effects will yield misleading results. In this study, we propose a novel algorithm, called WaveICA, which is based on the wavelet transform method with independent component analysis, as the threshold processing method to capture and remove batch effects for large-scale metabolomics data. The WaveICA method uses the time trend of samples over the injection order, decomposes the original data into multi-scale data with different features, extracts and removes the batch effect information in multi-scale data, and obtains clean data. The WaveICA method was tested on real metabolomics data. After applying the WaveICA method, scattered quality control samples (QCS) and subject samples in a PCA score plot of the original data were closely clustered, respectively. The average Pearson correlation coefficients for all peaks of the QCS increased from 0.872 to 0.972. Additionally, WaveICA significantly improved the classification accuracy for metabolomics data. The method was compared with three representative methods, and outperformed all of them. To conclude, WaveICA can efficiently remove batch effects while revealing more biological information. This method can be used in large-scale untargeted metabolomics studies to preprocess raw metabolomics data.

DeReuil, A.A., Birgenheier, L.P., 2019. Sediment dispersal and organic carbon preservation in a dynamic mudstone-dominated system, Juana Lopez Member, Mancos Shale. Sedimentology 66, 1002-1041.

https://doi.org/10.1111/sed.12532

Abstract A balance between primary production, rates of sediment accumulation or dilution, and biological or diagenetic destruction has long been considered a key control on organic carbon preservation in modern offshore marine environments. Additionally, current understanding of sediment transport processes in offshore environments has advanced in the last decade to include variable energy and dynamic mechanisms, requiring a re-evaluation of ancient deposits in these systems. The Juana Lopez Member of the Mancos Shale preserves organic carbon-rich mudstone interbedded and interlaminated with sandstone that records high energy traction flow conditions. Core, outcrop and geochemical data from the Juana Lopez Member were used to elucidate sediment provenance and processes controlling organic carbon preservation and distribution in this mudstone-dominated system. Five dominant lithofacies with varying grain size, sedimentary fabrics, composition and grain origins were differentiated and were deposited in three main environments: the

prodelta, fringe zone and low angle offshore ramp. Basal deposits of the Juana Lopez Member consist of siliceous sandstone-dominated, heterolithic deposits with characteristic sedimentary structures (for example, current ripples and normal grading) that indicate offshore-directed underflows, or hyperpycnites, delivered from the updip Ferron/Frontier deltaic system. In the upper portion of the Juana Lopez Member, a compositional change to biogenic carbonate-rich sandstone and mudstone is interpreted to be as a result of increased accommodation in central Utah (USA), associated base-level rise and shoreline-parallel sediment transport. Non-parallel laminated, organic carbon-rich mudstone is preserved throughout the Juana Lopez Member. Depositional fabrics and trace element signatures suggest that these deposits are the result of dynamic conditions at the sea floor and in the oxic to suboxic water column, further challenging the notion that organic-bearing mudstone is deposited solely through suspension settling in anoxic waters. Punctuated delivery of organic carbon laden sediment from mixed terrestrial and marine sources resulted in an event-bed style of organic carbon deposition and preservation.

Díaz-Urrutia, C., Ott, T., 2019. Activation of methane to CH3+: A selective industrial route to

methanesulfonic acid. Science 363, 1326-1329.


Abstract: Direct methane functionalization to value-added products remains a challenge because of the propensity for overoxidation in many reaction environments. Sulfonation has emerged as an attractive approach for achieving the necessary selectivity. Here, we report a practical process for the production of methanesulfonic acid (MSA) from only two reactants: methane and sulfur trioxide. We have achieved >99% selectivity and yield of MSA. The electrophilic initiator based on a sulfonyl peroxide derivative is protonated under superacidic conditions, producing a highly electrophilic oxygen atom capable of activating a C–H bond of methane. Mechanistic studies support the formation of CH3

+ as a key intermediate. This method is readily scalable with reactors connected in series for prospective production of up to 20 metric tons per year of MSA.

Editor's summary: Methane oxidation on the plus side. Industrial conversion of methane to alcohol derivatives involves a circuitous route that starts with overoxidation to carbon monoxide. More direct approaches in highly acidic media have shown promise at small scale but are not cost-effective. Díaz-Urrutia and Ott describe a reaction at pilot-plant scale that combines methane and sulfur trioxide directly in sulfuric acid to form methanesulfonic acid with no by-products (see the Perspective by Schüth). The reaction appears to proceed via a cationic chain mechanism initiated by a low concentration of added sulfonyl peroxide and propagated by CH3

+.



There is a reasonably extensive body of literature recording mass loss of polyhydroxyalkanoates (PHAs) (a class of biodegradable plastics) in the natural marine environment. However, to date, this research has been very disparate. Thus, it remains unclear what the timeframe for the biodegradation of such marine biodegradable plastics actually is. The aim of this work was to determine the rate of biodegradation of PHA in the marine environment and apply this to the lifetime estimation of PHA products. This provides the clarification required as to what ‘marine biodegradation of PHA’ means in practicality and allows the risks and benefits of using PHA to be transparently discussed. It was determined that the mean rate of biodegradation of PHA in the marine environment is 0.04–

0.09 mg·day−1·cm−2 (p = 0.05) and that, for example, a PHA water bottle could be expected to take between 1.5 and 3.5 years to completely biodegrade.



A series of core-flood tests were performed, together with nuclear magnetic resonance measurements of the initial and residual oil saturation states in the cores, to investigate the recovery and mobilization of bypassed oil using a two-step CO2 soaking and ‘huff and puff’ (huff-n-puff) injection method. Two main factors of interest were focused on: miscibility and size of the bypassed oil. During the initial soaking operation, we found that the ability to remove bypassed oil varies according to the mode used and decreases in the order: first-contact miscibility (FCM), multi-contact (MCM), and immiscibility (IM). The corresponding oil recovery factors are 66.3%, 48.0%, and 28.4%, respectively. FCM also facilitates activation of the bypassed oil to the greatest depth (≥6 cm), followed by MCM (∼3 cm). However, the associated oil recovery factors were found to decrease significantly as the bypassed-oil size was increased from the initial value of 6 cm to 20 cm – where even the FCM mode becomes inefficient. Such size of 6 or 10 cm makes the use of FCM reasonably hopeful (oil recovered: 66.3% and 48.2%, respectively). Smaller ones (6 cm; oil recovery: 48.0%) may be promising for MCM usage (where 3 cm is the best size), but, a size far smaller than 6 cm is needed for IM mode to be effective. Furthermore, in terms of the overall total recovery factor achieved using the two-step soaking and huff-n-puff procedure (bypassed-oil size: 6–20 cm), MCM is the best mode (85.6–86.7%), followed by FCM (69.4–74.0%), and then IM (56.9–59.2%). The size of the bypassed-oil has little effect on the huff-n-puff injection step, which implies this step has a much greater effective activation depth than that of the previous soaking step.

do Carmo, T.S., Moreira, F.S., Cabral, B.V., Dantas, R.C.C., de Resende, M.M., Cardoso, V.L., Ribeiro, E.J., 2019. Phosphorus recovery from phosphate rocks using phosphate-solubilizing bacteria. Geomicrobiology Journal 36, 195-203.

https://doi.org/10.1080/01490451.2018.1534901

In this paper, we are presenting a biological process to recover phosphorus by solubilizing low-grade phosphate rocks. To this end, the efficiency of different phosphate-solubilizing microorganism (PSM) species for solubilizing P from phosphate rocks using both pure cultures and associations. Nutritional conditions, phosphate rock concentrations, and reactor designs were tested. The genus Bacillus, especially Bacillus megaterium (ATCC 14581), was found to be the most promising PSM for solubilizing P. Production of organic acids and acidic pH values were shown to be directly related to P solubilizing. However, associations between tested microorganisms did not significantly enhance process efficiency. We conclude that nutritional factors of the medium are important to solubilization, and lower phosphate rock concentrations lead to better solubilization. The Air Lift reactor was promising for B. megaterium (ATCC 14581), but adaptations are needed for further tests.

Domingo-Almenara, X., Montenegro-Burke, J.R., Guijas, C., Majumder, E.L.W., Benton, H.P., Siuzdak, G., 2019. Autonomous METLIN-guided in-source fragment annotation for untargeted metabolomics. Analytical Chemistry 91, 3246–3253.

https://doi.org/10.1021/acs.analchem.8b03126

Computational metabolite annotation in untargeted profiling aims at uncovering neutral molecular masses of underlying metabolites and assign those with putative identities. Existing annotation strategies rely on the observation and annotation of adducts to determine metabolite neutral masses. However, a significant fraction of features usually detected in untargeted experiments remains unannotated, which limits our ability to determine neutral molecular masses. Despite the availability of tools to annotate, relatively few of them benefit from the inherent presence of in-source fragments in liquid chromatography-electrospray ionization-mass spectrometry. In this study, we introduce a strategy to annotate in-source fragments in untargeted data using low-energy tandem mass spectrometry (MS) spectra from the METLIN library. Our algorithm, MISA (METLIN-guided in-source annotation), compares detected features against low-energy fragments from MS/MS spectra, enabling robust annotation and putative identification of metabolic features based on low-energy spectral matching. The algorithm was evaluated through an annotation analysis of a total of 140 metabolites across three different sets of biological samples analyzed with liquid chromatography-mass spectrometry. Results showed that, in cases where adducts were not formed or detected, MISA was able to uncover neutral molecular masses by in-source fragment matching. MISA was also able to provide putative metabolite identities via two annotation scores. These scores take into account the number of in-source fragments matched and the relative intensity similarity between the experimental data and the reference low-energy MS/MS spectra. Overall, results showed that in-source fragmentation is a highly frequent phenomena that should be considered for comprehensive feature annotation. Thus, combined with adduct annotation, this strategy adds a complementary annotation layer, enabling in-source fragments to be annotated and increasing putative identification confidence. The algorithm is integrated into the XCMS Online platform and is freely available at http://xcmsonline.scripps.edu.



This study incorporates X-ray computed tomography (CT) technology into the in-situ observation of the xenon hydrate formation process in sand sediments under excess gas conditions. While the scanning images were used to obtain microscopic distribution information of the hydrate, we implemented the finite element method (FEM) to calculate the resistivity of the hydrate-bearing samples obtained from scanning images. Consequently, it was observed that the resistivity index (RI) versus hydrate saturation (Sh) data matched better with our new calculation model rather than the simple Archie formula fitting model (i.e. experimental fitting model). Besides, we calculated the resistivity versus the hydrate saturation curves based on digital rock models with idealized hydrate distributions. These distributions included adhesive type, cemented type and scattered type. Observation of microscopic distribution and simulation results indicated that the resistivity versus hydrate saturation exhibited certain differences for the three types of hydrate distributions. We also found that saturation exponent (n) is a function of the hydrate saturation (Sh), which can be applied in the proposed new calculation model in order to calculate the resistivity versus hydrate saturation data. This suggests that the established model is a useful methodology for the purpose of saturation calculations and reservoir identification in hydrate-bearing sediments.

Dong, X., Zhang, Y., Milton, J., Yerabolu, R., Easterling, L., Kenttämaa, H.I., 2019. Investigation of the relative abundances of single-core and multicore compounds in asphaltenes by using high-resolution

in-source collision-activated dissociation and medium-energy collision-activated dissociation mass spectrometry with statistical considerations. Fuel 246, 126-132.


Asphaltenes cause multiple problems in the petroleum industry, such as clogging crude oil transportation pipelines and fouling catalysts. Characterization of the structures of the compounds in asphaltenes is essential for addressing these problems. Two main categories of asphaltene molecular structures, single-core (island) and multicore (archipelago), have been agreed upon. However, their relative abundances in asphaltenes have been debated for decades. This may be partially due to the fact that many mass spectrometry studies carried out in both academia and industry make conclusions for the entire asphaltene sample based on information derived from a group of ionized asphaltenes with m/z values ranging from one up to ten. This approach makes the unvalidated assumption that the relative abundances of single- and multicore compounds are uniform within the entire sample. In this study, medium-energy collision-activated dissociation (MCAD) in a linear quadrupole ion trap/orbitrap high-resolution mass spectrometer was employed to explore the structures of asphaltene molecular ions with m/z values in the ranges of 350 ± 10, 450 ± 10, 550 ± 10 and 650 ± 10. The ions studied displayed different extents of decrease in their weighted average ring and double bond equivalence (RDBE) values when undergoing dissociation, suggesting that the abundances of single-core and multicore compounds are not uniform within the entire asphaltene samples. Therefore, traditional mass spectrometry approaches used to determine the relative abundances of single- and multicore asphaltene compounds may suffer from a sampling bias. However, in-source collision-activated dissociation (IS-CAD) is not susceptible to sampling bias because no ion selection is involved.

Drouin, N., Kubáň, P., Rudaz, S., Pedersen-Bjergaard, S., Schappler, J., 2019. Electromembrane extraction: Overview of the last decade. TrAC Trends in Analytical Chemistry 113, 357-363.


Sample preparation is a crucial step in any bioanalytical workflow. Nowadays, microextractions are very popular because of the reduction of the organic solvent and sample volumes, the analysis time, and the operating costs. Electromembrane extraction (EME) is one of the most recently reported liquid phase microextraction (LPME) techniques and was first described in 2006. It is based on the application of an electric field between two aqueous compartments separated by a layer of water-immiscible organic solvent, reducing the time needed for the extraction process to a few minutes, enabling extraction selectivity towards a broad range of molecule polarity (−5 < Log P < 5), recoveries up to 100%, and enrichment up to 100-fold. In this paper, EME literature was reviewed with special emphasis on recent mass transfer theory, and how this theory affects method development and the different technical configurations.

Druetta, P., Picchioni, F., 2019. Polymer and nanoparticles flooding as a new method for Enhanced Oil Recovery. Journal of Petroleum Science and Engineering 177, 479-495.


A new Enhanced Oil Recovery (EOR) method is proposed by combining the effects of a traditional polymer flooding and exploiting the advantages that nanotechnology presents in the oil industry. Thus, a novel technique is introduced and applied to a 2D reservoir model with a two-phase, five-component system (aqueous, oil phases and water, hydrocarbon, polymer, nanoparticles and salt). For

the polymer characterization, a novel approach is presented considering the polymer's architecture and its degradation in order to calculate the physical properties, which has never been reported in reservoir simulation. The presence of the nanoparticles affects mainly the rheological behavior and the wettability of the rock, increasing the oil phase mobility. Moreover, negative effects such as particle aggregation and sedimentation are also modeled using a novel formulation in reservoir simulation. The combined action of polymers and nanoparticles allowed increasing the recovery factors beyond standard EOR processes, and it represents a suitable alternative to replace traditional combined methods, such as Surfactant-Polymer (SP) or Alkaline-Surfactant-Polymer (ASP). This is due to the fact that the nanoparticles act, to a greater or lesser extent, on the wettability, rheological and interfacial properties of fluids and rock formation, which is complemented with the polymer's viscosifying properties. Moreover, economical factors could also render this technique more attractive, since the nanoparticles' associated costs are substantially lower than those from surfactant flooding. This simulation proves the potential of nanotechnology as a mean to boost traditional EOR techniques in order to further increase the operative life of mature oil fields.

Duman, A., Bozcu, A., 2019. Source rock potential of the Sayındere formation in the Şambayat oil field, SE Turkey. Petroleum Science and Technology 37, 171-180.

https://doi.org/10.1080/10916466.2018.1533856

Upper Campanian–Maastrichtian Sayındere Formation, located in southeastern Turkey, composed of pelagic limestone which was deposited relatively deep marine. In this study, well samples of the Sayındere Formation were analyzed by Rock-Eval pyrolysis and the oil sample from this unit were analyzed by GC, and GC-MS to assess source rock characteristics and hydrocarbon potential. The TOC values of the Sayındere Formation samples range from 0.34 to 4.65 wt.% with an average of 1.14 wt.% and organic matter have good TOC value. Hydrogen Index (HI) values range from 407 mg HC/g TOC to 603 mg HC/g TOC and indicates Type II kerogen. Tmax values are in the range of 434 - 442 °C and indicate early-mid mature stage. The Sayındere samples have fair to good hydrocarbon potential based on TOC contents, S2, and PY values. According to the HI versus TOC plot, most of the samples have good oil source. The oil sample contains predominant short-chain n-alkanes and plots in marine algal Type II field on a Pr/n-C17 versus Ph/n-C18 cross-plot indicating anoxic environment. Biomarker analysis shows that the deposition of oil source rock is carbonate-rich sediments.

Dutta, S.B., Shrivastava, R., Krishna, H., Khan, K.M., Gupta, S., Majumder, S.K., 2019. Nanotrap-enhanced Raman spectroscopy: An efficient technique for trace detection of bioanalytes. Analytical Chemistry 91, 3555–3560.


Reliable diagnosis of disease using body fluids requires sensitive and accurate detection of disease-specific analytes present in the fluid. In recent years, there has been increasing interest in using surface-enhanced Raman spectroscopy (SERS) for this purpose. The demonstrable signal enhancement and sensitivity of SERS makes it ideally suited for detection of a trace quantity of any analyte. However, lack of reproducibility along with large spatial variability in the measured Raman intensities due to differential (and often random) distribution of surface “hot spots” limits its routine clinical use. We propose here a technique, nanotrap-enhanced Raman spectroscopy (NTERS), for overcoming these long-standing limitations and challenges of SERS. In this technique, hot spots are formed by drying up a microvolume drop of the liquid, containing the mixture of nanoparticles and analytes in the focal volume of the Raman excitation laser, and the Raman signal is detected from

these spots containing the analytes localized within the nanoparticle aggregates. The performance of the technique was evaluated in detecting trace quantities of two Raman-active analytes, Rhodamine 6G (R6G) and urea. It was found that R6G and urea could be detected down to a concentration of 50 nM with signal-to-noise ratio (SNR) value of ∼75 and 4 mM with SNR value of ∼500, respectively. A comparison with SERS revealed that NTERS not only had significantly superior (around 2 orders of magnitude) signal enhancement but also had high reproducibility because of its intrinsic ability to form nanoparticle aggregates with high repetitiveness. Another advantage of NTERS is its simplicity and cost effectiveness as it does not require any specialized substrate.

Dwivedi, K.K., Chatterjee, P.K., Karmakar, M.K., Pramanick, A.K., 2019. Pyrolysis characteristics and kinetics of Indian low rank coal using thermogravimetric analysis. International Journal of Coal Science & Technology 6, 102-112.

https://doi.org/10.1007/s40789-019-0236-7

The present research work deals with the thermogravimetric analysis (TGA) and kinetic analysis of three typical Indian low rank coals selected from Indian coal mines at various temperature ranges. Experiments were performed at four different heating rate (50, 100, 150, 200 K/min) for three typical Indian low rank coal samples in a nitrogen atmosphere from temperature range 30–950 °C. The peak of temperature and mass loss for Indian low rank coal were evaluated. Current study also deals for the utilization and the behaviour of Indian low rank coal during the pyrolysis by using TGA. The activation energy for Indian low rank coal were calculated based on TGA data by using Friedman Method. Corresponding calculated mean value of activation energy for Indian low rank coal is found 49.132 kJ/mol. These experimental results help to explain and predict the behaviour of Indian low rank coal in practical applications.



Significance: The 2.1 billion-year-old sedimentary strata contain exquisitely preserved fossils that provide an ecologic snapshot of the biota inhabiting an oxygenated shallow-marine environment. Most striking are the pyritized string-shaped structures, which suggest that the producer have been a multicellular or syncytial organism able to migrate laterally and vertically to reach for food resources. A modern analogue is the aggregation of amoeboid cells into a migratory slug phase in modern cellular slime molds during time of food starvation. While it remains uncertain whether the amoeboidlike organisms represent a failed experiment or a prelude to subsequent evolutionary innovations, they add to the growing record of comparatively complex life forms that existed more than a billion years before animals emerged in the late Neoproterozoic.

Abstract: Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232–235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023–1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351–381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from the

Francevillian Basin. Combined microscopic, microtomographic, geochemical, and sedimentologic analyses provide evidence for biogenicity, and syngenicity and suggest that the structures underwent fossilization during early diagenesis close to the sediment–water interface. The string-shaped structures are up to 6 mm across and extend up to 170 mm through the strata. Morphological and 3D tomographic reconstructions suggest that the producer may have been a multicellular or syncytial organism able to migrate laterally and vertically to reach food resources. A possible modern analog is the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds at times of starvation. This unique ecologic window established in an oxygenated, shallow-marine environment represents an exceptional record of the biosphere following the crucial changes that occurred in the atmosphere and ocean in the aftermath of the great oxidation event (GOE).

Ellis, G.S., Zhang, T., Kralert, P.G., Tang, Y., 2019. Kinetics of elemental sulfur reduction by petroleum hydrocarbons and the implications for hydrocarbon thermal chemical alteration. Geochimica et Cosmochimica Acta 251, 192-216.


Although sulfur-containing compounds are known to play a significant role in the diagenic and catagenic processes that generate oil and gas, relatively little is known about the kinetics of reactions between elemental S and petroleum hydrocarbons. To investigate this subject, a series of closed-system pyrolysis experiments using paraffin, a low-sulfur oil, and a high-sulfur oil with and without elemental S were conducted, and first-order chemical kinetics were fit to the experimental results. The average value for the activation energy required to reduce elemental S to H2S and to thermochemically alter higher molecular weight hydrocarbons to methane was calculated to be 193 kJ mol−1 (46 kcal mol−1). The results of this study demonstrate that under typical geologic conditions the rate of reduction of elemental S to H2S by petroleum hydrocarbons is quite rapid. The maximum time for substantial amounts of elemental S to persist in contact with petroleum hydrocarbons is estimated to be no more than a few million years in cool reservoirs (e.g., <80 °C), and in hotter reservoirs (e.g., >120 °C) the half-life of elemental S may be as short as hundreds of years. Additionally, the presence of elemental S substantially lowers the onset temperature of hydrocarbon thermal chemical alteration (TCA). The activation energy for TCA of a low-sulfur oil to generate methane is estimated to be lowered by 92 kJ mol−1 (22 kcal mol−1) due to the presence of elemental sulfur. Consequently, the presence of elemental S in petroleum reservoirs is expected to lower the thermal stability of oil and decrease the maximum depth at which oil occurs within a basin (thermal deadline). The observed acceleration of hydrocarbon TCA is possibly due to organic sulfur compounds (e.g., thiols and sulfides) that form through the reaction of H2S or polysulfides with hydrocarbons and subsequently thermally degrade leading to the formation of sulfur radicals that in turn enhance TCA reactions.

Eshel, T., Erel, Y., Yahalom-Mack, N., Tirosh, O., Gilboa, A., 2019. Lead isotopes in silver reveal earliest Phoenician quest for metals in the west Mediterranean. Proceedings of the National Academy of Sciences 116, 6007-6012.


Significance: We offer here an answer to one of the most intriguing questions in ancient Mediterranean history: the timing/contexts and incentives of early Phoenician expansion to Mediterranean and Atlantic regions in Africa and Europe ∼3,000 years ago. This was enabled by a rare opportunity to analyze a very large sample set of ancient silver items from Phoenicia. An interdisciplinary collaboration combining scientific methods with precise archaeological data

revealed the Phoenicians’ silver sources. We propose that Phoenicians brought silver to the Levant from southwest Sardinia ∼200 years before they de facto settled there, and later, gradually, also from Iberia. We show that the quest for sliver was a major trigger for a long “precolonization” phase, during the 10th to 9th centuries BCE.

Abstract: When and why did the Phoenicians initiate long-term connections between the Levant and western Europe? This is one of the most hotly debated questions in ancient Mediterranean history and cultural research. In this study, we use silver to answer this question, presenting the largest dataset of chemical and isotopic analyses of silver items from silver hoards found in Phoenician homeland sites. Intertwining lead isotope analysis of silver items with precise archaeological context and chronology, we provide analytical evidence for the onset of Phoenician westward expansion. We suggest that the quest for silver instigated a long, exploratory phase, first in Anatolia (Asia Minor) and Sardinia, and subsequently in the Iberian Peninsula. This phase preceded the establishment of sustainable, flourishing Phoenician colonies in the West by over a century. In so doing, our results buttress the “precolonization” theory, accord it a firm chronological framework, and demonstrate that the quest for silver (and probably other metals) was an incentive for Phoenician westward expansion. Furthermore, our results show that the Phoenicians introduced innovative silver production methods to historic Europe.

Etemadifar, Z., Etemadzadeh, S.S., Emtiazi, G., 2019. A novel approach for bioleaching of sulfur, iron, and silica impurities from coal by growing and resting cells of Rhodococcus spp. Geomicrobiology Journal 36, 123-129.

https://doi.org/10.1080/01490451.2018.1514441

Coal is one of the most important sources of fossil energy on earth. However, direct combustion of coal with a high sulfur content can cause various environmental problems. Other constituents of coal that can cause environmental problems include iron oxide (hematite), iron hydroxide, and silica. In this study, growing and resting cells of Rhodococcus erythropolis strains PD1, R1, and FMF, and R. qingshengii were used in heterotrophic removal of sulfur and bioleaching of iron and silica from coal. All of the mentioned strains have an ability of dibenzothiophene (DBT) desulfurization via 4-S pathway. 2-hydroxybiphenyl, sulfate, and ferric ions (Fe3+) were assayed by Gibb’s test, barium chloride (BaCl2), and thiocyanate ions (SCN−), respectively. FTIR and XRF analyzer were used for detection of the coal bioleaching process by the selected strain of R. erythropolis (PD1). Results indicated that all strains have the ability to grow on coal as the sulfur source. Among them, strain PD1 produced the highest optical density and continued to grow even after 150-h incubation. In both growing- and resting-cells experiments, strain PD1 desulfurized coal most readily compared to other strains. Results of XRF showed that growing cells of strain PD1 had high desulfurizing ability of coal (46%) compared to resting cells in the absence of any carbon sources (24%). Growing cells of strain PD1 also leached 46% of the iron and 14% of the silicate after 7 days of incubation. Resting cells of PD1 leached 32% of the iron as determined by XRF analysis. Also, growing cells of PD1 removed most SiO2 from coal as detected and confirmed by FTIR and XRF. To the best of our knowledge, this is the first report on bioleaching of iron and silica from coal by R. erythropolis strain PD1, making it a suitable candidate for coal bioremediation.

Etiope, G., Oehler, D.Z., 2019. Methane spikes, background seasonality and non-detections on Mars: A geological perspective. Planetary and Space Science 168, 52-61.


The story of methane (CH4) on Mars continues to grow. A long series of CH4 detections (spikes, plumes, seasonal variations) and non-detections in the martian atmosphere suggest that CH4 is occasionally released from subsurface rocks, but also that an unknown process of rapid CH4 removal in the atmosphere must exist. The variability of the observations can be interpreted integrating concepts of subsurface geological gas source variability (CH4 seepage flux patterns), atmospheric chemistry (CH4 removal processes), and atmospheric circulation (CH4 transport and dilution). While the last two are widely studied, potential gas seepage patterns on Mars have never been discussed. In this work, we use the factors controlling gas seepage flux patterns observed on Earth to address key questions about the significance of the martian detections and non-detections. As on Earth, CH4 seepage on Mars must occur mainly through advection (non-diffusion) mechanisms, driven by pressure gradients and permeability, typically related to faults and fracture networks, which control release patterns, in terms of intensity, duration and variability. CH4 release may occur, therefore, whenever gas pressure and/or rock permeability increase (e.g., via destabilization of storage bodies such as clathrates or zeolites; breaching of seals such as permafrost; planetary stresses, impacts, or gas pressure build-up along faults). Rapid atmospheric pressure changes, due to storms and winds, may also play a role. All these forcings can lead to local, episodic, irregular or seasonal gas releases, which may explain the observations acquired so far if relatively rapid (month or day time-scales) mechanisms of CH4 removal exist in the lower atmosphere or near-surface. The release patterns cannot reveal whether CH4 is biologic or abiotic. If CH4 sensors operate discontinuously and only in one site or over limited regions, then, non-detections will be the rule and detections will be relatively rare. The chances of CH4 detection may increase if the observations are focused and repeated on specific, potential areas of gas release determined by geological analysis.

Evans, P.N., Boyd, J.A., Leu, A.O., Woodcroft, B.J., Parks, D.H., Hugenholtz, P., Tyson, G.W., 2019. An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology 17, 219-232.

https://doi.org/10.1038/s41579-018-0136-7

Methane is a key compound in the global carbon cycle that influences both nutrient cycling and the Earth’s climate. A limited number of microorganisms control the flux of biologically generated methane, including methane-metabolizing archaea that either produce or consume methane. Methanogenic and methanotrophic archaea belonging to the phylum Euryarchaeota share a genetically similar, interrelated pathway for methane metabolism. The key enzyme in this pathway, the methyl-coenzyme M reductase (Mcr) complex, catalyses the last step in methanogenesis and the first step in methanotrophy. The discovery of mcr and divergent mcr-like genes in new euryarchaeotal lineages and novel archaeal phyla challenges long-held views of the evolutionary origin of this metabolism within the Euryarchaeota. Divergent mcr-like genes have recently been shown to oxidize short-chain alkanes, indicating that these complexes have evolved to metabolize substrates other than methane. In this Review, we examine the diversity, metabolism and evolutionary history of mcr-containing archaea in light of these recent discoveries.

Faboya, O.L., Sonibare, O.O., Liao, Z., 2019. Biomarkers and isotopic characteristics of crude oils from a central Niger delta depobelt field, Nigeria. Petroleum Science and Technology 37, 346-353.

https://doi.org/10.1080/10916466.2018.1547753

Twelve crude oils samples from a field in the central depobelt in the Niger delta, Nigeria were analyzed for their biomarkers and isotopic composition by Gas chromatography?Mass spectrometry and Isotope mass spectrometry. The percentage C27, C28 and C29 steranes in the oils ranged from 35.80 to 39.9, 28.1 to 30.8 and 29.9 to 35.0, respectively. The distribution of molecular biomarkers and

isotopic composition in the oils indicated that they were formed from source rocks of a mixed source (marine and terrestrial kerogen) but with greater input from marine organic matter. The Pr/Ph ratios of the oil samples ranged from 1.2 to 2.3 and this indicated organic matter deposited under suboxic conditions. The vitrinite reflectance (%VRc) values calculated from methylphenanthrene index-1 (MPI-1) parameter ranged from 0.89 to 1.07 indicating oils generated at the peak of oil window.

Faggetter, L.E., Wignall, P.B., Pruss, S.B., Jones, D.S., Grasby, S., Widdowson, M., Newton, R.J., 2019. Mercury chemostratigraphy across the Cambrian Series 2 – Series 3 boundary: evidence for increased volcanic activity coincident with extinction? Chemical Geology 510, 188-199.


Flood basalt volcanism represented by the Kalkarindji Province (Australia) is temporally associated with a trilobite mass extinction at the Cambrian Series 2 – Series 3 boundary, providing one of the oldest potential links between volcanism and biotic crisis in the Phanerozoic. However, the relative timing of flood basalt volcanism (Kalkarindji Province, Australia) and the trilobite extinctions, first recorded in North America, is not known. Mercury (Hg) enrichment in the sedimentary record provides a potential proxy for volcanism which may facilitate improved chronologies of eruption and extinction. Here we report mercury records for three sections from mid-shelf strata of the Great Basin (western USA) that straddle the Series 2 – Series 3 boundary. One section (Oak Springs Summit, NV) features a Hg enrichment at the start of the extinction interval, but mercury anomalies are also present at lower levels. These older anomalies may record either earlier phases of Kalkarindji volcanism, eruptions in other locations, or may be the result of sedimentary and/or diagenetic processes affecting the Hg record. In the Carrara Formation at Emigrant Pass, CA, the precise extinction horizon is not well defined, but a carbon isotope anomaly (the Redlichiid-Olenellid Extinction Carbon isotope Event; ROECE) provides a stratigraphic tie point to the Oak Springs Summit section. At Emigrant Pass, Hg enrichments precede the ROECE interval and are absent in the inferred extinction zone. The Pioche Formation at Ruin Wash, NV, lacks Hg enrichment at the extinction horizon but contains older enrichments. The inconsistent Hg records between the three sections demonstrate that factors controlling Hg accumulation and preservation in marine sedimentary environments are not yet fully understood. The effects of redox fluctuations may complicate one-to-one association of sedimentary Hg enrichments and massive volcanism at the Cambrian Series 2 – Series 3 boundary and elsewhere in the geologic record.

Fan, S., Kind, T., Cajka, T., Hazen, S.L., Tang, W.H.W., Kaddurah-Daouk, R., Irvin, M.R., Arnett, D.K., Barupal, D.K., Fiehn, O., 2019. Systematic error removal using random forest for normalizing large-scale untargeted lipidomics data. Analytical Chemistry 91, 3590–3596.


Large-scale untargeted lipidomics experiments involve the measurement of hundreds to thousands of samples. Such data sets are usually acquired on one instrument over days or weeks of analysis time. Such extensive data acquisition processes introduce a variety of systematic errors, including batch differences, longitudinal drifts, or even instrument-to-instrument variation. Technical data variance can obscure the true biological signal and hinder biological discoveries. To combat this issue, we present a novel normalization approach based on using quality control pool samples (QC). This method is called systematic error removal using random forest (SERRF) for eliminating the unwanted systematic variations in large sample sets. We compared SERRF with 15 other commonly used normalization methods using six lipidomics data sets from three large cohort studies (832, 1162, and 2696 samples). SERRF reduced the average technical errors for these data sets to 5% relative

standard deviation. We conclude that SERRF outperforms other existing methods and can significantly reduce the unwanted systematic variation, revealing biological variance of interest.

Farooq, U., Nourani, M., Ivol, F., Årrestad, A.B., Øye, G., 2019. Adsorption of crude oil components on mineral surfaces followed by quartz crystal microbalance and contact angle measurements: The effect of oil composition, simulated weathering and dispersants. Energy & Fuels 33, 2359-2365.


Improved knowledge of interactions between crude oil and solid surfaces is of great importance for understanding oil spill responses as well as oil spill behavior on land and in the near-shore environment. Here, the goal was to study how crude oils with various physicochemical properties interacted with model shoreline surfaces. In addition, the influence of simulated weathering and addition of dispersants was investigated for selected crude oils. A quartz crystal microbalance was used to follow the adsorption from 13 different crude oils on silica, aluminosilicate, and calcium carbonate surfaces, whereas the corresponding wettability alterations were followed by contact angle measurements. The polar crude oil components adsorbed in considerably higher amounts on the calcium carbonate surfaces than on the silica and aluminosilicate surfaces. The simulated weathering of oils resulted in increased adsorption onto both the silica and aluminosilicate surfaces, whereas it had a little effect on the calcium carbonate surface. The presence of dispersants generally reduced the amounts adsorbed on the surfaces. In the presence of seawater, the crude oil with a higher total acid number interacted strongest with the calcium carbonate surface.



N-nitrosodimethylamine (NDMA) is a disinfection byproduct that has been classified as probable human carcinogen by the US Environmental Protection Agency. According to the published literature, natural dissolved organic matter (DOM) can be a source of NDMA precursors in drinking water. New advances in chemical characterization of DOM with high resolution mass spectrometry (HRMS) are allowing researchers to understand these ultra-complex mixtures.

The objective of this study is to investigate analytical methodologies based on HRMS to explore NDMA formation from natural waters. To this aim, different waters from drinking water reservoirs in Spain containing NDMA precursors (quantified by means of NDMA formation potential) in concentrations between 17 and 60 ng/L have been studied. The workflow includes DOM solid-phase extraction and Orbitrap analysis with and without chromatographic separation.

Here, we show that the molecular composition of DOM across the studied drinking water reservoirs is correlated with the NDMA formation potential. In particular, we found that NDMA formation potential is associated with compounds with high hydrogen saturation (H/C ≥ 1.5), corresponding also to reservoirs with higher background nutrient concentrations and wastewater indicators. Further chromatographic fractionation did not allow better definition of these possible precursors as they were present in different fractions of the chromatogram, suggesting that they were isomerically complex.

Fay, J.C., Liu, P., Ong, G.T., Dunham, M.J., Cromie, G.A., Jeffery, E.W., Ludlow, C.L., Dudley, A.M., 2019. A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. PLOS Biology 17, Article e3000147.

https://doi.org/10.1371/journal.pbio.3000147

Abstract: Strains of Saccharomyces cerevisiae used to make beer, bread, and wine are genetically and phenotypically distinct from wild populations associated with trees. The origins of these domesticated populations are not always clear; human-associated migration and admixture with wild populations have had a strong impact on S. cerevisiae population structure. We examined the population genetic history of beer strains and found that ale strains and the S. cerevisiae portion of allotetraploid lager strains were derived from admixture between populations closely related to European grape wine strains and Asian rice wine strains. Similar to both lager and baking strains, ale strains are polyploid, providing them with a passive means of remaining isolated from other populations and providing us with a living relic of their ancestral hybridization. To reconstruct their polyploid origin, we phased the genomes of two ale strains and found ale haplotypes to both be recombinants between European and Asian alleles and to also contain novel alleles derived from extinct or as yet uncharacterized populations. We conclude that modern beer strains are the product of a historical melting pot of fermentation technology.

Author summary: The budding yeast Saccharomyces cerevisiae has long been used to make beer. Yeast strains used to make ales are known to differ genetically and phenotypically from strains used to make wine and from strains isolated from nature, such as oak isolates. Beer strains are also known to be polyploid, having more than two copies of their genome per cell. To determine the ancestry of beer strains, we compared the genomes of beer strains with the genomes of a large collection of strains isolated from diverse sources and geographic locations. We found ale, baking, and the S. cerevisiae portion of lager strains to have ancestry that is a mixture of European grape wine strains and Asian rice wine strains and that they carry novel alleles from an extinct or uncharacterized population. The mixed ancestry of beer strains has been maintained in a polyploid state, which provided a means of strain diversification through gain or loss of genetic variation within a strain but also a means of maintaining brewing characteristics by reducing or eliminating genetic exchange with other strains. Our results show that ale strains emerged from a mixture of previously used fermentation technology.

Feldman, M., Fernández-Domínguez, E., Reynolds, L., Baird, D., Pearson, J., Hershkovitz, I., May, H., Goring-Morris, N., Benz, M., Gresky, J., Bianco, R.A., Fairbairn, A., Mustafaoğlu, G., Stockhammer, P.W., Posth, C., Haak, W., Jeong, C., Krause, J., 2019. Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia. Nature Communications 10, Article 1218.

https://doi.org/10.1038/s41467-019-09209-7

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

Feng, J., Liu, M., Zhao, J., Hu, P., Zhang, F., Sun, J.-H., 2019. Historical trends and spatial distributions of polycyclic aromatic hydrocarbons in the upper reach of the Huai River, China: Evidence from the sedimentary record. Applied Geochemistry 103, 59-67.


The historical trends and spatial distributions of 15 polycyclic aromatic hydrocarbons (PAHs) in sediments from the upper reach of the Huai River were investigated. The concentrations of total PAHs (ΣPAHs) in the surface sediments varied from 3.96 to 379 ng/g (average: 65.3 ng/g). PAHs in the surface sediments of the studied area were at a low level compared with some other rivers around the world. The component characteristics showed that four-ring PAHs were predominant. The principal component analysis-multiple linear regression (PCA/MLR) showed that PAHs in the surface sediments primarily originated from coal combustion and vehicular emissions, which accounted for 62.7% and 37.3% of ΣPAHs, respectively. The concentration of ΣPAHs in the sediment core ranged from 2.31 to 21.9 ng/g with deposition flux ranging from 1.91 to 33.3 ng/cm2/year. The historical pattern of PAHs correlated with the Chinese socioeconomic conditions during 1912–2014, confirming that PAHs are a sensitive tracer for anthropogenic activity. Since the 1980s, there was a sharp increase in PAHs concentrations in the studied core. PCA/MLR showed that PAHs in the sediment core were mainly from the burning of fossil fuels. The concentration of PAHs in the surface sediment and sediment core was affected by the content of total organic carbon and black carbon. The result revealed in this study could serve as a reference for the development of relevant remedial strategies for the management of the Huai River.

Feng, S., Cui, C., Li, K., Zhang, L., Shi, Q., Zhao, S., Xu, C., 2019. Molecular composition modelling of petroleum fractions based on a hybrid structural unit and bond-electron matrix (SU-BEM) framework. Chemical Engineering Science 201, 145-156.


In this paper, we developed a method to represent petroleum molecules and reconstruct the molecular composition of petroleum fractions. A hybrid framework combining structural units and a bond-electron matrix (SU-BEM) was proposed to represent petroleum molecules in a convenient way and retain all the detailed atomic information. The structural units and bond-electron matrix represent the basic structural components and the atom connectivity of petroleum molecules, respectively. The group contribution method was implemented in the framework to predict the physical and chemical properties of petroleum molecules based on their chemical structures. Good agreement was observed for the property calculations of pure low-carbon number components. A flexible probability density function (PDF) sequence module was developed and used in the sampling procedure to obtain the molecular quantities used in the compositional models. The PDF parameters, as well as molecular compositions, were optimized by minimizing the differences between predicted and experimental properties. The method was validated for applications involving diesel, vacuum gas oil, and fluid catalytic cracking slurry oil.

Feng, S., He, J., Tian, J., Lu, X., Yang, B., 2019. The characteristic and evolution of coal-forming swamp in Hanshuiquan district, Santanghu Coalfield, Xinjiang, NW China, during the Middle Jurassic: evidence from coal petrography, coal facies and sporopollen. International Journal of Coal Science & Technology 6, 1-14.

https://doi.org/10.1007/s40789-018-0230-5

Santanghu Coalfield is the largest integrated coalfield exploration area in China. The major coal seams developing in Xishanyao Formation (Middle Jurassic) are the high-quality steam coals characterized by large thickness, favorable horizontal continuity and high coal quality. In this paper, twenty-two samples were collected from the three typical boreholes in Hanshuiquan district, representing the 11 coal seam sequences (7#, 8#, 9#, 13#, 14#, 15#, 17#, 18#, 19#, 20#, 22#), respectively. The petrographic characteristics of the coal-bearing sequence in Xishanyao Formation were firstly summarized systematicly, and then the coal-forming swamp characteristics and succession mechanism of the coal seam in Xishanyao Formation were defined by analyzing the samples. The maceral composition, structure, geochemical and geophysical characteristics of coal are included in original genetic criteria of coal-forming swamp analysis. And the composition of coal petrography, maceral and microlithotype are the most frequently used parameters. Coal is composed of microscopic constituents and inorganic substances. The Xishanyao Formation maceral mainly consists of vitrinite (65.74%–97.01%), inertinite (1.93%–34%), and the exinite shows the mode of regular change. The coal-forming swamp in Xishanyao Formation possesses the characteristics of mainly marsh, wet forest swamp facies, and shallow water covered forest swamp facies, and a few of coal seams distribute in the deep water covered forest swamp facies. In addition, the sporopollens in Xishanyao Formation are mainly Pinaceae evergreen broad leaf and needle-leaved plants, Osmundaceae, Cyatheaceae and Lygodiaceae, indicating that the warm and humid tropic-subtropical climate conductive to the persistent growth of coal-forming plants in the Middle Jurassic. The coal-forming swamp shows the characteristics of vertically upward fluctuation through the periodic transition. It indicates a shallow-deep-shallow change process of the water covered depth in the swamp. This is the principal factor for the formation of the high-quality and continuous coal seam in Hanshuiquan district, Santanghu Coalfield.

Feng, X., Chen, Z.-Q., Benton, M.J., Wu, S., Bottjer, D.J., Thompson, J.R., 2019. A diverse trackway-dominated marine ichnoassemblage from the Lower Triassic in the northern Paleotethys: Ichnology and implications for biotic recovery. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 124-140.


We document a diverse ichnoassemblage from marine interbeds of the Lower Triassic terrestrial succession in the Houzhougongmiao (HZGM) section of Shaanxi Province, northwestern China. Integrated biostratigraphic data (bivalve, palynology and conchostracan) reveals that the ichnofossil-bearing marine beds are Griesbachian (Induan, Early Triassic) in age. The marine interbeds are interpreted to be the result of the earliest Triassic transgression of the Paleotethys Ocean northward onto the southern margin of the North China Craton. The HZGM ichnoassemblage includes 17 ichnospecies in 16 ichnogenera and is dominated by shallow-tier Asteriacites and Biformites produced by ophiuroids, the scratch marks or trackways Dimorphichnus, Diplichnites, and Monomorphichnus produced by arthropods, and a rare occurrence of the fish swimming trace Undichna. Of these, the hook-shaped imprints Biformites, representing the moving arm impressions of ophiuroids, are reported for the first time from the Lower Triassic. These trace-makers are interpreted to have lived in a low energy, semi-restricted, shallow embayment environment. Although possessing relatively high ichnodiversity, the HZGM ichnoassemblage differs clearly from other coeval diverse ichnocoenoses in the lack of complex burrow forms (i.e. Thalassinoides, Diplocraterion, or Rhizocorallium) and a mixed layer, and in having abundant shallow tiers. In addition, high ichnodiversity may occur at both high and low latitudes during the Griesbachian (or Induan). Accordingly, the resting trace or trackway-dominated ichnoassemblage from the HZGM section may represent the initial recovery of the trace-maker ecosystem after the Permian-Triassic mass extinction. Trace-makers such as arthropods and ophiuroids were perhaps opportunistic

organisms that proliferated in marginal marine settings when other biota were still suffering post-extinction biotic depletion and environmental stresses.

Feng, X., Chen, Z.-Q., Bottjer, D.J., Wu, S., Zhao, L., Xu, Y., Shi, G.R., Huang, Y., Fang, Y., Tu, C., 2019. Unusual shallow marine matground-adapted benthic biofacies from the Lower Triassic of the northern Paleotethys: Implications for biotic recovery following the end-Permian mass extinction. Earth-Science Reviews 189, 194-219.


We report two shallow marine, ichnofauna-bivalve-microbial mat biofacies from the Lower Triassic Xiahuancang Formation of the southern Qilian area, Qinghai Province, northwestern China, which was located at moderate-high paleolatitudes on the northern margin of the Paleotethys Ocean. Paleoenvironmental analyses show that Members I and II of the Xiahuancang Formation represent a shoreface and a lower shoreface to offshore transition setting, respectively. Biofacies 1, recognized from Member I, is characterized by a diverse ichnofauna (including deep-tiers of Rosselia and Diplocraterion), Claraia-dominated bivalves, and microbially induced sedimentary structures (MISSs). Biofacies 2, in succeeding Member II, is dominated by a diverse ichnofauna, epifaunal and shallow infaunal bivalves, and wrinkle structures. Primary co-occurrences, preservational features, and palimpsest or crosscutting relationships of all components within the biofacies indicate that microbial mats, bivalves, and trace-makers actively interacted with one another during deposition. They largely represent contemporaneous biotic associations. Microbial mats are interpreted to have grown under well-oxygenated conditions after storm deposition due to the association of deep-tiering infauna and diverse epifauna as well as well-developed cross-stratification, and the top layer of microbial mats could serve as an oasis for metazoans. Microbial mats not only proliferated in harsh environments, but also coexist with epifauna and deep-tiering infauna in well-oxygenated settings following the end-Permian crisis. Their occurrences in the Early Triassic are unrelated to environmental stresses, which are coincident with their sedimentologic record from other geological time intervals. Apparently, the southern Qilian ichnofauna-bivalve-microbial mat biofacies with juxtaposed epifauna, infauna and MISS- or wrinkle-related microbial mats represents a matground-adapted benthic metazoan ecosystem in the earliest Triassic, which provided sufficient oxygen, food, and other hydrodynamic conditions hospitable for metazoans and ecosystems to recover and reached a fairly high level (recovery stage 3) in a tough time when most biotas suffered biotic depletion and environmental stress. The biotic components in unique biofacies may represent a phase shift community in siliciclastic settings during the Early Triassic.

Fennel, K., Alin, S., Barbero, L., Evans, W., Bourgeois, T., Cooley, S., Dunne, J., Feely, R.A., Hernandez-Ayon, J.M., Hu, X., Lohrenz, S., Muller-Karger, F., Najjar, R., Robbins, L., Shadwick, E., Siedlecki, S., Steiner, N., Sutton, A., Turk, D., Vlahos, P., Wang, Z.A., 2019. Carbon cycling in the North American coastal ocean: a synthesis. Biogeosciences 16, 1281-1304.


A quantification of carbon fluxes in the coastal ocean and across its boundaries with the atmosphere, land, and the open ocean is important for assessing the current state and projecting future trends in ocean carbon uptake and coastal ocean acidification, but this is currently a missing component of global carbon budgeting. This synthesis reviews recent progress in characterizing these carbon fluxes for the North American coastal ocean. Several observing networks and high-resolution regional models are now available. Recent efforts have focused primarily on quantifying the net air–sea exchange of carbon dioxide (CO2). Some studies have estimated other key fluxes, such as the

exchange of organic and inorganic carbon between shelves and the open ocean. Available estimates of air–sea CO2 flux, informed by more than a decade of observations, indicate that the North American Exclusive Economic Zone (EEZ) acts as a sink of 160±80 Tg C yr−1, although this flux is not well constrained. The Arctic and sub-Arctic, mid-latitude Atlantic, and mid-latitude Pacific portions of the EEZ account for 104, 62, and −3.7 Tg C yr−1, respectively, while making up 51 %, 25 %, and 24 % of the total area, respectively. Combining the net uptake of 160±80 Tg C yr−1 with an estimated carbon input from land of 106±30 Tg C yr−1 minus an estimated burial of 65±55 Tg C yr−1 and an estimated accumulation of dissolved carbon in EEZ waters of 50±25 Tg C yr−1 implies a carbon export of 151±105 Tg C yr−1 to the open ocean. The increasing concentration of inorganic carbon in coastal and open-ocean waters leads to ocean acidification. As a result, conditions favoring the dissolution of calcium carbonate occur regularly in subsurface coastal waters in the Arctic, which are naturally prone to low pH, and the North Pacific, where upwelling of deep, carbon-rich waters has intensified. Expanded monitoring and extension of existing model capabilities are required to provide more reliable coastal carbon budgets, projections of future states of the coastal ocean, and quantification of anthropogenic carbon contributions.

Fernandes, C., Kankonkar, H., Meena, R.M., Menezes, G., Shenoy, B.D., Khandeparker, R., 2019. Metagenomic analysis of tarball-associated bacteria from Goa, India. Marine Pollution Bulletin 141, 398-403.


The beaches of Goa state in India are frequently polluted with tarballs, specifically during pre-monsoon and monsoon seasons. Tarballs contain hydrocarbons, including polycyclic aromatic hydrocarbons, which pose significant environmental risks. Microbes associated with tarballs reportedly possess capabilities to degrade toxic hydrocarbons present in tarballs. In this study, bacterial diversity associated with tarballs from Vagator and Morjim beaches of north Goa was analysed based on V3–V4 regions of 16S rRNA gene sequenced using Illumina Miseq Platform. The Proteobacterial members were dominant in both Vagator (≥85.5%) and Morjim (≥94.0%) samples. Many of the identified taxa have been previously reported as hydrocarbon degraders (e.g. Halomonas, Marinobacter) or possible human pathogens (e.g. Acinetobacter, Klebsiella, Rhodococcus, Staphylococcus, Vibrio). This is the first study reported on a metagenomic analysis of bacteria associated with tarballs from Goa.

Ferreira, I., Venâncio, C., Lopes, I., Oliveira, M., 2019. Nanoplastics and marine organisms: What has been studied? Environmental Toxicology and Pharmacology 67, 1-7.


Nowadays, there is an increased awareness on the threat that marine litter may pose to the marine environment. This review describes the major concerns related to plastic pollution, namely in terms of toxicity of different types and sizes of nanoplastics (particles smaller than 100 nm) to marine organisms, either producers or consumers. The available data show that nanoplastics may affect negatively organisms from different phyla with reported effects ranging from alterations in reproduction to lethality. Nevertheless, no information regarding marine vertebrates (e.g., fish) was found. Data show a high potential for bioaccumulation/biomagnification along marine food chains, since they can easily be retained inside organisms. The lack of standardized methodology for nanoplastics detection and the poor or inexistent legislation makes nanoplastics an environmental challenge.

Fetter, N., Blichert-Toft, J., Télouk, P., Albarède, F., 2019. Extraction of Pb and Zn from crude oil for high-precision isotopic analysis by MC-ICP-MS. Chemical Geology 511, 112-122.


Radiogenic and stable isotopic tracing of crude oils has not so far been undertaken, largely because of the difficulties of dealing with the low trace element contents of oil samples for high-precision isotopic measurements. Here, we present a novel analytical protocol that allows for precise and accurate determination of radiogenic Pb and stable Zn isotopic compositions on as little as 5 ml of crude oil from a variety of geographically, geologically, and environmentally diverse settings. The 41 Pb and Zn samples measured to validate the new protocol were separated from their respective crude oils by liquid-liquid extraction into an aqueous phase readily handled in a clean laboratory for subsequent purification of Pb and Zn by standard anion-exchange column chromatography. Lead and Zn isotopic compositions on the same 5 ml sample of crude oil were obtained by MC-ICP-MS on 95% of the total extracted Pb and Zn, while elemental concentrations were measured by Q-ICP-MS on 5% aliquots. To the best of our knowledge, the present technique is the first efficient procedure for Pb and Zn isotopic analysis of crude oil, which, owing to the elimination of the organic fraction at the liquid-liquid extraction stage, does not require any specialized equipment, neither for the wet chemistry nor for the mass spectrometry. The high extraction yields of the method and the low detection limits and high sensitivity of, respectively, Q-ICP-MS and MC-ICP-MS permit analysis of very small sample quantities (down to 2 ng and 100 ng, respectively, of Pb and Zn for isotopic analysis, and a few hundred pg for abundance measurements). Reproducibility is on a par with routine state-of-the-art Pb and Zn isotopic measurements of other types of geological materials, while total procedural blanks for both elements are negligible relative to the amounts of Pb and Zn typically separated from crude oil.

Figueirêdo, M.B., Jotic, Z., Deuss, P.J., Venderbosch, R.H., Heeres, H.J., 2019. Hydrotreatment of pyrolytic lignins to aromatics and phenolics using heterogeneous catalysts. Fuel Processing Technology 189, 28-38.


The pyrolysis of lignocellulosic biomass generates a liquid product, known as pyrolysis oil, that can be further processed into biofuels and value-added chemicals. During pyrolysis, cellulose and hemicelulose fractions are converted into a range of water-soluble sugar derivatives, for which several valorisation strategies exist. On the other hand, lignin is broken down into so-called pyrolytic lignin, a water-insoluble complex mixture of aromatic oligomers that requires different upgrading strategies than the sugar rich fraction. Here, we report an experimental study on the valorisation of pyrolytic lignin via catalytic hydrotreatment in the absence of an external solvent. A variety of carbon-supported noble-metal heterogeneous catalysts were tested (Ru/C, Pd/C, Pt/C and Rh/C), as well as conventional hydrotreatment catalysts (sulphided NiMo/Al2O3 and CoMo/Al2O3) to obtain valuable low molecular weight aromatic and phenolic compounds. Overall, depolymerized liquids were obtained with organic yields of up to 63 wt%. Pd/C was shown to be the best catalyst, yielding 59 wt% of monomers based on the organic product (i.e. 33 wt% based on pyrolytic lignin intake). While noble metal catalysts favored higher monomer yields, though with some over-reduction of aromatic rings to saturated hydrocarbons, sulphided catalysts were more efficient in deoxygenation and aromatization reactions, but yielded less monomers. The hydrocracking efficiency was shown to be strongly dependent on the reaction temperature. Based on the experimental data, a global reaction network is proposed. The high monomer yields reveal the potential of catalytic hydrotreatment for the upgrading of pyrolytic lignin into valuable phenolics and aromatics.

Fiskal, A., Deng, L., Michel, A., Eickenbusch, P., Han, X., Lagostina, L., Zhu, R., Sander, M., Schroth, M.H., Bernasconi, S.M., Dubois, N., Lever, M.A., 2019. Effects of eutrophication on sedimentary organic carbon cycling in five temperate lakes. Biogeosciences Discussions 2019, 1-35.


Even though human induced eutrophication has severely impacted temperate lake ecosystems over the last centuries, the effects on total organic carbon (TOC) burial and mineralization are not well understood. We study these effects based on sedimentary records from the last 180 years in five Swiss lakes that differ in trophic state. We compare changes in content of TOC and modeled TOC accumulation rates through time to historical data on algae blooms, water column anoxia, wastewater treatment, artificial lake ventilation, and water column phosphorus (P) concentrations. We furthermore investigate the effects of eutrophication on rates of microbial TOC remineralization and vertical distributions of microbial respiration reactions in sediments. Our results indicate that the history of eutrophication is well reflected in the sedimentary record. Subsurface peaks in sedimentary TOC coincide with past periods of elevated P concentrations in lake water. Sediments of eutrophic lakes show overall higher rates of microbial respiration, and a higher relative contribution of methanogenesis to total respiration. Yet, a clear impact of lake trophic state on the zonation of microbial respiration reactions is absent. Moreover, even though water column P concentrations have been reduced by ~ 80 % (range: ~ 50–90 %) since the period of peak eutrophication in the 1970s, TOC burial and accumulation rates have only decreased significantly (~ 20 and 25 %) in two of the five lakes. Hereby we found no clear relationship between the magnitude of the decrease in P concentrations and the change in TOC burial and accumulation rate. Instead, artificial lake ventilation, which is used to prevent water column anoxia in eutrophic lakes, may help sustain high rates of TOC burial and accumulation in sediments despite strongly reduced water column P concentrations. Our results provide novel insights into how eutrophication and eutrophication management practices affect organic carbon burial and the distribution of microbial respiration reactions in temperate lakes. These insights are important to understanding how anthropogenic activities affect the size of the carbon pool that is stored globally in lacustrine sediments.


https://doi.org/10.1038/s41579-019-0158-9

Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the ‘big five’ habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20–80% of cells in the subsurface exist as biofilms. Hence, overall, 40–80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.

Flores, A., Wang, X., Nielsen, D.R., 2019. Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production. Current Opinion in Biotechnology 57, 82-87.


Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ product separation are poised to help address this intrinsic problem, but suffer their own unique shortcomings. To improve and expand the utility of this versatile bioprocessing strategy, recent innovations have focused on developing more effective separation materials and novel process configurations, as well as adapting designs to accommodate semi-continuous modes of operation. As a result, integrated bioprocesses are finding new applications to aid the biosynthesis of an ever-growing list of bioproducts. Emerging applications, meanwhile, are exploring the further expansion of such designs to interface microbial and chemical catalysts, leading to new and versatile routes for the one-pot synthesis of an even greater diversity of renewable products.

Freedman, R., Rose, D., Sun, B., Brown, R.L., Malizia, T., 2019. Novel method for evaluating shale-gas and shale-tight-oil reservoirs using advanced well-log data. SPE Reservoir Evaluation & Engineering 22, 282-301.

https://doi.org/10.2118/181480-PA

We introduce a novel well-logging method for determining more-accurate total porosities, fluid volumes, and kerogen volumes in shale-gas and shale-tight-oil wells. Improved accuracy is achieved by self-consistently accounting for the effects of light hydrocarbons and kerogen on the log responses. The logging measurements needed to practice this method are bulk densities, nuclear-magnetic-resonance (NMR) total porosities, and total-organic-carbon (TOC) weight fractions. The TOC weight fractions and the matrix densities, which are used to interpret the bulk density measurements, are both derived from geochemical-tool measurements.

Most unconventional shale-gas and shale-tight-oil reservoirs contain some nonproducible immobile hydrocarbons. When immobile hydrocarbons are present, our method requires prior knowledge of in-situ total water volumes. The water volumes can be estimated from dielectric-tool measurements. In special cases (e.g., in some mature shale-gas reservoirs) where no immobile hydrocarbons are present, a dielectric tool is not needed. In such cases total water volumes are outputs of the method.

We discuss the response functions in shale reservoirs for measurements of bulk densities, NMR porosities, and TOC weight fractions and derive exact self-consistent solutions to the response equations. The algebraic solutions are used to compute shale total porosities, fluid volumes, and kerogen volumes. The predicted shale total porosities and fluid volumes are corrected for light-hydrocarbon effects on the measured bulk densities and NMR porosities and for kerogen effects on the bulk densities. It is shown that significant errors can be made in log-derived shale total porosities if NMR porosities or density-log porosities are assumed to represent true-shale porosities without applying proper corrections.

We discuss the application of the method to the analysis of logging data acquired in a mature shale-gas well drilled in the Marcellus Shale in the northeastern United States and to data acquired in a shale-tight-oil well drilled in the Permian Basin in west Texas. A multifrequency dielectric tool is used to determine in-situ total water volumes in the tight oil well. The mature shale-gas reservoir does

not contain immobile hydrocarbons, and, therefore, dielectric-logging measurements were not needed in this well. The results in both wells are shown to compare favorably with core data.

Frezzotti, M.L., Villa, I.M., Iannantuoni, G., 2019. Introduction to the Thematic set: Carbon forms, paths and processes in the Earth. Journal of the Geological Society 176, 335-336.


Carbon forms: paths and processes in the Earth is a thematic set of six papers arising from the lectures presented at the Lake Como School, held at Villa del Grumello, Como, Italy (15–20 October 2017), and organized by the Graduate School of Milano Bicocca. This collection of lecture notes focusses on the structure of carbon allotropes, the geodynamics of deep Earth's carbon transport and fixation at mantle conditions, carbon degassing by ascending magmas, and the vast tectonic carbon degassing at the Earth's surface.

New science is emerging for carbon, one of the fundamental elements for life, energy, and global climate change on our planet. Carbon is cycled between surface, atmosphere, and oceans. Most of the recyclable carbon is stored deep in the Earth. Ingassing from the atmo-hydrosphere into the mantle occurs by subduction; in the mantle carbon resides in solids such as diamonds and is transported by fluids and melts that migrate upward. Outgassing into the atmosphere is effected by volcanism and tectono-metamorphic soil emissions. The forms and processes of carbon ingassing and outgassing are still poorly constrained. There is as yet no consensus on how and when carbon transforms from solid to fluid phases and vice versa, nor even on the processes that regulate carbon fluxes between Earth's reservoirs. These emerging research themes are crucial to gain insights in the past and present evolution of our planet and constitute building blocks to address current challenges of climate change. The six papers of the present thematic set focus on the forms, paths, and processes of Earth's carbon.

Langenhorst & Campione (2018) explore the fundamental physical and chemical properties of ideal and real solid carbon forms as a function of pressure and temperature (P-T), and describe the ideal structural models of fundamental carbon allotropes. They show how the properties of graphene and diamond molecules vary with crystallite size. Imperfections in crystal structures of natural carbon allotropes are interpreted as fingerprints of the geological environment in which they formed.

Sverjensky (2019) provides the quantitative thermodynamic basis needed to carry out theoretical geochemical modeling of fluids and fluid-rock interactions from the surface to upper mantle conditions. He describes the general criteria for predicting equilibrium and non-equilibrium reactions, followed by a summary of how the thermodynamic activities of species are related to measurable concentrations through standard states and activity coefficients. The concept of aqueous speciation, and the way to calculate it, arises from this discussion. His DEW (Deep Earth Water) model includes a revised Helgeson-Kirkham-Flowers equation of state and revised predictive correlations for the estimation of equation of state coefficients. Finally, the DEW model is applied to the solubility and speciation of aqueous aluminium.

The third and fourth papers explore the nature of carbon reservoirs and carbon transport deep in the Earth's interior. Stagno (2019) reports the current state of research on naturally occurring deep carbon phases (e.g. diamond, carbides, carbonates, and carbonatitic melts) at mantle pressure and temperature conditions, carbon mobilization in the asthenospheric mantle by redox partial melting, and its sequestration during subduction by redox freezing processes. Through time, the redox state the Earth's mantle has strongly influenced the speciation of carbon from the mantle to mantle-derived magmas as well as from volcanic emissions. Tumiati & Malaspina (2018) illustrate how carbon can be a redox-controlling factor when it is transferred from the subducting plate to the mantle wedge.

They explore fluid-mediated processes at the slab-mantle interface considering different fluid/rock ratios. Comparing thermodynamic modeling with experimental results, they show how carbon speciation in C-O-H fluids can affect the stability of hydrous and carbonate minerals, and the solidus of peridotites.

Transfer of deep carbon to the Earth's surface constitutes the theme of the fifth and sixth papers. Moore & Bodnar (2019) estimate the amount and distribution of CO2 degassed by magmas, using as an example the Kilauea volcanic system (Hawaii). They calculate first-order estimates regarding: (i) the original concentration of CO2 in magma generated by melting a carbon-bearing source, (ii) the successive enrichment of CO2 in the melt during fractional crystallization, (iii) volatile saturation and exsolution of CO2 from a fluid-saturated melt, and (iv) the outgassing from the volcanic edifice. Frondini et al. (2018) review fluxes to the atmosphere by diffuse degassing of deep carbon from tectonic structures, concentrating on the case of the Italian Apennines. They report on the methods used to measure the regional flux of deep CO2 associated with groundwater circulation and comment on the relationships between the regional CO2 flux and areas of focused and diffuse gas emission from soil. Further, they illustrate the relationships between regional CO2 degassing and advective heat flow. Carbon balance of regional aquifers in the Apennine region shows that diffuse tectono-metamorphic CO2 degassing is the major component of the geological contribution to the atmosphere in Italy, prevailing over the CO2 degassed by active volcanoes.

Frondini, F., Cardellini, C., Caliro, S., Beddini, G., Rosiello, A., Chiodini, G., 2019. Measuring and interpreting CO2 fluxes at regional scale: the case of the Apennines, Italy. Journal of the Geological Society 176, 408-416.


Tectonically active regions are often characterized by large amounts of carbon dioxide degassing, and estimation of the total CO2 discharged to the atmosphere from tectonic structures, hydrothermal systems and inactive volcanic areas is crucial for the definition of present-day global Earth degassing. The carbon balance of regional aquifers is a powerful tool to quantify the diffuse degassing of deep inorganic carbon sources because the method integrates the CO2 flux over large areas. Its application to peninsular Italy shows that the region is characterized by specific CO2 fluxes higher than the baseline determined for the geothermal regions of the world, and that the amount of endogenous CO2 discharged through diffuse regional degassing (c. 2.1 × 1011 mol a−1) is the major component of the geological CO2 budget of Italy, definitely prevailing over the CO2 discharged by Italian active volcanoes and volcanoes with hydrothermal activity. Furthermore, the positive correlation between geothermal heat and deep CO2 dissolved in the groundwater of central Italy suggests that (1) the geothermal heat is transported into the aquifers by the same hot CO2-rich fluids causing the Italian CO2 anomaly and (2) the advective heat flow is the dominant form of heat transfer of the region.Supplementary material: The location, flow rate, extent of the hydrogeological basin, chemical and isotopic analyses of the 160 springs considered in this study, and the results of the carbon mass balance are reported in a table available at https://doi.org/10.6084/m9.figshare.c.4237025

Fru, E.C., Somogyi, A., Medjoubi, K., El Albani, A., Aubineau, J., Konhauser, K.O., Robbins, L.J., Lalonde, S.V., 2019. The rise of oxygen-driven arsenic cycling at ca. 2.48 Ga. Geology 47, 243-246.

https://dx.doi.org/10.1130/G45676.1

The Great Oxidation Event (GOE) at 2.45 Ga facilitated the global expansion of oxidized compounds in seawater. Here, we demonstrate that the GOE coincided with a sharp increase in arsenate and

arsenic sulfides in marine shales. The dramatic rise of these oxygen-sensitive tracers overlaps with the expansion of key arsenic oxidants, including oxygen, nitrate, and Mn(IV) oxides. The increase in arsenic sulfides by at least an order of magnitude after 2.45 Ga is consistent with the proposed transition to mid-depth continental-margin sulfide-rich waters following the GOE. At the same time, the strong increase in arsenate content, to ∼60% of the total arsenic concentration in shales, suggests that the oxidative component of the arsenic cycle was established for the first time in Earth’s history. These data highlight the global emergence of a new selective pressure on the survival of marine microbial communities across the GOE, the widespread appearance of toxic, oxidized chemical species such as arsenate in seawater.

Fu, D., Tong, G., Dai, T., Liu, W., Yang, Y., Zhang, Y., Cui, L., Li, L., Yun, H., Wu, Y., Sun, A., Liu, C., Pei, W., Gaines, R.R., Zhang, X., 2019. The Qingjiang biota—A Burgess Shale–type fossil Lagerstätte from the early Cambrian of South China. Science 363, 1338-1342.

http://science.sciencemag.org/content/363/6433/1338

Abstract: Burgess Shale–type fossil Lagerstätten provide the best evidence for deciphering the biotic patterns and magnitude of the Cambrian explosion. Here, we report a Lagerstätte from South China, the Qingjiang biota (~518 million years old), which is dominated by soft-bodied taxa from a distal shelf setting. The Qingjiang biota is distinguished by pristine carbonaceous preservation of labile organic features, a very high proportion of new taxa (~53%), and preliminary taxonomic diversity that suggests it could rival the Chengjiang and Burgess Shale biotas. Defining aspects of the Qingjiang biota include a high abundance of cnidarians, including both medusoid and polypoid forms; new taxa resembling extant kinorhynchs; and abundant larval or juvenile forms. This distinctive composition holds promise for providing insights into the evolution of Cambrian ecosystems across environmental gradients.

Editor's summary: A treasure trove of Cambrian secrets. Animal life exploded in diversity and form during the Cambrian period about 500 million years ago. Fu et al. describe an early Cambrian fossil site in China that contains a variety of specimens, more than half of which are previously undescribed (see the Perspective by Daley). The site rivals previously described Cambrian sites, such as the Burgess Shale, and should help to elucidate biological innovation and diversification during this period.

Fu, L., Zhou, T., Wang, J., You, L., Lu, Y., Yu, L., Zhou, S., 2019. NanoFe3O4 as solid electron shuttles to accelerate acetotrophic methanogenesis by Methanosarcina barkeri. Frontiers in Microbiology 10, 388. doi: 310.3389/fmicb.2019.00388.


Magnetite nanoparticles (NanoFe3O4) have been reported to facilitate direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens thereby improving syntrophic methanogenesis. However, whether or how NanoFe3O4 affects acetotrophic methanogenesis remain unknown. Herein, we demonstrate the unique role of NanoFe3O4 in accelerating methane production from direct acetotrophic methanogenesis in Methanosarcina-enriched cultrures, which was further confirmed by pure cultures of Methanosarcina barkeri. Compared with other nanomaterials of higher electrical conductivity such as carbon nanotubes (CNTs) and graphite, nanoFe3O4 with mixed valence Fe(II) and Fe(III) had the most significant stimulatory effect on methane production, suggesting its redox activity rather than electrical conductivity led to enhanced methanogenesis by M. barkeri. Cell morphology and spectroscopy analysis revealed that NanoFe3O4 penetrated into the cell

membrane and cytoplasm of M. barkeri. These results provide the unprecedented possibility that NanoFe3O4 in the cell membrane of methanogens serve as electron shuttles to facilitate intracellular electron transfer and thus enhance methane production. This work has important implications not only for understanding the mechanisms of mineral-methanogen interaction but also for optimizing engineered methanogenic processes.

Fu, W., Wang, Z., Yue, X., Zhang, J., Sun, B., 2019. Experimental study of methane hydrate formation in water-continuous flow loop. Energy & Fuels 33, 2176-2185.


As the offshore oil and gas fields are maturing, the water production rate from the reservoir is increasing progressively year by year. The methane hydrate formation in water-continuous systems has become a significant flow assurance issue for offshore oil and gas production. In this study, a group of methane hydrate formation experiments are designed to study characteristics of hydrate formation in the water-continuous flow loop, which were performed under void fractions from 2.6 to 5.0%, flow velocities from 1.24 to 1.57 m/s, subcooling temperatures from 4.5 to 7.2 °C, and hydrate particle concentration from 0 to 0.14 kg/kg. The methane hydrate formation process is considered as a mass transfer process, and the multiple influencing factors on the hydrate formation are analyzed experimentally, such as flow velocity, subcooling temperature, and hydrate particle concentration. Results show that higher flow velocity induces higher hydrate formation rate. Higher hydrate particle concentration results in lower hydrate formation rate. Thus, an integrated mass transfer coefficient is proposed, including the effect of the hydrate particle concentration and the flow velocity. In this work, the effect of subcoolings on the integrated mass transfer coefficient is found to be negligible. A corresponding mass transfer-limited hydrate formation model is proposed to predict methane hydrate formation in the water-continuous system, which is a function of the proposed integrated mass transfer coefficient, flow velocity, hydrate particle concentration, subcooling, and gas–liquid interfacial area. After comparing with experimental data, the proposed hydrate formation model shows its good agreement with experimental data.

Fu, X., Wang, J., Song, C., Wang, Z., Zeng, S., Wang, D., 2019. The Permian-Triassic transition in ocean island setting: Environmental disturbances and new high-resolution carbon-isotope record from the Qiangtang Basin, NW China. Palaeogeography, Palaeoclimatology, Palaeoecology 522, 40-51.


The Permian-Triassic boundary (PTB) events such as carbon-isotope excursion, volcanism, and environmental disturbances are not well understood in an ocean island setting. Here, we develop a new case study for the Permian-Triassic transition in the Qiangtang Basin, Tibet, by combining existing biostratigraphy, new carbon-isotope data, sedimentological data, UPb zircon age, mineralogical and geochemical data. These new data defined the Permian-Triassic transition age as about 252.3 ± 0.9 Ma, corresponding to the lowermost sea level. A long-term negative carbonate carbon isotope trend is present at the same stratigraphic level in different depositional environments, strongly suggesting its global nature. However, our new ocean island setting is characterized by an abrupt shift in carbon isotope values across the level, which is different from many chemostrtigraphic studies that show a gradual shift in carbon isotope values across the event horizon. The most likely explanation for the abrupt shift in δ13C values is a sedimentary hiatus at this level in the study section. Three-stage climatic models through the PTB in the ocean island setting are identified: Stage 1 is characterized by a warm and humid climate with moderate chemical weathering; while a hot and

humid climate with intense chemical weathering dominates stage 2; the climate in stage 3 is a relatively hot and arid climatic condition with weak chemical weathering.

Fuchsman, C.A., Paul, B., Staley, J.T., Yakushev, E.V., Murray, J.W., 2019. Detection of transient denitrification during a high organic matter event in the Black Sea. Global Biogeochemical Cycles 33, 143-162.

https://doi.org/10.1029/2018GB006032

N2 production by denitrification can occur in anoxic water or potentially inside organic particles. Here we compare data from the Black Sea, a permanently anoxic basin, during two organic matter regimes: suspended particulate organic matter concentrations were high in the oxycline after the spring bloom in March 2005 compared to lower organic matter concentrations in June 2005, May and October 2007, July 2008, and May 2001. For all cruises, N2 gas had a maximum in the suboxic zone (O2 < 10 μmol/L). During the high organic matter event (March 2005), an additional shallower N2 gas and δ15N-N2 maxima occurred above the suboxic zone in the oxycline where oxygen concentrations were 30-50 μmol/L. Examination of 16S rRNA indicated that anammox bacteria were not present in the oxycline. The δ15N of biologically produced N2 in the oxycline in March 2005 was significantly enriched (+7‰ to +38‰), not depleted, as would be expected from water column fractionation. A simple diffusion calculation indicated that ammonium produced from remineralization inside particles could be oxidized to nitrate and then completely consumed by denitrification inside the particle. In this calculation, half of denitrified N atoms originated from organic N [δ15N = 11‰] and half of N atoms originated from ambient nitrate [δ15N = 5‰–7‰], producing enriched δ15N‐N2 values. We suggest that denitrifiers were active in microzones inside particulates in hypoxic waters above the suboxic zone of the Black Sea. Denitrification in particles may also explain previous data from the oxycline above ocean oxygen deficient zones.

Fung, M.K., Schaller, M.F., Hoff, C.M., Katz, M.E., Wright, J.D., 2019. Widespread and intense wildfires at the Paleocene-Eocene boundary. Geochemical Perspectives Letters 10, 1-6.

https://www.geochemicalperspectivesletters.org/article1906

Discovery of impact spherules associated with the onset of the Carbon Isotope Excursion (CIE) that marks the Paleocene-Eocene (P-E) boundary (~56 Ma) indicates that the P-E transition was coincident with an extraterrestrial impact. Charcoal abundances increase >20 times background immediately above the P-E spherule layer at two Atlantic Coastal Plain palaeo-continental shelf localities located >200 km apart. Individual charcoal shards (~100 μm long; 58-83 wt. % carbon) show charred plant features. The carbon isotope ratio of charcoal (δ13Ccharcoal) through the peak shows that it originated from pre-impact vegetation that burned. We consider two scenarios to explain this widespread, synchronous increase in charcoal at the P-E boundary: 1) warming-induced, continental-scale drying; and 2) impact-induced wildfires. Differentiating between these two hypotheses depends critically on the observed sequence of events, which on the western North Atlantic margin is: the impact spherule horizon, followed by the peak in charcoal (derived from vegetation that grew before the CIE and impact), and finally the nadir of the CIE. Importantly, the pre-excursion δ13Ccharcoal remains constant through the CIE onset, requiring a dramatic increase in sedimentation. This work clarifies our understanding of the timing and sequence of events following an extraterrestrial impact at the P-E boundary.

Fustic, M., Strobl, R., Fowler, M., Jablonski, B.V., Martinius, A.W., 2019. Impact of reservoir heterogeneity on oil migration and the origin of oil-water contacts: McMurray Formation type section, Alberta, Canada. Marine and Petroleum Geology 103, 216-230.


This study documents and attempts to describe the processes leading to the formation and preservation of exposed oil, water, and paleo-gas contacts at the McMurray Formation type section, Alberta, Canada. The McMurray Formation type section, a part of the Athabasca Oil Sands Deposit (AOSD), the largest exhumed oil reservoir on Earth, is unparralled, still underutilized, natural laboratory for veryfing and refining existing, and developing new concepts, for oil migration and post oil-emplacement fluid diffusion and biodegradation processes in a sedimentologically complex reservoir setting. Exposures, coupled with adjacent borehole data, provide a three-dimensional insight into reservoir heterogeneities and their influence on oil migration, entrapment, post-emplacement fluid mixing, and biodegradation processes and products, in a hierarchical and chronological order from early charge to present-day conditions. The principles of oil above water and of horizontal or tilted oil/water contacts are challenged by outstanding examples of: (i) centimetre to decimetre scale inter-fingering oil-water stringers/contacts, created by capillary pressure differences and partial charge; (ii) irregular oil-water contacts in both clean and heterogeneous reservoirs characterized by gravitational effects caused by severe biodegradation that caused the formation of extra heavy-oil commonly referred to as “bitumen” that sank through the water column; (iii) occurrences of multiple metre-scale intervals with less than 50% oil saturation, commonly referred to as lean zones that formed during microbial gas generation following oil entrapment. Studied contacts provided excellent opportunity to study oil migration and charging mechanisms from pore and sedimentary bed to reservoir scale at various stages of oil migration into the reservoir, as well as oil, water, and gas re-migration within the reservoir (trap). Described exposures can play an additional role in advancing geoscience education, petroleum exploration, reservoir characterization, field development, and production optimization studies.

Gal, J.-F., 2019. An excursion into the history of chromatography: Mikhail Tswett, from Asti, Italy, to Tartu, Estonia. Chromatographia 82, 519-521.

https://doi.org/10.1007/s10337-019-03686-0

In 2010, in this Journal, I described two memorials in Tartu, Estonia, honouring scientists who worked on the development of chromatography, Teodor Lippmaa and Mikhail Semyonovich Tswett1 (Михаил Семëнович Цвет) [1]. The University of Tartu, founded in 1632 and reopened after various vicissitudes in 1802,2 has a long tradition in science and chemistry [2]. Its reopening took place under the initiative of George-Frederic Parrot [3], a German-speaking mathematician, physicist and chemist born in France.3

As reported in my 2010 note, during visits to the University of Tartu, I discovered a plaque (Fig. 2) in the University botanical garden (Fig. 1) commemorating the contribution of Mikhail Tswett to the Tartu Botanical Garden in 1917 and 1918. This, unfortunately too short, period of work in Tartu was due to the perturbations of the First World War and the poor physical condition of Mikhail Tswett. However, on March 24, 1917, he was appointed as professor of botany and director of the Botanical Gardens at the University of Tartu [4, 5]. It is interesting to note that Mikhail Tswett’s father, Semen Nikolaevich Tswett, had studied science at University of Tartu, which was held in high esteem in the Tswett family [6]. When Tartu was invaded by German troops in 1918, Mikhail Tswett left Tartu to Voronezh, Russia, where the University was relocated. He died in Voronezh on June 26, 1919, at the age of 47. This was a period of great political instability, the independence of Estonia was declared in

1918, and 1919 was the year of foundation of the first Estonian-language university, the centenary of which will be officially celebrated on the 1st of December 2019.

Not long after the publication of my note [1], I was visiting Asti, Italy, a town well known for wines and for its Palio, a dangerous bareback horse race run within the city. By chance, or by the so-called “serendipity”, I discovered a plaque commemorating the centenary of the birth of the discoverer of chromatography, Fig. 3, as noted in the commemorative inscription. My curiosity was excited and I would like to share my discovery.

This landmark celebrating Mikhail Tswett birth is situated under the arcades (Portici Pogliani) of Piazza Vittorio Alfieri, N° 5, about 4 m from the ground, close to the entrance of Hotel Reale (Royal Hotel). Just near the hotel entrance and the plaque, at N° 3, a historical pharmacy is also worth a stop,5 (Fig. 4), bearing in mind the remarkable “chemical affiliation” with the Tswett discovery of chromatography.

Hotel Reale, still in operation, is the exact place where Tswett was born on May 14, 1872. I was not able to collect more information among the Italian chemists’ community on the initiators and origin of this tribute. The birth of Mikhail Tswett was reported at the town hall on May 19, a date which is sometimes mistakenly reported as his birthday. His parents had come from Russia by ship to Genoa (Italy, Liguria), and arrived in Asti by train. They planned to spend an extended holiday in a resort at the beautiful Lake Maggiore, but the family had to stop urgently because of premature labour of the pregnant mother, Maria de Dorozza, of Italian origin. The birth appeared to have been difficult, and Maria died shortly after [7]. Little is known on the life of the mother [8]. The father took his premature and weak baby to Lausanne, Switzerland, where Mikhail Tswett was raised by a nurse. In 1885 Mikhail Tswett moved to Geneva [8], where he graduated from high school in 1891 and obtained his doctoral degree in 1896 [4].

Before his short period in Tartu, Tswett started a teaching career at St. Petersburg, Russia, then became an assistant at the University of Warsaw, Poland, and, later in the same University, professor of botany and agronomy at the Veterinary Institute, and professor of botany and microbiology at the Polytechnic Institute [8, 9].6 Several detailed accounts of his life, scientific achievements and difficulties in his career are available [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]. Two authors, Karl I. Sakodynskii (1930–1996) [15] and Leslie S. Ettre (1922–2010) [16] were the most prolific Tswett’s biographers.

Mikhail Tswett and Teodor Lippmaa were initially botanists, [17] but became recognized later by the chemist community. It is surprising that Tswett and Lippmaa are not cited in a history of analytical chemistry in Estonia covering the 19th and half of the twentieth century [18]. Fortunately, Tswett was cited in another account on the chemistry and chemistry-related sciences in Tartu [2]. Indeed, Mikhail Tswett was nominated for the Nobel Prize in 1918 [5].

Finally, it is notable that Asti and Tartu are the towns in which began and almost ended the life of Mikhail Semyonovich Tswett.

Footnotes

1. The English transcription of the Cyrillic Цвет is Tsvet, but the German transcription Tswett is mostly used; other transcriptions found in historical and scientific articles are Tsvett, Tswet, Zwet, and Cvet. The patronymic name (father's name) Семëнович is often transcript as Semenovich.

2. From 1802 to 1893, the teaching language at UT is German, the German name of Tartu being Dorpat. After the independence of Estonia, Estonian becomes the official language of the University. Russian biographers often mention the use of the former Russian name Yuriev (or Yur’ev) for Tartu.

3. The program of bilateral scientific exchanges between Estonia and France received the name of Parrot.

4. https://www.ut.ee/en/estoniasnationaluniversity100.5. This famous pharmacy was moved from the hospital of Santa Marta in 1867, and the owners keep old

pharmacy tools and pharmacopeias; see its Facebook site.6. Pictures of a memorial plaque celebrating the invention of chromatography by Mikhail Tswett (1901–1906),

and of the building of the Warsaw University on which this plaque is placed are shown in Ref [9].

References

1. Gal J-F (2010) A short note on the history of chromatography at the University of Tartu, Estonia. Chromatographia 72:203–204

2. Lenoir D (2009) Eliteuniversität des 19. Jahrhunderts” (Elite University of the 19th century). Nachrichten Chem 57:1100–1103; see also https://www.chem.ut.ee/en/about-institute/history, with links to two pdf files (accessed 21/09/2018); (i) Ilomets T, “Chemistry and Chemistry-Related Sciences at Tartu (Dorpat) University in 1802–1919”; (ii) Past V, “Chemistry at the University of Tartu in 1919–1947

3. Allik J, Konstabel K (2005) G. F. Parrot and the theory of unconscious inferences. J Hist Behav Sci 41:317–330

4. Ettre LS, Sakodynskii KI (1993) M. S. Tswett and the discovery of chromatography I: early work (1899–1903). Chromatographia 35:223–231

5. Ettre LS (1996) M. S. Tswett and the 1918 nobel prize in chemistry. Chromatographia 42:343–3516. Hais IM (1988) Tswett’s letters to Claparède. J Chromatogr 440:509–5317. Ettre LS (2003) M. S. Tswett and the Invention of chromatography. LC GC Eur 21(2–7):458–467

(published also in LC•GC North America, 2003) 8. Sakodynskii KI (1981) New data on M. S. Tswett’s life and work. J Chromatogr 220:1–289. Zolotov YuA (2003) The centenary of chromatography. J Anal Chem 58:703–705. (Translated from the

Russian edition Zhur. Anal. Khim. 2003, 58, 789–791) 10. Strain HH, Sherma J (1967) Michael Tswett’s contributions to sixty years of chromatography. J Chem Educ

44:235–23711. Sakodynskii KI (1970) M. S. Tswett - his Life and Work. Chromatographia 3:92–9412. Sakodynskii KI, Chmutov K (1972) M. S. Tswett chromatography. Chromatographia 5:471–47613. Berezkin VG (1989) Biography of Mikhail Semenovich Tswett and translation of Tswett’s preliminary

communication on a new category of adsorption phenomena. Chem Rev 89:279–28514. Livengood J (2009) Why was M. S. Tswett’s chromatographic adsorption analysis rejected? Studies History

Phil Sci 40:57–6915. Ettre LS (1996) In Memoriam K. I. Sakodynskii (1930–1996). Chromatographia 42:615–61616. Adlard T (2010) Leslie Stephen Ettre 1922–2010. Chromatographia 72:201–20217. Sander H, Meikar T, Magowska A (2014) The learned gardeners of the botanical gardens of the University

of Tartu and their activities (1803–1918). Acta Baltica Hist Sci 2:53–11018. Hödrejärv H (1997) History of analytical chemistry in Estonia (1800–1950). Fresenius J Anal Chem

357:191–196

Gal, J.-K., Kim, J.-H., Kim, S., Lee, S.H., Yoo, K.-C., Shin, K.-H., 2019. Application of the newly developed nutrient diol index (NDI) as a sea surface nutrient proxy in the East Sea for the last 240 years. Quaternary International 503, 146-152.


We assessed the applicability of the nutrient diol index (NDI) as a proxy for sea surface nutrients by analyzing sediments from a box core (ES14-BC03) collected in the southwestern continental slope of the East Sea, or the Japan Sea (hereafter the East Sea). The estimated sedimentation rate based on the 210Pb chronology was 0.15 cm yr−1 over the last 240 yrs. The NDI-derived phosphate (0.69 μmol L−1) and nitrate (8.63 μmol L−1) concentrations for the core-top sediment were within the average phosphate (0.26 ± 0.08 μmol L−1) and nitrate (3.38 ± 2.32 μmol L−1) concentration ranges for the last ∼20 years, accounting for both estimation error and variation in observational data. The distributions of the NDI-diols varied slightly through time, grouping into two distinct clusters (Cluster 1 and

Cluster 2) in both principle component analysis (PCA) and hierarchical clustering of principal components (HCPC). Cluster 2 represented a time period with higher relative abundances of the C28 and C30 1,14-diols, resulting in higher NDI-derived nutrient concentrations than those of other periods. Interestingly, during this period, the U37

K'-derived sea surface temperatures (SSTs) also decreased. These results indicate that higher surface nutrient conditions and colder SSTs occurred between 1884 CE and 1911 CE, which might be associated with stronger upwelling intensity at the study site. This study is the first application of the NDI to a down-core, demonstrating that the NDI can be a useful proxy that provides helpful information about past sea surface nutrient conditions.

Galasso, F., Fernandes, P., Montesi, G., Marques, J., Spina, A., Pereira, Z., 2019. Thermal history and basin evolution of the Moatize - Minjova Coal Basin (N'Condédzi sub-basin, Mozambique) constrained by organic maturation levels. Journal of African Earth Sciences 153, 219-238.


Kerogen concentrates obtained from Lopingian (Late Permian) to Upper Triassic mudrock lithologies of seven coal exploration boreholes, drilled in the Moatize – Minjova Coal Basin (N'Condédzi sub-basin, Mozambique), were studied by means of vitrinite reflectance (VR), spore fluorescence and spore colour, in order to constrain the thermal history and basin evolution by organic maturation levels. VR increases with depth, indicating organic maturation related to sediment burial for most of the boreholes. Modelled VR data indicate a regional palaeogeothermal gradient between 35 and 40 °C/km. Lower Jurassic doleritic intrusions observed in three boreholes had only local thermal effects without affecting the regional palaeogeothermal gradient. Two boreholes located near the basin margin show high palaeogeothermal gradients suggesting thermal processes other than heating due to burial were involved. These processes may have involved hot diagenetic fluids circulating through fault zones and/or permeable lithologies, locally elevating geothermal gradients. Circulation of these fluids was induced by lithostatic pressure due to rapid rates of sedimentation. These high sedimentation rates lead to the accumulation of a thick succession (over 2000 m) of Lopingian (Late Permian) to Upper Triassic siliciclastic sediments. All the organic maturation indices measured and the age of the successions indicate that organic maturation occurred during or after Late Triassic times. However, the presence of reworked Permian palynomorphs into Upper Triassic sediments and the absence of Middle Triassic sediments indicate an exhumation and erosion of Permian strata in Middle Triassic times. The organic maturation levels of the reworked palynomorph population are considerably higher than the indigenous Upper Triassic population, indicating that they attained higher burial temperatures prior to being reworked.



Aim of this work is locating how CO2 replacement into methane hydrate deposits may be performed, in order to increase both methane recovered and carbon dioxide stored quantities.

The experimental section deals with the study of natural gas hydrate formation process and replacement of methane, contained into water cages, with carbon dioxide. In particular, the formation of methane hydrate is analyzed to understand the parameters that most influence the replacement process. A total of 10 tests were carried out in a laboratory scale reactor. Test 1–8 were performed adopting thermal stimulation as replacement technique, while in Test 9 and Test 10 depressurization

was used. Results obtained have led to the conclusion that the rate of methane hydrate formation positively influences the percentage of CO2 stored, while the initial saturation of the sand pores has a negative effect. The presence of hydrate agglomerates hinders the gas transition preventing the replacement process. Finally, a greater quantity of CO2 hydrate, both via replacement process and via new hydrate formation, is related to a higher deposit structure preservation. As emerges from the experimental tests, the adopted replacement strategy influences the experimental relationships.

Ganeeva, Y.M., Barskaya, E.E., Okhotnikova, E.S., Timirgalieva, A.H., Yusupova, T.N., 2019. Study of hydrocarbons adsorbed in asphaltenes of Domanic Formation bitumoid. Petroleum Science and Technology 37, 479-485.

https://doi.org/10.1080/10916466.2018.1552969

Asphaltenes have adsorption and occlusion properties, and the study of the compounds adsorbed and occluded in them can characterize the evolutionary processes occurring in the oil reservoir. In this paper, the adsorption properties of asphaltenes isolated from bitumoid of Domanic formation of the Republic of Tatarstan (Russia) were studied. It was found that asphaltenes adsorbed to a greater extent the polar resins and to a lesser extent ? the nonpolar resins and the saturated hydrocarbons. It was shown that adsorbed resins were enriched in aromatic structures with poor alkyl substitution, and adsorbed saturated hydrocarbons were enriched in high molecular weight n-alkanes in comparison with compounds present in maltenes of bitumoid. Asphaltenes, after adsorbed compounds were extracted from them, became more carbonized. The assumption was made that vanadyl porphyrin complexes were occluded in asphaltenes rather than adsorbed on them.

Ganeeva, Y.M., Okhotnikova, E.S., Barskaya, E.E., Yusupova, T.N., Foss, L.E., Sotnikov, O.C., Remeev, M.M., Khisamov, R.S., 2019. The composition of organic matter of Domanic deposit of the Bavly field. Petroleum Science and Technology 37, 317-322.

https://doi.org/10.1080/10916466.2018.1542445

Core material taken from Zavolzhsky and Dankovo-Lebedyan horizons of the Bavly oil field attributed to the Domanic deposit is studied by thermal analysis methods. The content of total organic matter, the share of bitumoid and kerogen in it and their fractional composition are estimated. The features of fractional and hydrocarbon compositions of the bitumoids are revealed by thermal analysis, gas chromatography and IR spectroscopy methods. It is shown that, in some cases, the domanic deposit contains light hydrocarbons that can be extracted from the rock using solvents. An estimation of the oil-generating potential of the organic matter of the Zavolzhsky and Dankovo-Lebedyansky horizons is made.

Gao, L., Lu, X., Liu, H., Li, J., Li, W., Song, R., Wang, R., Zhang, D., Zhu, J., 2019. Mediation of extracellular polymeric substances in microbial reduction of hematite by Shewanella oneidensis MR-1. Frontiers in Microbiology 10, 575. doi: 510.3389/fmicb.2019.00575.


Extracellular electron transfer (EET) plays a fundamental role in microbial reduction/oxidation of minerals. Extracellular polymeric substances (EPS) surrounding the cells constitute a matrix that separates the cell’s outer membrane from insoluble minerals. The present study investigated the effect of EPS on EET processes during microbial reduction of hematite by the iron-reducing strain Shewanella oneidensis MR-1 (MR-1). Electrochemical characterization techniques were employed to

determine the influence of EPS components on the redox ability of MR-1. Cells removed EPS exhibited approximately 30% higher hematite reduction than regular MR-1 cells, and produced a current density of 56 μA cm-2, corresponding to 3–4 fold that of regular MR-1. The superior EET of EPS-deprived cells could be attributed to direct contact between outer membrane proteins and hematite surface, as indicated by more redox peaks being detected by cyclic voltammetry and differential pulse voltammetry. The significantly reduced current density of MR-1 cells treated with proteinase K and deoxyribonuclease suggests that the electron transfer capacity across the EPS layer depends mainly on the spatial distribution of specific proteins and electron shuttles. But exopolysaccharides in EPS tend to inhibit electron transfer although they favor the attachment of cells onto solid surface. Consistently, the charge transfer resistance of cells lacking EPS was only 116.3 Ω, or 44 times lower than that of regular cells (5,139.1 Ω). These findings point to a negative influence of EPS on EET processes for microbial reduction/oxidation of minerals.

García-Cicourel, A.R., Janssen, H.-G., 2019. Direct analysis of aromatic hydrocarbons in purified mineral oils for foods and cosmetics applications using gas chromatography with vacuum ultraviolet detection. Journal of Chromatography A 1590, 113-120.


Highly purified mineral oils are used in several pharmaceutical, foods and cosmetics applications. A fast and simple method was developed for the analysis of the total level of residual mineral oil aromatic hydrocarbons (MOAH) in these oils and in the intermediate oils that were sampled during the purification process. The method is based on gas chromatography with vacuum ultraviolet detection (GC-VUV) and relies on the spectral differences between the aliphatic and aromatic compounds in the sample. Because the detector provides a good selectivity for aromatics, direct quantification of the MOAH content is possible without the need for a laborious preseparation of the mineral oil. The method was successfully applied for the direct analysis of the MOAH levels of 18 different mineral oil samples. The aromatics contents obtained by GC-VUV were similar to those obtained using two conventional methods (NPLC-GC-FID and SPE-GC-FID), with no statistically significant difference. The detector response was linear over the concentration range tested (0.5–20 mg/mL) and the repeatability (RSD value) was less than 8%, which is better than the typical values for the conventional methods (up to 15% RSD). The minimum MOAH level that can be determined with this method is approximately 0.13%, making the GC-VUV method sufficiently sensitive for the analysis of all but the highest purity mineral oils.

Garcia, G.P., Sutour, S., Rabehaja, D., Tissandié, L., Filippi, J.-J., Tomi, F., 2019. Essential oil of the malagasy grass Elionurus tristis Hack. contains several undescribed sesquiterpenoids. Phytochemistry 162, 29-38.


Essential oils (EOs) obtained from aerial parts and roots of Elionurus tristis were investigated by GC, GC-MS, pc-GC and NMR. Both aerial parts and roots EOs contained common molecules such as α-pinene, camphene, trans-α-bergamotene and calarene. Moreover, we identified several unusual sesquiterpenes and four undescribed compounds, 7-epi-khusian-2-ol, 4,8-di-epi-acorone, 2-epi-ziza-5-en-2-ol and antsorenone. The last one exhibits an undescribed natural sesquiterpene skeleton. All undescribed compounds were isolated and fully characterized by MS, 1D and 2D-NMR. Furthermore, the formation pathway of the Antsorane skeleton is discussed.

Gascon, G., Negrin, J., Garcia-Montoto, V., Acevedo, S., Lienemann, C.-P., Bouyssiere, B., 2019. Simplification of heavy matrices by liquid–liquid extraction: Part I—How to separate LMW, MMW, and HMW compounds in maltene fractions of V, Ni, and S compounds. Energy & Fuels 33, 1922-1927.


A method using liquid–liquid extractions has been developed for matrix simplification and evaluated by gel permeation chromatography coupled with inductively coupled plasma and mass spectrometry. In this method, maltenes were dissolved in n-heptane and extractions with methanol (MeOH), acetonitrile (ACN), and dimethylformamide (DMF) were performed. The extraction with ACN is more efficient than that with MeOH for the removal of compounds with low-molecular weights (LMW) containing V (our reference element) and more selective than that with DMF (with this solvent, compounds with LMW and medium-molecular weights (MMW) are extracted). Thus, a sequential extraction was performed by applying ACN to selectively remove LMW compounds, followed by extractions with DMF of the resulting maltene to separate the MMW compounds from the high-molecular weights (HMW) compounds remaining in the final remnant maltene. The results show, for the first time in the literature, that it is possible to separate the three V and Ni species of compounds present in maltenes based on their molecular weights (HMW, MMW, and LMW).

Gastaldo, R.A., 2019. Ancient plants escaped the end-Permian mass extinction. Nature 567, 38-39.

https://www.nature.com/articles/d41586-019-00744-3

A global biodiversity crash 251.9 million years ago has revealed how ecosystems respond to extreme perturbation. The finding that terrestrial ecosystems were less affected than marine ones is unexpected.

Changes in Earth’s biodiversity recorded in fossils over various spatial and timescales reveal the comings and goings of species as they emerge and go extinct, and offer insights into how both species and the ecosystems they inhabit respond to perturbation. These patterns of the past provide models that might help us to understand the changes that life on Earth will experience in the future. The end-Permian mass extinction, often called the mother of mass extinctions1, is a focus of such studies. Large waves of extinctions occurred over a time interval of 60,000 to 120,000 years2 at the end of the Permian period, which lasted from 298.9 million to 251.9 million years ago. Fossil studies indicate that more than 90% of marine invertebrates went extinct3 as a consequence of extreme perturbations of the conditions on Earth, including intense volcanic activity. Writing in Nature Communications, Fielding et al.4 and Nowak et al.5 reveal what happened to terrestrial plants during the end-Permian crisis. Both contributions are well supported by an array of data, and both tell a slightly different story.

How terrestrial ecosystems were affected during the end-Permian mass extinction is not as well understood as the changes that occurred in marine ecosystems. There are biases in the fossil record of plants, and the invertebrate and vertebrate communities they supported, because the preservation potential of these organisms is highly dependent on the physico-chemical conditions of where they lived6. Larger plant components, such as leaves or stems (the macrofloral parts), are easily broken down, and this material is often recycled in the ecosystem. By contrast, plant reproductive material — spores and pollen — are protected by molecules that prevent degradation. Spores and pollen are produced annually at logarithmically higher numbers than other plant parts that sit above ground, which favours their preservation in sediments over more easily decayed plant structures.

Moreover, rocks from around the time of the extinction event are notoriously incomplete — sediments from certain times can be missing from ancient rock layers7. When this relative incompleteness of rock layers that would preserve fossil parts is added to the equation, interpreting patterns of species presence during this key episode in our planet’s history becomes complicated.

Fielding and colleagues report a regional study that uses the plant fossil record of spores, pollen and macrofloral remains in layers of rock from the Sydney Basin, Australia, in which layers from the time of the end-Permian crisis event are reported to be present. The authors present a comprehensive data set that includes an analysis of the layers, fossils and geochemistry within a known time frame. Synthesizing their data, the authors propose that the onset of a short-lived change in summer temperatures and a rise in seasonal temperatures across eastern Australia, about 370,000 years before the onset of the end-Permian marine extinction event, caused the regional collapse of Glossopteris flora (Fig. 1). Fossils of this extinct plant are preserved mainly in ancient wetlands, and it was the dominant type of forest species in the Southern Hemisphere. Other Southern Hemisphere records seem to show that Glossopteris survived for some time into the subsequent Triassic period (which lasted between 251.9 million and 201.3 million years ago) in Antarctica8, although exactly when they went extinct in the Triassic is unknown. Fielding and colleagues use the region-specific collapse of Glossopteris as a scenario for how vegetation might respond to current global warming. A regional loss in the Southern Hemisphere of a major plant group that has growth requirements highly sensitive to climate change, particularly in the temperature requirements for its essential processes, might be a harbinger of the plant group’s ultimate extinction.

Fielding and colleagues’ finding that the extinction of Glossopteris occurred about 370,000 years before the marine extinction event, and was coincident with the onset of massive volcanic activity, should now lead to investigations elsewhere in the Permian record to determine whether the loss of other wetland plants acts as a ‘canary in the coal mine’.

One long-held model9,10 for terrestrial ecosystem turnover and replacement of species between the Permian and the end of the Middle Triassic (between 251.9 million and around 237 million years ago) has focused on the effects of a global trend towards aridification. It was proposed that, after a worldwide collapse of plant communities and a mass extinction of species that cascaded through the food chain9, there was a change in the floral species across global landscapes by the Middle Triassic period. For the demise of Glossopteris, Fielding and colleagues find no evidence of an aridification trend in their region that would suggest that a hot terrestrial landscape promoted a mass extinction of plants during the time of the end-Permian crisis.

This conclusion of Fielding and colleagues’ regional work is supported by a comprehensive analysis of plant fossil records on a global scale conducted by Nowak and colleagues. The authors analysed the patterns of previously reported plant fossils from 259.1 million to around 237 million years ago, which spans the end-Permian mass extinction and the Early and Middle Triassic. They generated a database that includes information on more than 7,300 plant macrofossils and nearly 43,000 fossil records of pollen or spores. So far, this is the most comprehensive database generated for floral analysis before and after the end-Permian crisis. It amasses the evidence that has been considered by many palaeontologists to indicate a trend in mass extinction of terrestrial plants that mirrors that of the marine mass extinction9.

The authors present origination, extinction and turnover patterns at the level of species and genera on a stage-by-stage basis (stages being steps in the geological timescale). The diversity of genera was relatively constant across the time interval, although the species diversity of macrofloral fossils dropped 251.9 million years ago. The diversity of genera represented by spores and pollen remained constant across the time frame studied, although Nowak et al. note a small decline in species-level diversity around 251.9 million years ago. Of the groups of plants that have either pollen or spores, the

spore-bearing ferns, as well as the pollen-producing seed ferns and cycads, declined in diversity during this time, whereas the pollen-bearing conifers and ginkgos increased in diversity.

In contrast to prevailing wisdom, Nowak and colleagues demonstrate that land plants did not experience widespread extinction during Earth’s most severe biological crisis. Their conclusion is similar to that drawn for terrestrial vertebrates11. This leaves the relationship between the end-Permian marine mass extinction and the effect on land at the time enigmatic for now, and still up in the air for further investigation.

References1. Erwin, D. Sci. Am. 275, 72–78 (1996).2. Burgess, S. D., Bowring, S. & Shen, S. Z. Proc. Natl Acad. Sci. USA 111, 3316–3321 (2014).3. Payne, J. L. & Clapham, M. E. Annu. Rev. Earth Planet. Sci. 40, 89–111 (2012).4. Fielding, C. R. et al. Nature Commun. 10, 385 (2019).5. Nowak, H., Schneebeli-Hermann, E. & Kustatscher, E. Nature Commun. 10, 384 (2019).6. Behrensmeyer, A. K., Kidwell, S. M. & Gastaldo, R. A. Paleobiology 26, 103–147 (2000).7. Gastaldo, R. A., Neveling, J., Geissman, J. W. & Kamo. S. L. Geol. Soc. Am. Bull. 130, 1411–1438 (2018).8. Collinson, J. W., Hammer, W. R., Askin, R. A. & Elliot, D. H. Geol. Soc. Am. Bull. 118, 747–763 (2006).9. Benton, M. J. Phil. Trans. R. Soc. A 376, 20170076 (2018).10. Smith, R. H. M. & Botha-Brink, J. Palaeogeogr. Palaeoclimatol. Palaeoecol. 396, 99–118 (2014).

Gastaldo, R.A., Neveling, J., Geissman, J.W., Li, J., 2019. A multidisciplinary approach to review the vertical and lateral facies relationships of the purported vertebrate-defined terrestrial Permian–Triassic boundary interval at Bethulie, Karoo Basin, South Africa. Earth-Science Reviews 189, 220-243.


The stratigraphic section at Bethulie, South Africa, is reported to contain the vertebrate-defined Permian–Triassic boundary succession in the terrestrial realm of the Karoo Basin. The model of vertebrate turnover, from the Daptocephalus to Lystrosaurus Assemblage Zones, tightly constrains the boundary sequence to a short stratigraphic interval where siltstone color begins to change from greenish gray to grayish red, the latter color interpreted to be a consequence of aridification. The biological response to this facies change has been termed “the Great Dying,” and the sedimentary rocks that are preserved are ascribed to a playa lake depositional setting. This drying event is believed to be contemporaneous across the basin, although previous studies have shown that the facies appears at multiple horizons at all purported Permian–Triassic boundary sections in the basin.

Here, we report results of a multidisciplinary effort to characterize the vertebrate assemblage-zone boundary interval exposed at Bethulie using the lithostratigraphic, petrographic, geochemical, and rock magnetic properties of these rocks. In this stratigraphic succession at its “type” location, the 3-m thick assemblage-zone boundary interval is distinguished by thick beds of greenish-gray, greenish-gray mottled to grayish-red, and grayish-red siltstone, all of which change facies characteristics laterally along strike. Specifically, about 220 m to the southeast of the type section, sediments lose all grayish-red coloration, whereas the interval becomes laminated to the northwest. Petrographically, most siltstone is homogenized, with few burrows and small-scale cross-bedded structures with mudchips. There are no gypsiferous or calcareous beds, nor is there evidence of disturbed structures, authigenic breccia, or pseudomorphs associated with dessication. Mean elemental composition of both greenish-gray and grayish-red beds are indistinguishable, geochemically, and both are dominated by illite and chlorite clay species. Mössbauer spectroscopic analyses reveal the presence of

a small concentration of fine-grained hematite in the grayish-red siltstone, with its presence mainly found as coatings on clay minerals. Rock magnetic experiments (isothermal remanent magnetization, acquisition and backfield DC demagnetization; magnetic hysteresis; susceptibility vs. temperature) yield data that demonstrate no essential differences between the different colored siltstones. And, both lithologies host mangnetite/maghematite and hematite. Our results do not support the previous interpretation that this inferred Permian–Triassic boundary interval represents the onset of playa lake deposits under conditions of aridification. Rather, our evidence supports the existence of a “wet” landscape at what is considered the Daptocephalus/Lystrosaurus assemblage-zone boundary.

George, B.G., Ray, J.S., Kumar, S., 2018. Geochemistry of carbonate formations of the Chhattisgarh Supergroup, central India: implications for Mesoproterozoic global events. Canadian Journal of Earth Sciences 56, 335-346.

https://doi.org/10.1139/cjes-2018-0144

The Chhattisgarh Supergroup is one of the major Proterozoic marine sedimentary sequences of India. It consists of largely undeformed and unmetamorphosed siliciclastic, volcaniclastic, and carbonate formations deposited in two sub-basins, Hirri and Bharadwar, separated by an Archean greenstone belt. In spite of its apparent importance for Mesoproterozoic oceanic records, very few geochemical studies have been carried in the basin. Here, we present results of our high resolution geochemical and C–O–Sr isotopic studies in two carbonate formations of the supergroup: the Charmuria and the Chandi. We observe elevated δ13C values increasing from 2.6‰ to 3.6‰ in these formations, which is consistent with the globally reported late Mesoproterozoic values. Such consistently positive δ13C values are attributed to increased organic carbon burial in the basin margins during the deposition of these carbonates. Based on the principles of δ13C isotope stratigraphy, we suggest a depositional age between 1.0 and 1.2 Ga for these carbonates which form the upper part of the supergroup. The lowest 87Sr/86Sr ratios obtained from the Charmuria and Chandi formations, 0.70723 and 0.70816, respectively, are more radiogenic than the contemporaneous seawater, suggesting that the Sr isotopic system of the formations are altered. Based on the similarity in the δ13C values, we stratigraphically correlate the carbonate formations of the Raipur Group in both the Hirri and Bharadwar sub-basins. We also present a compilation of available δ13C and 87Sr/86Sr records from all the Proterozoic sedimentary successions of India and compare it with the global datasets. We find that while the Indian basins possess records of the Bitter Springs and Shuram δ13C anomalies, they lack evidence for the other major global events of the Proterozoic.

Geweely, N.S., Afifi, H.A., Ibrahim, D.M., Soliman, M.M., 2019. Efficacy of essential oils on fungi isolated from archaeological objects in Saqqara excavation, Egypt. Geomicrobiology Journal 36, 148-168.

https://doi.org/10.1080/01490451.2018.1520938

The archeological objects constitute an important part of the worldwide cultural heritage. The impact of the fungal activity on the deterioration of cultural heritage is a global problem and their preservation over time is a challenging task. Antifungal activities of 12 essential oils (EOs) (black cumin, castor, cinnamon, clove, cumin, garlic, geranium, lavender, lemongrass, menthe, olive, and thyme) were examined against 16 fungal species isolated from three tested archaeological objects (wall painting stone, wooden statue, and pottery coffin) from Saqqara stores in Egypt. Molecular identification was carried out for the highly frequent species (Aspergillus niger, A. flavus and Rhizopus oryzae) in the three tested archaeological samples. Antifungal activity and minimal

inhibitory concentration (MIC) of the tested EOs with different concentrations (0.125, 0.25, 0.5, 0.75, 1 μl/ml) were measured.

The most efficient EOs were thyme (MIC ranged from 0.25–0.75μl/ml) followed by clove (MIC ranged from 0.25–1 μl/ml) and geranium, (MIC ranged from 0.5–1 μl/ml). Thymol (37.1%) and p-Cymene (26.32%) were the active constituents of thyme, while Triacetin (69.36%) and eugenol (28.67) were the most efficient components of clove oil followed by geranium active components (à-Citronellol 20.62% and Geraniol 14.43%). Aspergillus niger was the most resistance species, while Fusarium oxysporum and Penicilium citrinium were the most susceptible ones.

Gielnik, A., Pechaud, Y., Huguenot, D., Cébron, A., Riom, J.-M., Guibaud, G., Esposito, G., van Hullebusch, E.D., 2019. Effect of digestate application on microbial respiration and bacterial communities' diversity during bioremediation of weathered petroleum hydrocarbons contaminated soils. Science of The Total Environment 670, 271-281.


Digestate is an organic by-product of biogas production via anaerobic digestion processes and has a great potential as soil fertilizer due to concentrated nutrients. In this study, we examined digestate as a potential nutrient and microbial seeding for bioremediation of weathered (aged) petroleum hydrocarbon contaminated soils. We analysed 6 different treatments in microcosm using two industrial soils having different textures: a clay rich soil and a sandy soil. After 30 days of incubation, the highest total petroleum hydrocarbons (TPH) removal was observed in microcosms containing digestate together with bulking agent (17.8% and 12.7% higher than control in clay rich soil and sandy soil, respectively) or digestate together with immobilized bacteria (13.4% and 9% higher than control in clay rich soil and sandy soil, respectively). After digestate application microbial respiration was enhanced in sandy soil and inhibited in clay rich soil due to aggregates formation. After bulking agent addition to clay rich soil aggregates size was reduced and oxygen uptake was improved. Application of digestate to soil resulted in the development of distinct microbial groups in amended and non-amended soils. Genera containing species able to degrade TPH like Acinetobacter and Mycobacterium were abundant in digestate and in soil amended with digestate. Quantification of alkB genes, encoding alkane monoxygenase, revealed high concentration of these genes in digestate bacterial community. After application of digestate, the level of alkB genes significantly increased in soils and remained high until the end of the treatment. The study revealed great potential of digestate as a nutrient and bacteria source for soil bioremediation.


https://doi.org/10.1029/2018JB015847

The Korea Institute of Geoscience and Mineral Resources conducted depressurization experiments at various gas hydrate saturation conditions, using mini pressure cells, to determine critical gas hydrate saturation. Their results indicated that it is necessary to carry out a numerical simulation in connection with the experiments to determine the critical gas hydrate saturation at numerous conditions that could not be incorporated into the experiments. In this study, a numerical simulation model, which simulated a mini pressure cell, was developed to verify the results of the aforementioned experiments. The changes in the fluid density and computer tomography values showed a similar trend. The validated numerical simulation model was used to determine the

dissociation behaviors and productivities for various gas hydrate saturation levels (10?80%). As the gas hydrate saturation increased, the fluid permeability decreased. The gas hydrate dissociation was slowed by this correlation, and the production of gas and water was delayed at 50?60% gas hydrate saturation. Thus, the critical gas hydrate saturation was determined to be 50-60% for the experimental conditions of the field production test at the Ulleung Basin, East Sea, Korea. A pressure difference was noticed between the production and injection points due to the pressure propagation being delayed at critical gas hydrate saturation. Verifying the results of the experiments proved useful to understanding the dissociation and multiphase flow patterns in various depressurization scenarios.

Giorio, C., Bortolini, C., Kourtchev, I., Tapparo, A., Bogialli, S., Kalberer, M., 2019. Direct target and non-target analysis of urban aerosol sample extracts using atmospheric pressure photoionisation high-resolution mass spectrometry. Chemosphere 224, 786-795.


Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous atmospheric pollutants of high concern for public health. In the atmosphere they undergo oxidation, mainly through reactions with ·OH and NOx to produce nitro- and oxygenated (oxy-) derivatives. In this study, we developed a new method for the detection of particle-bound PAHs, nitro-PAHs and oxy-PAHs using direct infusion into an atmospheric pressure photoionisation high-resolution mass spectrometer (APPI-HRMS). Method optimisation was done by testing different source temperatures, gas flow rates, mobile phases and dopants. Samples were extracted with methanol, concentrated by evaporation and directly infused in the APPI source after adding toluene as dopant. Acquisition was performed in both polarity modes. The method was applied to target analysis of seasonal PM2.5 samples from an urban background site in Padua (Italy), in the Po Valley, in which a series of PAHs, nitro- and oxy-PAHs were detected. APPI-HRMS was then used for non-target analysis of seasonal PM2.5 samples and results compared with nano-electrospray ionisation (nanoESI) HRMS. The results showed that, when samples were characterised by highly oxidised organic compounds, including S-containing compounds, like in summer samples, APPI did not bring any additional information with respect to nanoESI in negative polarity (nanoESI(-)). Conversely, for winter samples, APPI(-) could detect a series of aromatic and poly-aromatic compounds, mainly oxidised and nitrogenated aromatics, that were not otherwise detected with nanoESI.

Godfray, G., Seetharamaiah, J., 2019. Geochemical and well logs evaluation of the Triassic source rocks of the Mandawa basin, SE Tanzania: Implication on richness and hydrocarbon generation potential. Journal of African Earth Sciences 153, 9-16.


Selected core and cutting samples from the Triassic succession of the Mbuo claystone and the Nondwa shale were collected from the Mandawa-7, Mbuo-1 and Mbate-1 wells, onshore Mandawa basin, to understand the hydrocarbon generation potential. Earlier studies show that Mbuo claystone and Nondwa shale source rocks have fair to good generation potential based on percent total organic carbon (TOC) with kerogen type II/III, but no detailed studies include the potential for hydrocarbon generation from Triassic source rocks in the Mandawa basin. Detailed parameters like TOC, level of organic maturity (LOM), net to gross (NTG) ratio and integrated geochemical and well log analysis approaches are applied to understand the generation potential of the Triassic source rocks. The results show that TOC derived from well log analysis ranges from 0.01 to 11 wt percent (wt%), clearly including fair to good average TOC values with less than 0.5 NTG for both the Mbuo claystone and the Nondwa shales using a marginal cut-off value of 0.5 wt% TOC. The S1 and S2 values range from

0.1 to 1.7mgHC/g Rock and 1.2–17.2mgHC/g Rock respectively. The cross plot between TOC and S1 and S2 values from Rock Eval shows that these source rocks have low potential for hydrocarbon generation, and that S1 and S2 are independent to the thermal maturity. Integrating results obtained from various studies shows that both Mbuo claystone and Nondwa shales in the Mbate-1 and Mandawa-7 wells have poor hydrocarbon generation potential in their respective organic-rich intervals.

Golsanami, N., Sun, J., Liu, Y., Yan, W., Chen, L., Jiang, L., Dong, H., Zong, C., Wang, H., 2019. Distinguishing fractures from matrix pores based on the practical application of rock physics inversion and NMR data: A case study from an unconventional coal reservoir in China. Journal of Natural Gas Science and Engineering 65, 145-167.


Our main scheme in this study was distinguishing between fracture porosity and matrix porosity in coalbed methane reservoirs through a novel approach which is the joint usage of NMR transverse relaxation (T2) measurements and rock physics modeling based on Levenberg-Marquardt (LM) algorithm. For this purpose, NMR T2 relaxation curves of 34 water-saturated coal samples, prepared and processed in the laboratory, were measured and the pore size distribution inside them was investigated. Subsequently, matrix and fracture porosity were separated based on the threshold T2 relaxation time (90–110 ms) which was achieved through our particularly designed fracturing experiments (this is different from the common T2 cutoff). The T2 measurements were performed in the laboratory using our NMR machine. After that, a rock physics scheme based on Levenberg-Marquardt algorithm was applied to independently estimate matrix porosity and fracture porosity from the samples' statistic mechanical properties including compressional wave velocity (Vp), shear wave velocity (Vs), bulk modulus (K), shear modulus (G), Young's modulus (E), and Poisson's ratio (ν) which were all carefully measured in the laboratory. Afterward, both types of the abovementioned porosities were comprehensively characterized and the obtained achievements were listed. Once finished with this step, the 3D structure of the entire reservoir was extracted using the recorded data inside 32 drilled wells, and then the established models were upscaled and the unique and independent contour maps of fracture porosity and matrix pore porosity were drawn over the entire reservoir area.

The proposed novel approach provides the kind of information about fractures of the media which is not obtainable with either of NMR or rock physics methods when they are used individually. This study established a novel discussion investigating application of rock physics relationships in order to determine fracture porosity of the coal reservoirs. The approach was used to successfully investigate and characterize pore-only porosity and fracture-only porosity of a coalbed methane reservoir. According to the obtained results, joint usage of rock physics modeling and LM algorithm would be considered as a reliable technique in quick or deeper exploration of unconventional coal reservoirs.



Algal-derived dissolved organic matter (ADOM) originating from lysed Microcystis aeruginosa cells was investigated as precursor material to form disinfection by-products upon disinfection with free chlorine. Non-targeted ultrahigh resolution 12 Tesla negative mode electrospray ionization Fourier

transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed high molecular diversity in solid-phase extracted and ionizable components of Microcystis aeruginosa ADOM. The toxin microcystin LR was effectively degraded by free chlorine, which was expected. However, we found a high diversity of disinfection by-products associated with the addition of free chlorine to the water-soluble and solid-phase extractable fraction of ADOM and of double-bond moieties in abundant and known unsaturated fatty acids. Aromatic DOM precursors were absent from known metabolites of Microcystis aeruginosa and no evidence for aromatic disinfection by-products (DBPs) was found, despite N-containing compounds. A large diversification of N-containing molecular formulas was observed after chlorination, which seems indicative for the breakdown and oxidation of larger peptides. Additionally, a diverse group of N-compounds with presumed chloramine functional groups was observed. This study highlights the importance to evaluate ADOM and its ability to form different DBPs when compared to allochthonous or terrestrially-derived DOM.

González-Nicolás, A., Cihan, A., Petrusak, R., Zhou, Q., Trautz, R., Riestenberg, D., Godec, M., Birkholzer, J.T., 2019. Pressure management via brine extraction in geological CO2 storage: Adaptive optimization strategies under poorly characterized reservoir conditions. International Journal of Greenhouse Gas Control 83, 176-185.


Industrial-scale injection of CO2 into the subsurface increases the fluid pressure in the reservoir, which if not properly controlled can potentially lead to geomechanical damage (i.e., fracturing of the caprock or reactivation of faults) and subsequent CO2 leakage. Brine extraction is one approach for managing formation pressure, effective stress, and plume movement in response to CO2 injection. The management of the extracted brine can be expensive (i.e., due to transportation, treatment, disposal, or re-injection), with added cost to the carbon capture and sequestration (CCS); thus, minimizing the volume of extraction brine is of great importance to ensure that the economics of CCS are favorable. The main objective of this study is to demonstrate the use of adaptive optimization methods in the planning of brine extraction and to investigate how the quality of initial site characterization data and the use of newly acquired monitoring data (e.g. pressure at observation wells) impact the optimization performance. We apply an adaptive management approach that integrates monitoring, calibration, and optimization of brine extraction rates to achieve pre-defined pressure constraints. Our results show that reservoir pressure management can be extremely benefited by early and high frequency pressure monitoring during early injection times, especially for poor initial reservoir characterization. Low frequencies of model calibration and optimization with monitoring data may lead to optimization problems because either pressure buildup constraints are violated or excessively high extraction rates are proposed. The adaptive pressure management approach may constitute an effective tool to manage pressure buildup under uncertain reservoir conditions by minimizing the volumes of extracted brine while controlling pressure buildup.

Goodarzi, F., Haeri-Ardakani, O., Gentzis, T., Pedersen, P.K., 2019. Organic petrology and geochemistry of Tournaisian-age Albert Formation oil shales, New Brunswick, Canada. International Journal of Coal Geology 205, 43-57.


Lacustrine oil shale and shale samples of the Tournaisian-age Albert Formation in New Brunswick, Canada, taken from six locations, were analyzed by organic petrology using reflected white and fluorescence light microscopy and by Rock-Eval pyrolysis to determine their depositional environment and hydrocarbon generating potential. Calcium, Th, and Ca contents of the samples were

also determined using ICPMS. The results were compared to the Big Marsh lacustrine oil shale of Carboniferous age in Nova Scotia.

Organic matter consists mostly of filamentous alginite, bacterial remains, and matrix bituminite, which fluoresce green to dark-yellow. Organic matter was deposited in a lake basin. The regular layering of algal remains and wrapping around mineral particles indicate deposition in a low energy setting below wave base, which resulted in the stratification of the organic matter and the enclosing mineral matrix. There are also fluorescing to non-fluorescing bitumens present in parts of the Albert oil shale. The bitumens were incorporated as a result of hydrocarbon migration during deposition of the oil shales (the two are considered to be syn-sedimentary) because the bitumens are part of the regular rock layering and the fact that the organic matter is wrapped around mineral grains. The bitumens in the Albert oil shales consist of fluorescing wurtzilite and non-fluorescing albertite.

The Albert oil shales have lower input of terrestrial sediments containing Th and are carbonate-rich. The variation of Th/U ratio and TOC (wt%) indicates that the Albert oil shales have different mineralogy than those from the Big Marsh ones. There are two types of carbonates particles in the Albert oil shale; a) syngenetic angular particles, which are suspended in the organic matter but may also occur as micrite, and b) rounded to angular and possibly transported particles containing oil inclusions. As a result, variations in Th/U and calcium divided the oil shales into: a low-calcium lacustrine type (which includes the Big Marsh oil shale); the Albert oil shale and shale deposited far from the Albert Mine; and few samples from a deposit close to the Albert Mine that have high calcium content and some of them contained oil inclusions. The higher TOC of samples collected from the bitumen mining area in the Albert Mine is related to bitumen impregnation due to hydrocarbon migration. Variation of HI (mg HC/g/TOC) and authigenic uranium in the Albert oil shale indicates that depositional environment was more anoxic than most of the oil shales in the Big Marsh deposit.

Rock-Eval pyrolysis data and accompanying organic petrology analysis indicate that the samples are mostly immature to marginally mature as indicated by %Ro, ran of 0.60–0.68 and variation in the fluorescence Red/Green and Blue/Green and Blue (R/G, B/G, B) quotients. Variations in maturity indicators (such as HI and Tmax) are caused by other factors, such as quantity of organic matter in the samples. The Hydrogen Index (HI) vs. Tmax plot of the oil shales displays a wide range of HI within a narrow Tmax range of 438–442 °C indicating immature to marginally mature Type I kerogen. There is a slight trend of increasing Tmax into the oil window with increasing HI, likely due to the extreme mass of hydrocarbons in these samples, which requires higher energy to breakdown, rather than burial-related thermal maturity. Maturity of the Albert oil shale increases from east to west within the study area as indicated by the westward increase of all three fluorescent quotients of both filamentous algae and matrix bituminite and in the %Ro. The reflectance of the Albert oil shales, measured on vitrinite, is mostly suppressed compared to the nearby Mapleton organic-lean shale in New Brunswick. There is also a correlation between HI and %Ro, ran in the oil shale samples studied; the higher is the HI, the lower is the %Ro.

The majority of the oil shale samples have a very high potential for hydrocarbon extraction using the ex-situ methodology (at 30 L/t) and the upper 20% of the samples have the potential for in-situ extraction (at 60 L/t).

Gray, D.A., Dugar, G., Gamba, P., Strahl, H., Jonker, M.J., Hamoen, L.W., 2019. Extreme slow growth as alternative strategy to survive deep starvation in bacteria. Nature Communications 10, Article 890.

https://doi.org/10.1038/s41467-019-08719-8

Bacteria can become dormant or form spores when they are starved for nutrients. Here, we find that non-sporulating Bacillus subtilis cells can survive deep starvation conditions for many months. During this period, cells adopt an almost coccoid shape and become tolerant to antibiotics. Unexpectedly, these cells appear to be metabolically active and show a transcriptome profile very different from that of stationary phase cells. We show that these starved cells are not dormant but are growing and dividing, albeit with a doubling time close to 4 days. Very low nutrient levels, comparable to 10,000-fold diluted lysogeny broth (LB), are sufficient to sustain this growth. This extreme slow growth, which we propose to call ‘oligotrophic growth state’, provides an alternative strategy for B. subtilis to endure nutrient depletion and environmental stresses. Further work is warranted to test whether this state can be found in other bacterial species to survive deep starvation conditions.

Grubel, K., Chouyyok, W., Heldebrant, D.J., Linehan, J.C., Bays, J.T., 2019. Octane-on-demand: Onboard separation of oxygenates from gasoline. Energy & Fuels 33, 1869-1881.


Increasing numbers of standards for emissions and fuel economy drive the need to downsize spark ignition internal combustion engines. To accommodate this change while reducing engine knock, fuels with higher octane numbers are needed. However, studies have shown that octane requirements are not uniform across the vehicle drive cycle, leading to inefficient use of the high-octane fuel components. One approach shown to substantially increase fuel economy through the efficient use of high-octane fuel components is a dual-fuel solution called octane-on-demand. Octane-on-demand supplies fuel that has the required octane rating, as dictated by the engine torque demands, by delivering the proper ratio of high- and low-octane fuels. Barriers associated with introducing two fuels in the marketplace for an octane-on-demand approach can be overcome using an onboard separation system to separate a single fuel, such as a market E10 gasoline, into a high-octane oxygenate, such as ethanol, and a lower-octane base fuel. Onboard separation systems currently under evaluation rely on pervaporation membranes, which lose efficiency as the oxygenate is removed, leading to inefficient use of this valuable fuel component. Here, we present liquid–solid and liquid–liquid chemical separation strategies that may provide advantages over membrane separation. This paper introduces applications of tailored chemical reactions, solid sorbent materials, and ionic liquids that are shown to have a high oxygenate recovery and utility beyond ethanol to potential future oxygenate additives, such as isomers of butanol.

Gruber, N., Clement, D., Carter, B.R., Feely, R.A., van Heuven, S., Hoppema, M., Ishii, M., Key, R.M., Kozyr, A., Lauvset, S.K., Lo Monaco, C., Mathis, J.T., Murata, A., Olsen, A., Perez, F.F., Sabine, C.L., Tanhua, T., Wanninkhof, R., 2019. The oceanic sink for anthropogenic CO2 from 1994 to 2007. Science 363, 1193-1199.


Abstract: We quantify the oceanic sink for anthropogenic carbon dioxide (CO2) over the period 1994 to 2007 by using observations from the global repeat hydrography program and contrasting them to observations from the 1990s. Using a linear regression–based method, we find a global increase in the anthropogenic CO2 inventory of 34 ± 4 petagrams of carbon (Pg C) between 1994 and 2007. This is equivalent to an average uptake rate of 2.6 ± 0.3 Pg C year−1 and represents 31 ± 4% of the global anthropogenic CO2 emissions over this period. Although this global ocean sink estimate is consistent with the expectation of the ocean uptake having increased in proportion to the rise in atmospheric

CO2, substantial regional differences in storage rate are found, likely owing to climate variability–driven changes in ocean circulation.

Editors's summary: The state of ocean CO2 uptake. The ocean is an important sink for anthropogenic CO2 and has absorbed roughly 30% of our emissions between the beginning of the industrial revolution and the mid-1990s. This effect is an important moderator of climate change, but can we count on it to remain as strong in the future? Gruber et al. calculated the ocean uptake of anthropogenic CO2 for the interval from 1994 to 2007, which continued as expected. They also observed clear regional deviations from this pattern, suggesting that there is no guarantee that uptake will remain as robust with time.

Guan, H., Xu, L., Wang, Q., Chen, D., Wu, N., Mao, S., 2019. Lipid biomarkers and their stable carbon isotopes in ancient seep carbonates from SW Taiwan, China. Acta Geologica Sinica - English Edition 93, 167-174.

https://doi.org/10.1111/1755-6724.13772

Four massive brecciated, chimney‐like, and slender pipe network carbonate samples (JA‐4, JA‐5, JX‐8 and BG‐12) were collected from southwestern Taiwan, which were suggested to have formed as a result of anaerobic oxidization of methane (AOM). Considering that the environmental conditions of the carbonates precipitation and the sources of carbon and organic matter need to be further declared, molecular fossils and compound‐specific carbon isotopic investigations of the carbonates were conducted in this study. According to lipid biomarkers of 2,6,10,15,19‐pentamethyleicosane (PMI) and squalane diagnostic to methanotrophic archaea, as well as the extremely low δ13C values (as low as –113.4‰) detected in samples JA‐4, JA‐5 and JX‐8, these carbonates were revealed to be a result of AOM. Based on the varied δ13C values of characteristic archaea biomarkers in specific samples, biogenic methane was proposed to be responsible for the formation of samples JA‐4 and JA‐5, whereas a mixed carbon source of 13C‐depleted methane and 13C‐enriched residual CO2 from methanogenesis was suggested for the carbonate of JX‐8 due to the co‐occurrence of a highly positive δ13Ccarb value (+8‰) and a moderate 13C depletion of PMI. The low content of AOM‐related biomarkers and the absence of indicators for ANME‐2 suggested that these carbonates were formed in weak seep settings. By comparison, no typical lipid biomarkers for methanotrophic archaea was detected in carbonate BG‐12. The short‐chain and long‐chain n‐alkanes accounted for 30% and 45% of all hydrocarbons, respectively, with a CPI value of 1.2, suggesting that the n‐alkanes were derived from both marine organisms and terrestrial inputs. A low thermal maturity could be revealed by the incomplete equilibrium value of the C31αβ 22S/(22S+22R) ratio (0.5), and the carbonate BG‐12 was probably deposited in a suboxic condition indicated by a value of Pr/Ph ratio (2.5).

Guo, K., Lv, Y., He, L., Luo, X., Yang, D., 2019. Separation characteristics of water-in-oil emulsion under the coupling of electric field and magnetic field. Energy & Fuels 33, 2565-2574.


In order to reveal the dehydration mechanism under the coupling of an electric field and a magnetic field, the dehydration rate of water-in-oil emulsions was tested after the treatment by a rapid evaluation experiment system, where an electric field and a magnetic field could be generated synchronously. The main factors that cause the coupling action were analyzed quantitatively. The results showed that the single steady magnetic field had no obvious effect on dehydration of

emulsions. However, the dehydration rate of emulsions in the coupling field of the ac electric field and the steady magnetic field was superior to that of the single ac electric field, and the increase of particle size of the dispersed phase was conducive to improving the dehydration efficiency. For the coupling effect of the dc electric field and the steady magnetic field, the dehydration rate had no obvious improvement compared with the single dc electric field. Moreover, the calculation results showed that the polarization–magnetism force generated by transient polarization was the main factor for the efficient separation of oil and water under the coupling field of the ac electric field and the steady magnetic field.

Guo, Q., Yu, J., Zhao, Y., Liu, T., Su, M., Jia, Z., Zhao, Y., Mu, Z., Yang, M., 2019. Identification of fishy odor causing compounds produced by Ochromonas sp. and Cryptomonas ovate with gas chromatography-olfactometry and comprehensive two-dimensional gas chromatography. Science of The Total Environment 671, 149-156.


Disgusting fishy odor problems have become a major concern in drinking water quality, and are commonly related to algal proliferation in source water. Unlike the typical musty/earthy odorants 2-methylisoborneol (MIB) and geosmin, identification of the corresponding fishy odorants is still a big challenge. In this study, two species of fishy-odor-producing algae, Ochromonas sp. and Cryptomonas ovate, were cultured to explore the odor production characteristics and typical odorants. When algae were ruptured in the stationary and decline phases, fishy odor intensities of 4 to 8 characterized by FPA were produced. However, some frequently reported aldehydes that could cause fishy odor, including n-hexanal, 2-octenal, heptanal, 2,4-heptanal and 2,4-decadienal, were not detected in either of the cultured algae. The possible fishy odor-causing compounds were further identified by combining gas chromatography-olfactometry (GC-O/MS) and comprehensive two-dimensional gas chromatography (GC × GC-TOFMS) using retention indices (RIs). From GC-O/MS analysis, twelve and six olfactometry peaks with various odor characteristics were identified in Ochromonas sp. and Cryptomonas ovate, respectively, of which three and two olfactometry peaks showed fishy odor characteristics. 2-Nonenal, 2,4-octadienal, fluorene and 2-tetradecanone were identified as fishy odorants in Ochromonas sp., and 1-octen-3-ol, 6-methyl-5-hepten-2-one, 1-octen-3-one, 2-nonenal and 2,4-octadienal were identified in Cryptomonas ovate. Other identified compounds, including butyl butanoate (fragrant odor), ionone (fragrant odor), bis (2-chloroisopropyl) ether (chemical odor) etc., did not show fishy features. Therefore, the fishy odor might be a synthetic and comprehensive odor, which resulted from the combination of different odorants and their synergistic effects. The results of this study will be helpful for understanding fishy odor problems, which will provide support for fishy odor management and control in the drinking water industry.

Guo, X., Wang, J., 2019. The chemical behaviors of microplastics in marine environment: A review. Marine Pollution Bulletin 142, 1-14.


Microplastics are widely existed in marine and coastal environments, which aroused global concern in recent years. This review mainly summarized the interactions of organic pollutants and metals with microplastics based on environmental monitoring results and laboratory results reported by literatures. Firstly, the type, properties, and distribution of microplastics in the environment were briefly reviewed. Secondly, the property changes of microplastics after degradation were discussed. Thirdly, the concentrations of pollutants on microplastics in global environments were summarized. Then the effect of the factors (e.g. types and properties of microplastics, types of pollutants, and

environmental conditions) on the sorption behaviors of microplastics were discussed in detail. Finally, the influences of microplastics on marine organisms were briefly evaluated.

Guzman, M.S., Rengasamy, K., Binkley, M.M., Jones, C., Ranaivoarisoa, T.O., Singh, R., Fike, D.A., Meacham, J.M., Bose, A., 2019. Phototrophic extracellular electron uptake is linked to carbon dioxide fixation in the bacterium Rhodopseudomonas palustris. Nature Communications 10, Article 1355.

https://doi.org/10.1038/s41467-019-09377-6

Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. EEU is performed by prevalent phototrophic bacterial genera, but the electron transfer pathways and the physiological electron sinks are poorly understood. Here we show that electrons enter the photosynthetic electron transport chain during EEU in the phototrophic bacterium Rhodopseudomonas palustris TIE-1. Cathodic electron flow is also correlated with a highly reducing intracellular redox environment. We show that reducing equivalents are used for carbon dioxide (CO2) fixation, which is the primary electron sink. Deletion of the genes encoding ruBisCO (the CO2-fixing enzyme of the Calvin-Benson-Bassham cycle) leads to a 90% reduction in EEU. This work shows that phototrophs can directly use solid-phase conductive substances for electron transfer, energy transduction, and CO2 fixation.

Haeusler, M., Trinkaus, E., Fornai, C., Müller, J., Bonneau, N., Boeni, T., Frater, N., 2019. Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal. Proceedings of the National Academy of Sciences 116, 4923-4927.


Significance: Fully upright and balanced posture is one of the hallmarks of humanity, and it has long been seen as present among all members of the genus Homo. However, recent considerations of Neandertal vertebrae have concluded that these late archaic humans, who were both behaviorally and phylogenetically close to ourselves, lacked fully developed spinal curvatures and must therefore have had precarious postures. Reassessment and virtual reconstruction of the La Chapelle-aux-Saints 1 Neandertal skeletal remains provides direct anatomical evidence that he, and by extension other Neandertals, possessed the usual human lower back and neck curvature (lordosis). It is therefore time to move beyond making Neandertals less human and focus on the subtle shifts in Late Pleistocene human biology and behavior.

Abstract: Although the early postural reconstructions of the Neandertals as incompletely erect were rejected half a century ago, recent studies of Neandertal vertebral remains have inferred a hypolordotic, flat lower back and spinal imbalance for them, including the La Chapelle-aux-Saints 1 skeleton. These studies form part of a persistent trend to view the Neandertals as less “human” than ourselves despite growing evidence for little if any differences in basic functional anatomy and behavioral capabilities. We have therefore reassessed the spinal posture of La Chapelle-aux-Saints 1 using a new pelvic reconstruction to infer lumbar lordosis, interarticulation of lower lumbar (L4-S1) and cervical (C4-T2) vertebrae, and consideration of his widespread age-related osteoarthritis. La Chapelle-aux-Saints 1 exhibits a pelvic incidence (and hence lumbar lordosis) similar to modern humans, articulation of lumbar and cervical vertebrae indicating pronounced lordosis, and Baastrup disease as a product of his advanced age, osteoarthritis, and lordosis. Our findings challenge the view of generally small spinal curvatures in Neandertals. Setting aside the developmentally abnormal

Kebara 2 vertebral column, La Chapelle-aux-Saints 1 is joined by other Neandertals with sufficient vertebral remains in providing them with a fully upright (and human) axial posture.

Hakimi, M.H., Alaug, A.S., Al Faifi, H.J., Alramisy, G.A., Lashin, A.A., 2019. Late Jurassic Safer Salt Member in the Al-Jawf sub-basin of NW Sabatayn Basin, Yemen: geochemical evaluation of organic-rich oil-source rock potential. Petroleum Science and Technology 37, 645-654.

https://doi.org/10.1080/10916466.2018.1560325

Late Jurassic Safer shales in the Al-Jawf sub-basin are analyzed to evaluate the organic matter input, depositional conditions and petroleum generation potential. The shales have high organic matter, with TOC values of 1.0-13.5% and they contain predominantly Types II and III kerogen, referring to mainly oil- and gas-prone. These kerogens are indicative for dominate marine algal component and some terrestrial organic matter input as indicated from biomarkers. Moreover, the presence of the gammacerane also confirmed a high salinity stratification condition and suggests that the dominate Type II kerogen is rich-sulphur kerogen (Type II-S). The vitrinite reflectance (VRo%) and Rock-Eval pyrolysis Tmax data indicate that the analyzed shales are immature.

Hakimi, M.H., Alaug, A.S., Alramisy, G.A., Ahmed, A.F., 2019. Petroleum that has migrated into an outcropping of the Jurassic Ayad Salt Dome of Shabwah depression, Yemen. Petroleum Science and Technology 37, 296-304.

https://doi.org/10.1080/10916466.2018.1542441

Two oil seep samples were collected from outcropping Jurassic Ayad Salt Dome of Shabwah depression. The results of this study have been used to provide information of the origin of the oil seeps and the type of organic matter and maturity of their potential source rock in the basin. Although these are surface oil seeps, their high saturated hydrocarbon content indicates that they are non-degraded oils, probably due to an arid environment of the thick salt sediments. The analyzed oil seep samples are characterized by full complement of n-alkanes, a very high component of phytane, relatively low CPIs of less than unity, and an unusually high content of aliphatic HCs. These features suggest that the analyzed oil seeps are generated from an algal marine organic matter in the source rock that deposited under highly anoxic hypersaline conditions and indicate a moderately low level of maturity. The geochemical characteristics of the analyzed oil seeps in this study are similar and consistent with the source rock characteristics of the Safer Member in the Sabatayn Basin.

Hakimi, M.H., Alaug, A.S., Mohialdeen, I.M.J., Kahal, A.Y., Abdulelah, H., Hadad, Y.T., Yahya, M.M.A., 2019. Late Jurassic Arwa Member in south-eastern Al-Jawf sub-basin, NW Sabatayn Basin of Yemen: Geochemistry and basin modeling reveal shale-gas potential. Journal of Natural Gas Science and Engineering 64, 133-151.


The current study evaluated the source rock characteristics, thickness, and lithology of the Late Jurassic Arwa Member to provide information about both conventional and unconventional resource systems in the Al-Jawf sub-basin. Three exploratory wells in the south-eastern portion of the Al-Jawf sub-basin were used for the source rock geochemistry and basin modeling study. Results from the geochemical and basin modeling indicate that the Arwa Member is a self contained source-reservoir whose shales are considered as gas-prone source rocks, and have generated large amounts of thermogenic gas through secondary cracking of oils at high thermal maturity levels. The geochemical

results reveal that the Arwa shales currently contain Type III and IV kerogen in a gas-window maturity stage and are shale-gas resources. The basin models illustrate that the late Jurassic to early Miocene age was the peak-oil generation window of the Arwa shale source rock, with a transformation ratio (TR) of 10–85%. Most of the oil was expelled along micro-fractures caused by the pressure of oil generated within the Arwa shales, which was then trapped in the carbonate reservoir rocks within the Arwa Member itself. The oil retained in the Arwa carbonate rocks was partially and/or completely cracked into gas between the early Miocene and the present-day. This thermogenic gas was generated due to high thermal maturity caused by Tertiary volcanic rocks. Assuming a thickness of 360–1590 m and partial and/or complete cracking of retained oil to gas, the Arwa Shale Member could have a huge gas-generation potential.

Halloran, L.J.S., Brunner, P., Hunkeler, D., 2019. COMPEST, a PEST-COMSOL interface for inverse multiphysics modelling: Development and application to isotopic fractionation of groundwater contaminants. Computers & Geosciences 126, 107-119.


In the geosciences, inverse problems, wherein observations corresponding to model outputs are known and model parameters are unknown, are commonplace. Many of these problems involve coupled physical, chemical, and other processes that can be modelled using forward finite-element models. Here, we present a novel interface, COMPEST, that connects the parameter estimation and uncertainty analysis package, PEST, with the finite-element modelling package, COMSOL Multiphysics. To demonstrate some of the capabilities of this approach, we also develop and present a novel model for the degradation and transport of chlorohydrocarbons in low-permeability units. This model integrates isotopic fractionation arising from degradation and diffusion. Three implementations of this model with increasing complexity are used to demonstrate the functionality of the developed interface. This linkage provides a means for parameter estimation, uncertainty analysis, and singular value decomposition to gain insight into the behaviour, identifiability, and interdependence of the various parameters in the model. COMPEST is written so as to be suited to a wide range of scientific and engineering applications and thus can be used to link any COMSOL model with PEST. This enables the use of advanced inverse modelling techniques previously unavailable to COMSOL users.

Hameed, S., Sharma, A., Pareek, V., Wu, H., Yu, Y., 2019. A review on biomass pyrolysis models: Kinetic, network and mechanistic models. Biomass and Bioenergy 123, 104-122.


Pyrolysis converts biomass into liquid, gaseous and solid fuels. This work reviews the existing models for biomass pyrolysis, including kinetic, network and mechanistic models. The kinetic models are based on the global reaction mechanisms and have been extensively used for a wide range of biomass under various operating conditions. Major emphases have been on the network models as these models predict the structural changes during biomass pyrolysis. Key aspects of various network models include reaction schemes, structural characteristics and applications to CFD simulations. Recent advances in understanding reaction mechanisms using mechanistic models have been summarized. Importance of inherent inorganic species in biomass pyrolysis is also critically analysed. Future studies of biomass pyrolysis modelling should focus on developing multiscale models considering reactions of all biomass components (i.e., cellulose, hemicellulose, lignin, inorganic species and extractives) and potential interactions.

Hammershøj, R., Birch, H., Redman, A.D., Mayer, P., 2019. Mixture effects on biodegradation kinetics of hydrocarbons in surface water: Increasing concentrations inhibited degradation whereas multiple substrates did not. Environmental Science & Technology 53, 3087-3094.


Most biodegradation tests are conducted using single chemicals at high concentrations, although these chemicals are present in the environment as mixtures at low concentrations. A partitioning-based platform was recently developed for biodegradation testing of composed mixtures of hydrophobic chemicals at ng/L to μg/L concentrations. We used this platform to study the concentration and mixture effect on biodegradation kinetics. Biodegradation tests were conducted in 20 mL vials using environmental water samples as inocula. Passive dosing was applied (1) to vary initial test concentrations of individual test compounds and (2) to vary the number of mixture components between 1 and 16. Automated solid-phase microextraction coupled to gas chromatography–mass spectrometry was used to measure substrate depletion relative to abiotic controls. The number of mixture components had no or only a limited effect on the biodegradation half times for three compounds when tested at environmentally relevant concentrations. In contrast, longer lag phases and half lives were observed for single compounds when tested at higher concentrations that approached aqueous solubility. The obtained results support that simultaneous testing of multiple chemicals at low concentrations can accelerate the generation of biodegradation kinetic data, which are more environmentally relevant compared with data from tests conducted with single chemicals at much higher concentrations.

Han, B., Song, Z., Li, Q., Zheng, L., 2019. Evaluation of new diagnostic ratios of naphthalenes and fluorenes by identifying severely weathered oils collected in laboratory simulations and coastal weathering experiments. Archives of Environmental Contamination and Toxicology 76, 508-517.

https://doi.org/10.1007/s00244-018-0570-6

The composition and physical properties of spilled oil have great changes during the seriously weathering process. It brings great difficulties to the source identification of oil spill. So, the stable and trustworthy diagnostic ratios (DRs) for accurate identification of severely weathered spilled oils are very important. The explosion of Sinopec pipeline happened on November 22, 2013 at Qingdao, China. Local beaches at Jiaozhou Bay were polluted by spilled oils. We have collected original spilled oil samples from an area free from human interference near the oil leakage point after the accident. Synchronized with actual beach weathering, laboratory experiments were conducted to simulate oil weathering for 360 days by using the collected original spilled oil samples. Based on the t test and the repeatability limit method, 65 DRs of naphthalenes and fluorenes were screened. Fifteen DRs, namely, C2Nap/(C2Nap + C3Nap), C2Nap/(C2Nap + C4Nap), C2Nap/total Nap, C3Nap/(C3Nap + C4Nap), C3Nap/total Nap, C4Nap/total Nap, C2Flu/(C2Flu + C3Flu), C2Flu/total Flu, C2Nap/(C2Nap + Flu), C2Nap/(C2Nap + C1Flu), C2Nap/(C2Nap + C2Flu), C2Nap/(C2Nap + C3Flu), C3Nap/(C3Nap + Flu),C3Nap/(C3Nap + C1Flu), total Nap/(total Nap + total Flu), have maintained remarkable stability during the simulated weathering experiments and field weathering process. These stable ratios can retain the characteristics of oil source during weathering. They are very beneficial to improve the accuracy of identifying the source of severely weathered oil and can be used as an effective supplement to existing index system for source identification.



As one of the major hydrocarbon source rocks, deeply buried (4500–7000 m) Ordovician marine carbonates are important reservoir rocks in Tahe Oilfield, Tarim Basin, NW China. Most of the observed diagenetic features are genetically related to the meteoric water due to the multistage structural uplifts and subsequent paleo-exposure, weathering and erosion experienced by the carbonate strata. There is very limited study on the petrological and geochemical constraints on fluids types and formation mechanisms of the Ordovician carbonate reservoirs in this region. In order to investigate to the mechanism and characteristics of karstification, this paper integrated petrographic studies, elements and C, O, Sr isotopes geochemistry and fluid inclusions, and revealed the origin and types of diagenetic fluids, with which the dissolution and development of secondary porosity enhances reservoir properties of the Ordovician carbonates. Through this study, vugs and pores generated from epigenetic meteoric dissolution were observed to partially destroyed due to subsequent compaction, filling and cementation. Meteoric water, hydrothermal fluids and formation water are the three main types of diagenetic fluids in the Ordovician carbonate rocks of Tahe Oilfield. This paper investigated the values of key parameters related to perception, and figured out the precipitation types of calcites by methods of comparisons. Comparing to carbonate matrix, some calcite cements exhibit the features of relatively negative values of δ18O, a relatively wide range of δ13C, higher ratios of 87Sr/86Sr, and low to medium homogenization temperatures. These may indicate the precipitation of calcite cement from meteoric water. Respectively high ΣREE and obvious positive Eu anomaly, lower δ18O, higher δ13C value, higher 87Sr/86Sr ratios, combined with abnormal high homogenization temperatures of some calcites could confirm their precipitations from hydrothermal fluids. Respectively higher δ18O values and lower 87Sr/86Sr ratios of some calcite cements suggest their precipitations from formation water. The dissolution of meteoric water is the most important karstification and controlled by carbonic acid solution recharge conditions. Hydrothermal activity can promote the thermochemical sulfate reduction (TSR) and have certain dissolution ability. The paper established the models of meteoric water and hydrothermal fluids karstification. In practice, the results would work as a useful reference for the exploration of deeply burial carbonate reservoirs and hydrocarbon in carbonate strata of basins around the world.

Han, Y., John, G.F., Clement, T.P., 2019. Understanding the thermal degradation patterns of hopane biomarker compounds present in crude oil. Science of The Total Environment 667, 792-798.


In-situ burning (ISB) is a common oil spill response technique used for managing marine oil spills. The burnt residues generated from ISB can have several toxic compounds and therefore their impacts on aquatic ecosystem are of major environmental concern. When quantifying the fate of the toxic compounds in ISB residues, C30-αβ hopane is routinely used as a conservative biomarker since it has shown to be resistant to most natural weathering processes. However, a recent laboratory study has shown that C30-αβ and other hopane compounds have the potential to degrade when crude oil was physically burnt under controlled conditions. When crude oil is burnt, the temperature of the oil can raise up to 350–500 °C; however, so far, no one has studied the fate of hopanes when crude oil is simply heated to very high temperatures. In this study, we hypothesize that heating crude oil to very high temperatures would result in the degradation of hopane compounds. Results of our study show that C30-αβ hopane in crude oil will start to degrade at around 160 °C and the degradation pattern follows first order kinetics. Other types of hopanes and their diagnostic ratios can also change when the oil is exposed to severe heating conditions. We conclude that removal of hopane biomarkers via thermal degradation is a possible depletion pathway during ISB. Therefore, caution should be exercised when using hopanes as conservative biomarker compounds for characterizing ISB residues.

Hanson, A.J., Luek, J.L., Tummings, S.S., McLaughlin, M.C., Blotevogel, J., Mouser, P.J., 2019. High total dissolved solids in shale gas wastewater inhibit biodegradation of alkyl and nonylphenol ethoxylate surfactants. Science of The Total Environment 668, 1094-1103.


Hydraulic fracturing fluids are injected into unconventional oil and gas systems to stimulate hydrocarbon production, returning to the surface in flowback and produced waters containing a complex mixture of xenobiotic additives and geogenic compounds. Nonionic polyethoxylates are commonly added surfactants that act as weatherizers, emulsifiers, wetting agents, and corrosion inhibitors in hydraulic fracturing fluid formulations. Understanding the biodegradability of these ubiquitous additives is critical for produced water pre-treatment prior to reuse and for improving treatment trains for external beneficial reuse. The objective of this study was to determine the effect of produced water total dissolved solids (TDS) from an unconventional natural gas well on the aerobic biodegradation of alkyl ethoxylate and nonylphenol ethoxylate surfactants. Changes in surfactant concentrations, speciation and metabolites, as well as microbial community composition and activity were quantified over a 75-day aerobic incubation period. Alkyl ethoxylates (AEOs) were degraded faster than nonylphenol ethoxylates (NPEOs), and both compound classes and bulk organic carbon biodegraded slower in TDS treatments (10 g L−1, 40 g L−1) as compared to controls. Short-chain ethoxylates were more rapidly biodegraded than longer-chain ethoxylates, and changes in the relative abundance of metabolites including acetone, alcohols, and carboxylate and aldehyde intermediates of alkyl units indicated metabolic pathways may shift in the presence of higher produced water TDS. Our key finding that polyethoxylated alcohol surfactant additives are less labile at high TDS has important implications for produced water management, as these fluids are increasingly recycled for beneficial reuse in hydraulic fracturing fluids and other purposes.

Hanson, C.A., Müller, A.L., Loy, A., Dona, C., Appel, R., Jørgensen, B.B., Hubert, C.R.J., 2019. Historical factors associated with past environments influence the biogeography of thermophilic endospores in Arctic marine sediments. Frontiers in Microbiology 10, 245. doi: 210.3389/fmicb.2019.00245.


Selection by the local, contemporary environment plays a prominent role in shaping the biogeography of microbes. However, the importance of historical factors in microbial biogeography is more debatable. Historical factors include past ecological and evolutionary circumstances that may have influenced present-day microbial diversity, such as dispersal and past environmental conditions. Diverse thermophilic sulphate-reducing Desulfotomaculum are present as dormant endospores in marine sediments worldwide where temperatures are too low to support their growth. Therefore, they are dispersed to here from elsewhere, presumably a hot, anoxic habitat. While dispersal through ocean currents must influence their distribution in cold marine sediments, it is not clear whether even earlier historical factors, related to the source habitat where these organisms were once active, also have an effect. We investigated whether these historical factors may have influenced the diversity and distribution of thermophilic endospores by comparing their diversity in 10 Arctic fjord surface sediments. Although community composition varied spatially, clear biogeographic patterns were only evident at a high level of taxonomic resolution (>97% sequence similarity of the 16S rRNA gene) achieved with oligotyping. In particular, the diversity and distribution of oligotypes differed for the two most prominent OTUs (defined using a standard 97% similarity cutoff). One OTU was dominated by a single ubiquitous oligotype, while the other OTU consisted of ten more spatially localised oligotypes that decreased in compositional similarity with geographic distance. These

patterns are consistent with differences in historical factors that occurred when and where the taxa were once active, prior to sporulation. Further, the influence of history on biogeographic patterns was only revealed by analysing microdiversity within OTUs, suggesting that populations within standard OTU-level groupings do not necessarily share a common ecological and evolutionary history.

Hao, G., Shan, X., Li, F., Tong, L., Liu, Y., Wang, S., Zhang, J., Zhao, C., 2019. Characteristics of geochemistry and biodegradation for oil sand extracts in western slope of Songliao Basin Acta Petrolei Sinica 40, 308-321.

http://www.syxb-cps.com.cn/EN/abstract/abstract5643.shtml#

The degradation occurred to the crude oil in the migration process from central depression to the margin of Songliao Basin, thus forming the oil sand reservoir in the western slope, where the extracts of oil sand are non-liquid with high density and viscosity. In Taobao-Xiaotaipingshan-Xibeigou-Tumuji area along the migration direction, for the oil sand extracts in Upper Cretaceous Yaojia Formation, the content of saturated aromatic hydrocarbons decreases with the depth shallowing, the content of unsaturated asphaltene increases, the carbon isotopes of whole oil and saturated hydrocarbon become heavier. The parameters above present an opposite variation trend in the single-well samples of Xiaotaipingshan area. Based on GC-MS analysis, the degradation levels of oil sand extracts are Wenger 2-8, the n-alkanes and isoprenoid alkanes in saturated hydrocarbons of most samples are missing, hopanes are partially degraded, and 25-norhopanes are detected in Xiaotaipingshan area. With the decreasing of depth in Taobao-Tumuji area, the biodegradation levels increase gradually. Biomarkers parameters present regular variations, such as tricyclic terpane/pentacyclic triterpane, C27 diasteranes/regular sterane, dibenzothiophene/phenanthrene, and etc. In Xiaotaipingshan area, the mass fractions of 25-norhopanes and corresponding hopanes as well as their ratios present that the biodegradation levels increase with the increasing of depth, the degradation resistance of hopanes increase with the carbon number increasing, and 22R homohopanes have greater biodegradation resistance than 22S homohopanes. at the western slope of Songliao Basin, the degradation laws of oil sand extracts are as below: in the migration process from a deep anaerobic environment to a surface aerobic environment, the degradation level of oil sand extracts gradually increases with the increasing of depth and water saturation in the single-well sample.

Hart, M.B., Leighton, A.D., Hampton, M., Smart, C.W., 2019. Global bioevents and the Cretaceous/Paleogene boundary in Texas and Alabama: Stratigraphy, correlation and ocean acidification. Global and Planetary Change 175, 129-143.


With increasing levels of atmospheric pCO2 the oceans are becoming progressively more acidic, with the impact of a lowered pH beginning to affect the calcification of numerous invertebrate groups, including foraminifers, pteropods, heteropods and calcareous nannoplankton. Research on the ecology of foraminifera in the Mediterranean Sea, Gulf of California, Caribbean Sea and elsewhere has shown how modern assemblages are responding to acidification. Experimental work in mesocosms and laboratory cultures are also adding to our knowledge of the response to pH changes. Near Ischia (Italy), natural CO2 vents amongst sea grass meadows are creating low pH environments in which it is possible to observe the response of benthic foraminifera. At a pH of 7.8 the foraminiferal assemblages are already becoming less diverse and below pH 7.6 there are often no calcite-secreting benthic foraminifera. In the Gulf of California, in a deeper-water setting, natural CO2

(and methane) vents are also lowering sea floor pH. The foraminifera show the impact of this change, although the relatively high carbonate saturation ensures that calcite-secreting foraminifers are able to

live and reproduce in these relatively low pH environments, only becoming impacted by dissolution effects once dead. Using data from the Cretaceous–Paleogene boundary in Texas, Alabama and north-west Europe it is clear that the plankton was severely impacted by surface water acidification while the relatively shallow water benthic foraminifera show little change and no visible signs of post-mortem dissolution due to ocean acidification.

Hartnady, M.I.H., Kirkland, C.L., 2019. A gradual transition to plate tectonics on Earth between 3.2 to 2.7 billion years ago. Terra Nova 31, 129-134.

https://doi.org/10.1111/ter.12378

Zircon crystals precipitated from granitoid magmas contain a robust record of the age and chemistry of continental magmatism spanning some 4.375 Ga of Earth history, a record that charts initiation of plate tectonics. However, constraining when exactly plate tectonics began to dominate crustal growth processes is challenging as the geochemical signatures of individual rocks may reflect local subduction processes rather than global plate tectonics. Here we apply counting statistics to a global database of coupled U?Pb and Hf isotope analyses on magmatic zircon grains from continental igneous and sedimentary rocks to quantify changes in the compositions of their source rocks. The analysis reveals a globally significant change in the sources of granitoid magmas between 3.2 and 2.7 Ga. These secular changes in zircon chemistry are driven by a coupling of the deep (depleted mantle) and shallow (crustal) Earth reservoirs, consistent with a geodynamic regime dominated by Wilson cycle style plate tectonics.

Hasenfratz, A.P., Jaccard, S.L., Martínez-García, A., Sigman, D.M., Hodell, D.A., Vance, D., Bernasconi, S.M., Kleiven, H.F., Haumann, F.A., Haug, G.H., 2019. The residence time of Southern Ocean surface waters and the 100,000-year ice age cycle. Science 363, 1080-1084.


Abstract: From 1.25 million to 700,000 years ago, the ice age cycle deepened and lengthened from 41,000- to 100,000-year periodicity, a transition that remains unexplained. Using surface- and bottom-dwelling foraminifera from the Antarctic Zone of the Southern Ocean to reconstruct the deep-to-surface supply of water during the ice ages of the past 1.5 million years, we found that a reduction in deep water supply and a concomitant freshening of the surface ocean coincided with the emergence of the high-amplitude 100,000-year glacial cycle. We propose that this slowing of deep-to-surface circulation (i.e., a longer residence time for Antarctic surface waters) prolonged ice ages by allowing the Antarctic halocline to strengthen, which increased the resistance of the Antarctic upper water column to orbitally paced drivers of carbon dioxide release.

Editor's summary: Resetting the glacial timer. The periodicity of glacial cycles changed from 100,000 to 41,000 years during the middle of the Pleistocene epoch. Why? Hasenfratz et al. measured the oxygen isotope composition and magnesium/calcium ratio in benthic and planktonic foraminifera from the Antarctic in order to reconstruct changes in the rate of transfer of ocean water from the depths to the surface over the past 1.5 million years (see the Perspective by Menviel). The emergence of the 100,000-year cycle coincided with a reduction in deep-water supply and a freshening of the surface ocean. This slowing may have caused more prolonged ice ages by making the Antarctic less responsive to orbitally paced drivers of carbon dioxide release.


https://doi.org/10.1007/s00128-018-2518-y

Ten plant species were grown in constructed wetlands (CWs) to remediate water containing 2% (w/v) crude oil. The plant species with better growth and biomass production were Typha latifolia and Cyperus laevigatus, and they were significantly correlated (R2 = 0.91) with hydrocarbon degradation. From T. latifolia and C. laevigatus, 33 hydrocarbon-degrading bacterial strains were isolated from the rhizosphere, and root and shoot interiors. More diversified bacteria were found in the rhizosphere and endosphere of C. laevigatus than those of T. latifolia. The predominant cultural hydrocarbon-degrading bacteria were shown to belong to the genera Pseudomonas, Acinetobacter and Bacillus. In addition to genes involved in hydrocarbon degradation, most of the bacteria displayed multiple plant growth promoting (PGP) activities. This study suggests the importance of selecting suitable bacterial strains with hydrocarbon degradation and PGP activities for improving the efficacy of CWs used in remediating water contaminated with crude oil.

Hattori, K., Desrochers, A., Pedro, J., 2018. Provenance and depositional environment of organic-rich calcareous black shale of the Late Ordovician Macasty Formation, western Anticosti Basin, eastern Canada. Canadian Journal of Earth Sciences 56, 321-334.


The organic-rich Macasty shale in the Gulf of St. Lawrence was deposited in the Late Ordovician during the Taconic orogeny. The orogeny involved explosive volcanism and thrusting of allochthonous rocks in the eastern margin of North America. Neodymium isotope compositions of the shale show that the provenance is predominantly Grenvillian granite–gneissic rocks, which were widely exposed north of the basin, with little contribution from Taconic igneous rocks. The bulk composition and the presence of detrital kaolinite suggest that the Grenvillian source rocks underwent intense weathering before erosion. Fine-grained detritus was deposited in the Anticosti Basin, where abundant organic activity kept the sediment–water interface under anoxic conditions. This proposed interpretation is supported by the enrichment of redox-sensitive elements, such as As, V, and U, and by high δ34S for pyrite. Calcite cement formed in the pore space of sediments during the diagenesis at temperatures below 60 °C. The low-temperature diagenetic conditions are consistent with the preservation of abundant organic matter in the shale.

Hay, W.W., DeConto, R.M., de Boer, P., Flögel, S., Song, Y., Stepashko, A., 2019. Possible solutions to several enigmas of Cretaceous climate. International Journal of Earth Sciences 108, 587-620.

https://doi.org/10.1007/s00531-018-1670-2

The nature of the warm climates of the Cretaceous has been enigmatic since the first numerical climate models were run in the late 1970s. Quantitative simulations of the paleoclimate have consistently failed to agree with information from plant and animal fossils and climate sensitive sediments. The ‘cold continental interior paradox’ (first described by DeConto et al. in Barrera E, Johnson C (eds) Evolution of the Cretaceous Ocean/climate system, vol 332. Geological Society of America Special Paper, Boulder, pp 391–406, 1999), has been an enigma, with extensive continental interiors, especially in northeast Asia, modeled as below freezing in spite of plant and other evidence to the contrary. We reconsider the paleoelevations of specific areas, particularly along the

northeastern Siberian continental margin, where paleofloras indeed indicate higher temperatures than suggested by current climate models. Evidence for significant masses of ice on land during even the otherwise warmest times of the Cretaceous is solved by reinterpretation of the δ18O record of fossil plankton. The signal interpreted as an increase in ice volume on land is the same as the signal for an increase in the volume of groundwater reservoirs on land. The problem of a warm Arctic, where fossil floras indicate that they never experienced freezing conditions in winter, could not be solved by numerical simulations using higher CO2 equivalent greenhouse gas concentrations. We propose a solution by assuming that paleoelevations were less than today and that there were much more extensive wetlands (lakes, meandering rivers, swamps, bogs) on the continents than previously assumed. Using ~ 8 × CO2 equivalent greenhouse gas concentrations and assuming 50–75% water surfaces providing water vapor as a supplementary greenhouse gas on the continents reduces the meridional temperature gradients. Under these conditions the equatorial to polar region temperature gradients produce conditions compatible with fossil and sedimentological evidence.

He, W., Zhou, J., 2019. Structural features and formation conditions of mud diapirs in the Andaman Sea Basin. Geological Magazine 156, 659-668.

https://doi.org/10.1017/S0016756818000018

Data from offshore oil and gas explorations have revealed that mud diapirs occur widely not only at continental margins but also in foreland basins and may have played an important role in the entrapment of oil and gas. Although the structural features and formation mechanism of salt diapirs have been extensively investigated, mud diapirs are still not fully understood, largely due to the difficulty of identifying them from seismic data. In this paper, the structural features and main controlling factors of mud diapirs in the Andaman Sea Basin are investigated based on seismic profiles combined with drilling data and regional tectonic settings. The results show that there are five types of mud diapir in the Andaman Sea Basin: turtleback mud diapir, mud dome, piercing mud diapir, mud volcano and gas chimney-like mud diapir. Turtleback mud diapirs mainly occur in the southern segment of the accretionary wedge of the Andaman Sea Basin, which is far from the Bengal Fan and characterized by low deposition rate and strong compression tectonic setting. Piercing mud diapirs exist mainly in the central segment of the accretionary wedge, which is close to provenances of sediments and characterized by rapid sedimentation rates, large mudstone thickness and transpressional tectonic setting. Mud domes and mud volcanoes mainly occur in the northern segment of the accretionary wedge, which is characterized by rapid sedimentation rates, large mudstone thickness and sedimentary wedge growth tectonic setting. The gas chimney-like mud diapirs only occur in the northern segment of the back-arc depression close to the Sagaing strike-slip fault belt, which is characterized by high deposition rate, large mudstone thickness and high geothermal gradient. These features suggest that thick mudstone deposit, rapid sedimentation rates, large geothermal gradient, strong tectonic stress and gravitational spreading and sliding may have prompted the formation of mud diapirs in the Andaman Sea Basin.



Trichloromethane (TCM) is a frequently detected and persistent groundwater contaminant. Recent studies have reported that two closely related Dehalobacter strains (UNSWDHB and CF) transform TCM to dichloromethane, with inconsistent carbon isotope effects (ε13CUNSWDHB = −4.3 ± 0.45‰;

ε13CCF = −27.5 ± 0.9‰). This study uses dual element compound specific isotope analysis (C; Cl) to explore the underlying differences. TCM transformation experiments using strain CF revealed pronounced normal carbon and chlorine isotope effects (ε13CCF = −27.9 ± 1.7‰; ε13ClCF = −4.2 ± 0.2‰). In contrast, small carbon and unprecedented inverse chlorine isotope effects were observed for strain UNSWDHB (ε13CUNSWDHB = −3.1 ± 0.5‰; ε37ClUNSWDHB = 2.5 ± 0.3‰) leading to opposing dual element isotope slopes (λCF = 6.64 ± 0.14 vs λUNSWDHB = −1.20 ± 0.18). Isotope effects of strain CF were identical to experiments with TCM and Vitamin B12 (ε13CVitamin B12 = −26.0 ± 0.9‰, ε13ClVitamin B12 = −4.0 ± 0.2‰, λVitamin B12 = 6.46 ± 0.20). Comparison to previously reported isotope effects suggests outer-sphere-single-electron transfer or SN2 as possible underlying mechanisms. Cell suspension and cell free extract experiments with strain UNSWDHB were both unable to unmask the intrinsic KIE of the reductive dehalogenase (TmrA) suggesting that enzyme binding and/or mass-transfer into the periplasm were rate-limiting. Nondirected intermolecular interactions of TCM with cellular material were ruled out as reason for the inverse isotope effect by gas/water and gas/hexadecane partitioning experiments indicating specific, yet uncharacterized interactions must be operating prior to catalysis.

Heidbreder, L.M., Bablok, I., Drews, S., Menzel, C., 2019. Tackling the plastic problem: A review on perceptions, behaviors, and interventions. Science of The Total Environment 668, 1077-1093.


The excessive production and consumption of plastic has serious consequences on the environment and human health. The reduction of plastic has therefore become a major global challenge. As technical solutions might be insufficient to curb the problem, a perspective highlighting the impact of human behavior is needed. The current literature review provides an overview of the existing social-scientific literature on plastic, ranging from risk awareness, consumers' preferences, and predictors of usage behavior to political and psychological intervention strategies. By reviewing the literature, we aim to identify potential factors for future interventions to reduce plastic consumption. The 187 studies reviewed show that people much appreciate and routinely use plastic, despite a pronounced awareness of the associated problems. Habits, norms, and situational factors seem to be especially predictive for plastic consumption behavior. Both political and psychological interventions are potentially effective, although long-term effects are often uncertain. The review closes with implications for behavior-based solutions and future research, which should combine interdisciplinary approaches and take into account cultural differences.

Hennhoefer, D., Al Suwaidi, A., Bottini, C., Helja, E., Steuber, T., 2019. The Albian to Turonian carbon isotope record from the Shilaif Basin (United Arab Emirates) and its regional and intercontinental correlation. Sedimentology 66, 536-555.

https://doi.org/10.1111/sed.12493

The sedimentary record of the Arabian Shelf offers a unique opportunity to study the Cretaceous (Albian–Turonian) greenhouse climate from a palaeoequatorial perspective. In particular, hemipelagic to pelagic carbonate successions from the extensive Shilaif intra‐shelf basin have the potential to produce an excellent record of carbon cycle perturbations during this interval. This study presents a 269 m thick chemostratigraphic (carbonate δ13C and δ18O) record from the Middle Albian to Early Turonian of central Abu Dhabi (United Arab Emirates), representing over 14 Myr of uninterrupted carbonate sedimentation. The Mauddud to Shilaif formations represent outer ramp to basinal intra‐shelf carbonates with variations from laminated organic‐rich to clean bioturbated intervals. Isotopic evidence of the latest Albian Anoxic Event (Oceanic Anoxic Event 1d), Middle Cenomanian Event I

and the Cenomanian–Turonian Anoxic Event (Oceanic Anoxic Event 2) are confirmed and biostratigraphically calibrated by means of calcareous nannofossils. The carbon isotope record allows correlation with other regional records and well‐calibrated records across the Tethyan Ocean and represents a significant improvement of the chronostratigraphic framework of the United Arab Emirates (Shilaif) and Oman (Natih) intra‐shelf basins. The study further confirms that low carbon isotope values corresponding to the two source rock intervals in the Shilaif Formation clearly precede the isotopic expressions of Oceanic Anoxic Event 1d and Oceanic Anoxic Event 2.

Herkenhoff, K.E., Squyres, S.W., Arvidson, R.E., Cole, S.B., Sullivan, R., Yingst, A., Cabrol, N., Lee, E.M., Richie, J., Sucharski, B., Bell III, J.F., Calef, F., Chapman, M., Edgar, L., Franklin, B., Geissler, P., Hurowitz, J., Jensen, E., Johnson, J.R., Kirk, R., Lanagan, P., Leff, C., Maki, J., Mullins, K., Redding, B., Rice, M., Sims, M., Soderblom, L., Spanovich, N., Springer, R., Sunda, A., Vaughan, A., 2019. Overview of Spirit microscopic imager results. Journal of Geophysical Research: Planets 124, 528-584.

https://doi.org/10.1029/2018JE005774

Abstract: This paper provides an overview of Mars Exploration Rover Spirit Microscopic Imager (MI) operations and the calibration, processing, and analysis of MI data. The focus of this overview is on the last five Earth years (2005–2010) of Spirit's mission in Gusev crater, supplementing the previous overview of the first 450 sols of the Spirit MI investigation. Updates to radiometric calibration using in‐flight data and improvements in high‐level processing are summarized. Released data products are described, and a table of MI observations, including target/feature names and associated data sets, is appended. The MI observed natural and disturbed exposures of rocks and soils as well as magnets and other rover hardware. These hand‐lens‐scale observations have provided key constraints on interpretations of the formation and geologic history of features, rocks, and soils examined by Spirit. MI images complement observations by other Spirit instruments, and together show that impact and volcanic processes have dominated the origin and evolution of the rocks in Gusev crater, with aqueous activity indicated by the presence of silica‐rich rocks and sulfate‐rich soils. The textures of some of the silica‐rich rocks are similar to terrestrial hot spring deposits, and observations of subsurface cemented layers indicate recent aqueous mobilization of sulfates in places. Wind action has recently modified soils and abraded many of the rocks imaged by the MI, as observed at other Mars landing sites.

Plain Language Summary: The Microscopic Imager (MI) on NASA's Spirit rover returned the highest‐resolution images of the Martian surface available at the time of the 2004–2010 mission. Designed to survive 90 Mars days (sols) and search for evidence of water in the past, Spirit returned data for 2210 sols, far exceeding all expectations. This paper summarizes the scientific insights gleaned from the thousands of MI images acquired during the last 5 years of the mission, supplementing the summary of the first 450 sols of the Spirit MI investigation published previously (Herkenhoff et al., 2006). Along with data from the other instruments on Spirit, MI images guided the scientific interpretation of the geologic history of the rocks and soils observed in Gusev crater on Mars. We conclude that the geologic history of the area explored by Spirit has been dominated by impacts and volcanism, and that water, perhaps very hot water, was involved in the evolution of some of the rocks and soils. More recently, winds have moved soil particles and abraded rocks, as observed elsewhere on Mars. These results have improved our understanding of Mars' history and informed planning of future missions to Mars.

Hernandez-Baez, D.M., Reid, A., Chapoy, A., Tohidi, B., 2019. Determination of distribution factors for heavy n-alkanes (nC12-nC98) in high temperature gas chromatography. Journal of Chromatography A 1591, 138-146.


The ultimate purpose of this research work is to get an insight into the incomplete elution of heavy n-alkanes which along with thermal cracking, is one of the two main factors questioning the reliability of High Temperature Gas Chromatography (HTGC) analysis of heavy oils. For this purpose, knowledge of how the Distribution Factors vary with temperature is an essential requirement in the GC modelling.

This study provides an extension of the data set of distribution factors for n-alkanes up to nC98H198 in a HT5 GC column over the temperature range 10 °C–430 °C, and introduces a method to determine the distribution coefficient of heavy n-alkanes by using two complimentary HTGC modes: i.) High-Efficiency mode, for efficient resolution with a long column operated at low flow rate with n-alkanes elution rate up to nC64, and ii.) true SimDist mode, with a short column operated at high flow rate for inefficient resolution with n-alkanes elution rate up to nC100.

Furthermore, this study demonstrates the use of the in-house obtained distribution factors as the main input in the in-house GC model for the prediction of the retention times. Its validation has been carried out using distribution factors obtained at both constant flow rate and constant inlet pressure operating conditions, with an average relative error in the GC modelling at the same operating conditions of 4.4% for the former and 1.5% for the latter.

This new extension of the data set of heavy n-alkanes distribution factors provides the basis for studying the partitioning and incomplete elution of heavy n-alkanes in HTGC analysis. Also, these new distribution factors can be used as input in GC modelling, to determine the optimum analytical conditions to improve the separation process and thus the HTGC practices.

Hernandez-Baez, D.M., Reid, A., Chapoy, A., Tohidi, B., Bounaceur, R., 2019. Establishing the maximum carbon number for reliable quantitative gas chromatographic analysis of heavy ends hydrocarbons. Part 3. Coupled pyrolysis-GC modeling. Energy & Fuels 33, 2045-2056.


The purpose of this research work is to determine the maximum single carbon number (SCN) which can be reliably quantified using High Temperature Gas Chromatography (HTGC) analysis of heavy oil hydrocarbons, accounting for (i) thermal cracking risk and (ii) the non/incomplete elution. To that end, an in-house coupled numerical Pyrolysis-GC model has been developed, capable of calculating the degree of elution and of simulating the migration, partitioning, and pyrolysis conversion of a mixture of 11 heavy n-alkanes spanning the range from nC14H30 to nC80H16 throughout the GC column. On the basis of this model and using a commonly used column configuration and temperature program, two conclusions have been made: (i) half of the mass injected of nC80 thermally decomposed before nC70 has eluted, suggesting a possible coelution of both nC70 and the pyrolysis products of nC80 and therefore making the HTGC analysis of nC70 and heavier n-alkanes no longer reliable, and (ii) alkanes heavier than nC70 take progressively longer to elute completely from the column, compromising the resolution of the peaks, i.e., nC70 takes 2.5 min and nC80 takes 8.5 min. Moreover, nC80 remained 12.9 min in the isothermal plateau before complete elution, implying that the nC80 peak will be overlooked and masked by the FID plateau signal, in combination with column

bleed products. Therefore, in the case study the maximum reliable SCN which can be quantitatively analyzed with HTGC will be the lighter components than nC70.



Biochar has been proposed as a soil amendment in agricultural applications due to its advantageous adsorptive properties, high porosity, and low cost. These properties allow biochar to retain soil nutrients, yet the effects of biochar on bacterial growth remain poorly understood. To examine how biochar influences microbial metabolism, Escherichia coli was grown in a complex, well-defined media and treated with either biochar or activated carbon. The concentration of metabolites in the media were then quantified at several time points using NMR spectroscopy. Several metabolites were immediately adsorbed by the char, including l-asparagine, l-glutamine, and l-arginine. However, we find that biochar quantitatively adsorbs less of these metabolic precursors when compared to activated carbon. Electron microscopy reveals differences in surface morphology after cell culture, suggesting that Escherichia coli can form biofilms on the surfaces of the biochar. An examination of significant compounds in the tricarboxylic acid cycle and glycolysis reveals that treatment with biochar is less disruptive than activated carbon throughout metabolism. While both biochar and activated carbon slowed growth compared to untreated media, Escherichia coli in biochar-treated media grew more efficiently, as indicated by a longer logarithmic growth phase and a higher final cell density. This work suggests that biochar can serve as a beneficial soil amendment while minimizing the impact on bacterial viability. In addition, the experiments identify a mechanism for biochar’s effectiveness in soil conditioning and reveal how biochar can alter specific bacterial metabolic pathways.

Hodson, A.J., Nowak, A., Redeker, K.R., Holmlund, E.S., Christiansen, H.H., Turchyn, A.V., 2019. Seasonal dynamics of methane and carbon dioxide evasion from an open system pingo: Lagoon Pingo, Svalbard. Frontiers in Earth Science 7, 30. doi: 10.3389/feart.2019.00030.

https://www.frontiersin.org/article/10.3389/feart.2019.00030

The processes associated with the release of CH4 and CO2 from sub-permafrost groundwaters are considered through a year-long monitoring investigation at a terrestrial seepage site in West Spitsbergen. The site is an open system pingo thought to be associated with the uplift of a former sea-floor pockmark in response to marked isostatic recovery of the coastline following local ice sheet loss over the last 10000 years. We find that locally significant emissions of CH4 and (less so) CO2 to the atmosphere result from a seepage < 1 L s-1 that occurs all year. Hydrological and meteorological conditions strongly regulate the emissions, resulting in periodic outbursts of gas-rich fluids following ice fracture events in winter, and significant dilution of the fluids in early summer by meltwater. Evasion of both gases from a pond that forms during the 100 day summer (45.6 + 10.0 gCH4-C m-2 and 768 + 211 gCO2-C m-2) constitute between roughly 20 and 40% of the total annual emissions (223 gCH4-C m-2 a-1 and 2040 gCO2-C m-2 a-1). Seasonal maximum dissolved CH4 concentrations (up to 14.5 mg L-1 CH4) are observed in the fluids that accumulate beneath the winter ice layer. However, seasonal maximum dissolved CO2 levels (up to 233 mg L-1) occur during late summer. Differences between the δ13C-CH4 composition of the winter samples (average 58.2 +/- 8.01 ‰ (s.d.)) and the late summer samples (average 66.9 +/- 5.75 ‰ (s.d.)) suggest minor oxidation during temporary storage beneath the winter ice lid, although a seasonal change in the methane source could also be

responsible. However, this isotopic composition is strongly indicative of predominantly biogenic methane production in the marine sediments that lie beneath the thin coastal permafrost layer. Small hotpots of methane emission from sub-permafrost groundwater seepages therefore deserve careful monitoring for an understanding of seasonal methane emissions from permafrost landscapes.

Hoffmann, N., Rein, J., Sachsenberg, T., Hartler, J., Haug, K., Mayer, G., Alka, O., Dayalan, S., Pearce, J.T.M., Rocca-Serra, P., Qi, D., Eisenacher, M., Perez-Riverol, Y., Vizcaíno, J.A., Salek, R.M., Neumann, S., Jones, A.R., 2019. mzTab-M: A data standard for sharing quantitative results in mass spectrometry metabolomics. Analytical Chemistry 91, 3302–3310.


Mass spectrometry (MS) is one of the primary techniques used for large-scale analysis of small molecules in metabolomics studies. To date, there has been little data format standardization in this field, as different software packages export results in different formats represented in XML or plain text, making data sharing, database deposition, and reanalysis highly challenging. Working within the consortia of the Metabolomics Standards Initiative, Proteomics Standards Initiative, and the Metabolomics Society, we have created mzTab-M to act as a common output format from analytical approaches using MS on small molecules. The format has been developed over several years, with input from a wide range of stakeholders. mzTab-M is a simple tab-separated text format, but importantly, the structure is highly standardized through the design of a detailed specification document, tightly coupled to validation software, and a mandatory controlled vocabulary of terms to populate it. The format is able to represent final quantification values from analyses, as well as the evidence trail in terms of features measured directly from MS (e.g., LC-MS, GC-MS, DIMS, etc.) and different types of approaches used to identify molecules. mzTab-M allows for ambiguity in the identification of molecules to be communicated clearly to readers of the files (both people and software). There are several implementations of the format available, and we anticipate widespread adoption in the field.

Hong, H., Zhao, L., Fang, Q., Algeo, T.J., Wang, C., Yu, J., Gong, N., Yin, K., Ji, K., 2019. Volcanic sources and diagenetic alteration of Permian–Triassic boundary K-bentonites in Guizhou Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 141-153.


Terrestrial Permian–Triassic boundary (PTB) sequences in South China usually contain one to three ash beds (K-bentonites), which provide evidence of a possible trigger for the terrestrial mass extinction and are useful as a distinct marker for correlation of the PTB boundary interval from terrestrial to marine areas. Here, we investigate the clay mineralogy and geochemistry of ash beds in the Zhejue and Jiucaichong sections, representing paludal and lacustrine environments, respectively, in order to better understand the source(s) and preservation of these ash beds. The two Zhejue K-bentonites exhibit similar compositions that are distinctly different from that of the Jiucaichong K-bentonite. The former contain mainly clay minerals with minor quartz, anatase, and lepidocrocite, and the clay minerals in these layers are mainly R1 and R3 mixed-layer illite/smectite (I/S) and well-crystallized to poorly-crystallized kaolinite, whereas the latter consists mainly of R3 I/S with minor quartz, feldspars, and anatase. The former have higher CIA values (92.2 and 93.8) than the latter (79.4), indicating more intense chemical weathering that may have been related to deposition in a paludal setting with high organic acid concentrations in pore fluids. These K-bentonites also exhibit differences in major-element chemistry (MgO and K2O contents are higher at Jiucaichong due to lesser weathering intensity and, possibly, early diagenetic uptake from pore fluids), REE chemistry

(Jiucaichong exhibits a larger Eu anomaly), and Nd isotopic compositions (Zhejue K-bentonites have 143Nd/144Nd ratios of 0.512436 and 0.512400, higher than the 0.512190 ratio for Jiucaichong). Although some of these compositional differences may be related to the dissimilar chemical environments in which diagenesis occurred (i.e., paludal vs lacustrine), the differences in Eu anomalies and Nd isotopic compositions imply heterogeneous volcanic ash sources. The source of these K-bentonites was probably a continental volcanic arc located on the paleo-southern margin of the South China Craton, within which multiple volcanic vents may have been active concurrently.

Hu, S., Chen, X., Wang, R.-q., Yang, L., Bai, X.-h., 2019. Natural product applications of liquid-phase microextraction. TrAC Trends in Analytical Chemistry 113, 340-350.


As a simple, rapid, green, and highly-efficient sample-preparation technique, liquid-phase microextraction has been successfully coupled with various instrumental analysis methods and widely applied to determine target analytes (especially trace or ultratrace) from different natural products. In this review, the study is centered on the up-to-date (2017/2018) applications and progresses of various liquid-phase microextractions, mainly including dispersive liquid-liquid microextraction, floating solidification liquid-phase microextraction, hollow fiber liquid-phase microextraction and electromembrane extraction and other novel procedures in the analysis of the endogenous chemical compositions, such as active, nutritional and toxic components from plants as well as disease marker, hormone, neurotransmitters from animals. Finally, future development and applications of liquid-phase microextraction in complex sample analysis are prospected.

Hu, Z., Gao, H., Ramisetti, S.B., Zhao, J., Nourafkan, E., Glover, P.W.J., Wen, D., 2019. Carbon quantum dots with tracer-like breakthrough ability for reservoir characterization. Science of The Total Environment 669, 579-589.


Predictions have shown that our demand for oil and gas will continue to grow in the next decade, and future supply will become more reliant on tertiary recovery and from nonconventional resources. However, current reservoir characterization methodologies, such as well logs, cross-well electromagnetic imaging and seismic methods, have their individual limitations on detection range and resolution. Here we propose a pioneering way to use carbon quantum dots (CQDs) as nanoparticle tracers, which can be transported through a reservoir functioning as conventional tracers, while acting as sensors to obtain useful information. These hydrothermally produced CQDs from Xylose possess excellent stability in high ionic strength solutions, durable absorbance and fluorescence ability due to multi high-polarity functional group on their surfaces. Consistency between our on-line ultraviolet–visible (UV–Vis) spectroscopy and off-line Confocal laser scanning microscopy (CLSM) measurements confirms that CQDs have the tracer-like migration capability in glass beads-packed columns and sandstone cores, regardless of particle concentration and ionic strength. However, their migration ability is undermined in the column packed with crushed calcite grains with positive charge. We also demonstrate that quantitative oil saturation detection in unknown sandstone core samples can be achieved by such CQDs based on its breakthrough properties influenced by the presence of oil phase.

Hua, H., Cai, Y., Xiao, S., Li, G., 2019. Diverse biomineralizing animals in the terminal Ediacaran Period herald the Cambrian explosion. Geology 47, 380-384.

https://doi.org/10.1130/G45949.1

The origin and radiation of biomineralizing metazoans represents an important evolutionary innovation in the history of life. The earliest known skeletal metazoans are dominated by four genera in the terminal Ediacaran Period (ca. 550–539 Ma), followed by the diversification of new and diverse shelly fossils in the early Cambrian Period (ca. 539–510 Ma). Thus, terminal Ediacaran skeletal fossils and early Cambrian shelly fossils are commonly regarded as two distinct assemblages, with little overlap in stratigraphic distribution and taxonomic composition, implying a possible extinction event and a subsequent radiation event at the Ediacaran-Cambrian boundary. However, it has been shown recently that some Ediacaran skeletal taxa may have extended into the early Cambrian, indicating evolutionary continuity between these two assemblages. Here we document an assemblage of diverse skeletal fossils from the terminal Ediacaran Dengying Formation in South China. This assemblage is dominated by terminal Ediacaran taxa such as Cloudina and Sinotubulites, but also contains rare elements that morphologically resemble early Cambrian shelly fossils. This finding suggests that terminal Ediacaran skeletal animals are more diverse than previously thought and further reinforces the evolutionary continuity of biomineralizing animals across the Ediacaran-Cambrian transition.

Huang, X.-M., Wu, Y., Cui, J.-T., Wang, F.-H., Wang, X., Li, Y.-F., Wu, W.-Y., 2019. Applications of high-resolution mass spectrometry in determination of chlorinated paraffins. Chinese Journal of Analytical Chemistry 47, 323-334.


Chlorinated paraffins (CPs) are a new class of persistent organic pollutants and have aroused great concern of many environmental scientists, due to their ubiquity in various environmental media and biotas. Given their relative low levels in environmental samples, CPs need to be enriched and cleaned up before instrumental analysis. CPs consist of thousands of congeners and isomers, thus posing grand challenges to eliminate the mass interference by homologues and other organohalogen compounds during instrumental examination. Fortunately, high-resolution mass spectrometry (HRMS) owns the powerful ability to solve this key problem owing to its high mass resolution. This review introduces the methods of pretreatment and instrumental analysis of CPs-containing samples in the environment, mainly illustrating the application of gas chromatography and liquid chromatography coupled with HRMS (i.e. GC-HRMS and LC-HRMS). The existing issues and prospects of future study are also discussed.

Huang, X., Li, T., Gao, H., Zhao, J., Wang, C., 2019. Comparison of SO2 with CO2 for recovering shale resources using low-field nuclear magnetic resonance. Fuel 245, 563-569.


Adsorption isotherms of pure CH4, C2H6, CO2, and SO2 are measured on one typical shale sample using the static volumetric method. The adsorption capacity of the above four gases is then compared to elucidate the affinity of each gas species on shale. Nuclear magnetic resonance (NMR) technique is then used to investigate how SO2 and CO2 exert the influence on the adsorbed CH4 and C2H6 on the organic shale. Based on the measured adsorption isotherms, SO2 presents the strongest adsorption capacity among the four gases, and is followed by C2H6, CO2, and CH4. It suggests that SO2 can be served as a potential agent for recovering the heavier hydrocarbon species, i.e., C2H6, from organic shale, while CO2 may be only suitable for the shale CH4 recovery. After introducing CO2 or SO2, based on the variation of T2 spectrum of the “CH4 or C2H6-saturated” shale sample, we infer that the

adsorbed CH4 can be readily replaced by CO2 and SO2 from shale surface. However, the adsorbed C2H6 molecules are less probably replaced by CO2 compared to SO2. In addition, the amount of desorbed CH4 and C2H6 resulted from CO2 is much smaller than that of SO2, suggesting the superiority of SO2 for shale resource recovery. We expect this strategy will inspire new perspectives for the recovery of shale resources using the method of flue-gas treatment.

Huang, X., Zhao, Y.-P., Wang, X., Pan, L., 2019. Adsorption-induced pore blocking and its mechanisms in nanoporous shale due to interactions with supercritical CO2. Journal of Petroleum Science and Engineering 178, 74-81.


Supercritical carbon dioxide (sCO2) has recently been used to recover hydrocarbons from shale formations due to its advantages in boosting production, saving water, and minimizing environmental impacts. Meanwhile, CO2 is sealed up underground, which would cut down the greenhouse gas emissions and reduce global warming. However, current knowledge regarding how sCO2 interacts with shale, especially its nanopores which are responsible for adsorption, migration and storage of oil and gas, has been lacking. Here we show that after sCO2 adsorption, the total pore volume decreases by ∼20% in nanoporous shale, majorly by up to 60% in the range of 0.85–2.0 nm. We analyze the morphology and composition changes in shale, and show that the nanopore is either closed up or newly opened, with more closed pores than new ones. We for the first time propose that this adsorption-induced pore blocking phenomenon is jointly voluminal and geochemical resulted from physisorption, associative chemisorption and dissociative chemisorption of sCO2 in shale. Our results help to effectively assess the hydrocarbon production capacity in shale gas reservoirs using CO2-fracking technique, and the CO2 storage potential in shale formations.

Huang, Y., Chen, Z.-Q., Zhao, L., Stanley, G.D., Yan, J., Pei, Y., Yang, W., Huang, J., 2019. Restoration of reef ecosystems following the Guadalupian–Lopingian boundary mass extinction: Evidence from the Laibin area, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 8-22.


The Guadalupian–Lopingian boundary (GLB), also Middle–Late Permian boundary, mass extinction severely destroyed metazoan reef ecosystems, although some studies argued that both biotic and environmental turnover across the GLB are not so obvious. When compared with prolifically developed reefs in the Capitanian, the Wuchiapingian reef examples appear depauperate and almost 89% of the carbonate production in these bioconstructions was lost. Here, we report a typical sponge reef from the Wuchiapingian stage in the Tieqiao section, central Guangxi Province, South China. The Tieqiao reef might represent the only example of a Wuchiapingian metazoan reef in the eastern Palaeo-Tethys region. It provides insight into ecosystem restoration following the GLB extinction. Major constructors of the Tieqiao reef are sponges (Peronidella, Parauvanella, Sollasia, Tabulozoa, and Amblysiphonella), algae (Anthracoporella, Archaeolithporella, Permocalculus, Gymnocodium) and Tubiphytes. This reef is well constrained as middle–late Wuchiapingian in age by the Clarkina orientalis conodont zone. Carbonate carbon isotope excursions experienced negative spikes near the GLB and multiple perturbations in the early–middle Wuchiapingian, and remained relatively stable during re-establishment of metazoan reefs in middle–late Wuchiapingian. Conodont oxygen isotopes showed that the sea surface temperature (SST) was extremely high, >30°C during late Capitanian time, punctuated by a short cooling event and global regression associated with the GLB extinction, and followed by high SST and rapid rise in sea level in the early Wuchiapingian. The reemergence of the Tieqiao reef coincided with the initial cooling in surface oceans and sea-level fall during the

middle–late Wuchiapingian. Accordingly, reef ecosystems experienced a long-term depletion worldwide in early–middle Wuchiapingian time and then recovered ~2.5Myr after the GLB extinction based on estimate in integration of both conodont biostratigraphy and radiometric ages.



Adsorption of dissolved organic matter (DOM) onto soils plays an important role in the mobility and stabilization of organic carbon in soils; however, little attention has been paid to changes in the molecular components of soil DOM during adsorption on soils. In the present study, molecular fractionation of DOM induced by adsorption on a red soil was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. The results indicated that compounds high in unsaturation or polarity or rich in oxygen had a high affinity to soil surfaces, while aliphatic compounds with few oxygenated groups and low polarity compounds were preferentially retained in solution. Among soil fractions with different particle sizes, the fine clay fraction with high iron content and surface area was the main contributor to the adsorptive fractionation of DOM. Comparison of the molecular fractionation of DOM derived from adsorption on soil with iron removed and on soil minerals with various iron contents and surface areas further indicated that iron containing minerals in the soil provided the major adsorptive sites and determined the molecular fractionation of DOM at the soil-water interface. The results provide molecular information for further understanding mechanisms underlying the persistence and mobility of organic carbon in soils.

Hughes, S.S., Haberle, C.W., Kobs Nawotniak, S.E., Sehlke, A., Garry, W.B., Elphic, R.C., Payler, S.J., Stevens, A.H., Cockell, C.S., Brady, A.L., Heldmann, J.L., Lim, D.S.S., 2018. Basaltic terrains in Idaho and Hawai‘i as planetary analogs for Mars geology and astrobiology. Astrobiology 19, 260-283.

https://doi.org/10.1089/ast.2018.1847

Field research target regions within two basaltic geologic provinces are described as Earth analogs to Mars. Regions within the eastern Snake River Plain of Idaho and the Big Island of Hawai‘i, the United States, provinces that represent analogs of present-day and early Mars, respectively, were evaluated on the basis of geologic settings, rock lithology and geochemistry, rock alteration, and climate. Each of these factors provides rationale for the selection of specific targets for field research in five analog target regions: (1) Big Craters and (2) Highway lava flows at Craters of the Moon National Monument and Preserve, Idaho, and (3) Mauna Ulu low shield, (4) Kīlauea Iki lava lake, and (5) Kīlauea caldera in the Kīlauea Volcano summit region and the East Rift Zone of Hawai‘i. Our evaluation of compositional and textural attributes, as well as the effects of syn- and posteruptive rock alteration, shows that basaltic terrains in Idaho and Hawai‘i provide a way to characterize the geology and major geologic substrates that host biological activity of relevance to Mars exploration. This work provides the foundation to better understand the scientific questions related to the habitability of basaltic terrains, the rationale behind selecting analog field targets, and their applicability as analogs to Mars.



The interactions between shales and supercritical carbon dioxide (ScCO2) as well as the influence of these interactions on the pore structure and the surface functional groups play a key role in long-term CO2 geological sequestration. To investigate the effect of ScCO2 treatment on the performance of high-pressure CO2 adsorption, three shale samples selected from different formations were treated with ScCO2 in a geochemical reactor to simulate the in situ geological sequestration process. The high-pressure adsorption behaviors of CO2 on untreated and ScCO2-exposed shale samples were measured by gravimetric method at 45 °C and pressures up to 18 MPa. Characterization methods included scanning electron microscope (SEM), thermogravimetric analysis (TGA), X-ray diffraction (XRD), low-pressure gases adsorption (LP-GA), element analysis (EA) and X-ray photoelectron spectroscopy (XPS). The experimental results indicated that ScCO2 fluid could significantly alter the structural and physicochemical properties of shales, leading to the variations in high-pressure CO2 adsorption capacity of shales. The moisture and oxygen contents in the ScCO2-exposed samples were lower than those in the untreated samples. XPS analysis showed that the relative content of the organic oxygen-containing functional groups (C–O, C=O, O–C–O and COO−) in the raw shale samples decreased after the ScCO2 treatment. After long-term ScCO2 immersion, the maximum CO2 adsorption capacity of the shale samples exhibited a decreasing trend when compared to the raw samples, which was linked to the changes in the specific surface area of the micro- and mesopores as well as the oxygen-containing functional groups. The results obtained in this paper provide a basis for further evaluation of CO2 storage mechanisms.

Hulin, C., Mercury, L., 2019. Capillarity-driven supersolubility in dual-porosity systems. Geochimica et Cosmochimica Acta 252, 144-158.


Capillary phenomena are widespread in unsaturated media such as soils, building stones, deep depleted aquifers and still gas storage/sequestration reservoirs. Processes linked to capillarity depend on pore size and environmental conditions such as relative humidity. When capillary forces are high, water’s internal pressure can reach negative values representative of a tensile state. In those conditions, the capillary tensile water provokes compaction in moist granular materials. In geochemical terms, thermodynamics predict a significant effect on the solvent properties of tensile water. However, very little experimental work has validated thermodynamics models or shown the porosity arrangements that make capillarity a significant player to control the geochemical balance and poromechanics of porous media. In this study, we designed an experimental setup in glass microtubes (ø 200 µm) conducive to capillary tension. In the tubes, salts (halite and sodium sulfate) precipitated from an evaporating solution to build a strongly contrasted dual-porosity system. Large pore bodies (ø 200 µm) coexisted with nanometric pores that induced capillary tension in the whole volume. We observed mineral–liquid interactions (mass gain/loss, crystal shaping), especially how salt solubility changed as a function of capillary conditions. The water’s tensile state increased salt solubility, changing the reactions’ equilibrium constants at constant composition as predicted by thermodynamics. In addition, mineral grains showed clear evidence of poromechanical tensile stress, driving salts to move towards the interior of the tube or to crack. The results showed the potential significance of capillarity in heterogeneous porous media including nanopores. They should be considered in relation to how porous structures change, in the contexts of increasing droughts due to climate changes and increasing excavation work in deep sedimentary basins.

Huo, F., Wang, X., Xu, Z., Huang, H., Li, J., 2019. Characteristics and genesis of the Ordovician crude oil in the RePu area, Halahatang sag, Tarim Basin, China. Petroleum Science and Technology 37, 581-588.

https://doi.org/10.1080/10916466.2018.1558242

The RePu area is located in the Tarim Basin, China. Based on the exploration and development, this paper analyzed the characteristics of the Ordovician crude oil and the source rocks by gas chromatography-mass spectrometry. The Ordovician carbonatite reservoir oil in this area exhibited light component, rich chain hydrocarbon and poor aromatic hydrocarbon. The composition of C7 compound showed the advantage of n-heptane, which belonged to type I generative kerogen, and it was deep buried highly mature crude oil. The crude oil biomarker compounds all exhibited high content of long-chain tricyclic terpanes and high Ts/Tm values. The large presence of alkane aromatization compounds indicated strong reducing environmental conditions during crude oil formation. By comprehensive judgment that the main oil source of the Ordovician reservoirs in the RePu area was the Cambrian source rock.

Hutchins, R.H.S., Prairie, Y.T., del Giorgio, P.A., 2019. Large-scale landscape drivers of CO2, CH4, DOC, and DIC in boreal river networks. Global Biogeochemical Cycles 33, 125-142.

https://doi.org/10.1029/2018GB006106

The boreal biome is characterized by extremely dense and complex fluvial networks that are closely coupled to land. Reconstructing the role that these fluvial networks play in regional carbon (C) budgets requires identifying landscape and environmental drivers of riverine C that operate at the whole network scale and that can be applied across landscapes. Here we explore drivers of CO2, CH4, and dissolved organic (DOC) and inorganic C (DIC) across 190 streams and rivers spanning 8 Strahler orders over an area of 500,000 km2 of heterogeneous boreal landscape in Québec, focusing on those drivers that can be readily obtained from remote sensing data. Each C species (except DIC) could be modeled as a function of a proximal network-scale property, such as flow distance or elevation, but adding regional structure to these models greatly improved predictions. These modeled regional effects were similar for DOC, CO2, and CH4 and were strongly related to average regional soil organic content and especially to NPP, the latter integrating regional differences in climate and other environmental factors. These results suggest that there may be regional C baselines determined by a combination of landscape and climate features, which simultaneously influence the average CO2, DOC, and CH4 within fluvial networks, albeit through different underlying mechanisms and with varying degrees of influence on each C species. The latter two C species appear to be more sensitive to regional differences in soil, NPP, and climate than CO2 or DIC, and therefore more likely to shift under future scenarios of change in northern landscapes.

Ibarra, D.E., Rugenstein, J.K.C., Bachan, A., Baresch, A., Lau, K.V., Thomas, D.L., Lee, J.-E., Boyce, C.K., Chamberlain, C.P., 2019. Modeling the consequences of land plant evolution on silicate weathering. American Journal of Science 319, 1-43.

http://www.ajsonline.org/content/319/1/1.abstract

It has long been recognized that the advent of vascular plants in the Paleozoic must have changed silicate weathering and fundamentally altered the long-term carbon cycle. Carbon cycle models are frequently employed to quantify the effect of this state change in the Earth system. These models have suggested that plants likely played a key role in modulating atmospheric CO2 in the past, with

the largest plant-induced changes to the system in the late Paleozoic. These studies have, for the most part, focused on the effects of plants on weathering via their impacts on the soil environment. Yet, plants also modify the hydrological cycle, which may also have had implications for global weathering. Here, we evaluate the consequences of plant evolutionary innovation that have not been previously incorporated into carbon cycle models by coupling a one-dimensional vapor transport model to a reactive transport model of silicate weathering. Using this cascade of models, we investigate: 1) how evolutionary shifts in plant transpiration may have enhanced silicate weathering through increased downwind transport of water vapor to continental interiors; 2) the importance of deeply-rooted plants and their associated microbial communities in increasing soil CO2 and weathering zone length scales; and, 3) the coupled effect of these two processes on weathering rates.

The hydrologic balance for our modeling approach is framed by energy/supply constraints (encapsulated through Budyko relationships) calibrated for minimally vegetated-, vascular plant forested-, and angiosperm-worlds. Using constraints for atmospheric vapor-transport over continents and terrestrial weathering fluxes, we find that the emergence of widespread transpiration and associated inland vapor recycling associated with the advent of deep-rooted vascular plants over the later Devonian increases weathering solute concentrations by a factor of 1.64 to 2.39 for a fixed atmospheric CO2. The later domination of ecosystems by angiosperms in the late Cretaceous and Cenozoic, and the subsequent increase in transpiration fluxes, increased weathering solute concentrations by 7 to 55 percent leading to a cumulative total increase in weathering solute concentrations by a factor of 1.70 to 2.55. Partitioning of the vapor recycling effects and feedbacks on the weathering thermodynamics indicates that 55 percent of the increases in weathering concentrations are due to the thermodynamic effects of soil CO2 with the remaining 45 percent attributable to hydrologic effects. Our estimates of the relative changes in weathering solute concentrations caused by land plant evolution are of a similar magnitude to relative flux scaling relationships implemented in existing carbon cycle models such as GEOCARBSULF (Berner, 2006), COPSE (Bergman and others, 2004), and GEOCLIM (Le Hir and others, 2011). As Phanerozoic plant evolution resulted in a more efficient generation of weathering solutes, a weaker dependence of silicate weathering on physical forcing factors such as temperature, pH of rainwater, tectonics, and prevailing lithology, must have resulted. Consequently, we postulate that terrestrial plant evolution likely contributed to a more stable climate system over the Phanerozoic.

Imai, M., Mikami, K., Suganuma, T., Tsuchiya, Y., Nakagawa, K., Takahashi, S., 2019. Determination of binary diffusion coefficients between hot liquid solvents and bitumen with X-ray CT. Journal of Petroleum Science and Engineering 177, 496-507.


The Steam Assisted Gravity Drainage (SAGD) process has been used for in-situ thermal bitumen recovery in Canada. Nevertheless, there are several drawbacks that could impair the SAGD performance. One of the main drawbacks of SAGD is nontrivial consumption of energy to generate steam. To curtail the consumption of steam, many SAGD variants have been proposed. For example, Vapor Extraction (VAPEX) was proposed as a solvent-based cold production method and Solvent-Assisted SAGD (SA-SAGD) was proposed as a solvent-assisted hybrid method. In those solvent-based/assisted methods, the dissolution of solvents in bitumen enhances the in-situ oil mobility.

The speed of the mixing between solvents and bitumen in solvent-based/assisted recovery processes is dictated by dispersive mass flux which is proportional to the transverse dispersion coefficient. Diffusion coefficient, tortuosity and transverse dispersivity should be quantified to characterize the transverse dispersion coefficient. In this research, the diffusion coefficients of solvents in Athabasca bitumen were determined with X-ray computed tomography (CT).

A medical X-ray CT scanner was used to capture the diffusion phenomenon occurring between fresh liquid solvents and bitumen. The experiments were designed to reproduce the in-situ high pressure, high temperature condition (3.5 MPa, 135C) where solvent and bitumen actually interact at the vapor chamber edge in the SA-SAGD process. Using our new °experimental system, we successfully measured molecular diffusion coefficients at the condition of the vapor chamber edge for the first time.

In conclusion, the binary diffusion coefficients between solvents and bitumen were successfully measured at the condition where the mixing of solvents and bitumen actually occurs in the SA-SAGD process. The characterized diffusion coefficients will be input parameters for the reservoir simulation and semi-analytical models.



Aim of present work was to assess in-planta association potential of isolated endophytic bacterial strain Pseudomonas sp. (J10) (KY608252) with two cultivars of Lolium perenne L. (small & jumbo) and Arabidopsis thaliana L. for total petroleum hydrocarbon (TPH) degradation, alkane monooxygenase (alkb) gene expression and phytotoxicity analysis. A plant-microbe phytoremediation system was established to investigate the bacteria's ability to colonize the plant body and quantification of alkb gene to help withstand TPH stress in soil as well as in hydroponics. A real-time PCR method was developed to analyze bacterial colonization and survival within the plant body. Analysis revealed that J10 efficiently colonized all the tested plant species and expressed alkb gene under hydrocarbon stress ranging between 3.7 × 102–3.9 × 106 in A. thaliana and L. perenne (small), respectively. The colonization was more pronounced in soil as compared to hydroponic system. J10 inoculation reduced phytotoxicity and suggested that inoculation had a positive effect on plant growth under stress conditions as compared to control. L. perenne (small) showed significant TPH removal efficiency (45.6%) followed by L. perenne jumbo (24.5%) and A. thaliana (6.2%). In hydroponics, L. perenne (small) degraded about 28.2% TPH followed by L. perenne (jumbo) as 24.4%. Potential of the indigenously isolated plant endophytes may be exploited further for phytoremediation efficiency and industrial applications.

Islam, M.S., Sun, J., Li, X., Leng, X., 2019. Seasonal sinking rates of transparent exopolymer particles (TEP) concentrations with associated carbon flux in adjacent Bohai Sea and Yellow Sea. Biogeosciences Discussions 2019, 1-43.


To study the seasonal transparent exopolymer particles (TEP) distributions, sedimentation and its impacts on carbon cycle in north Chinese seas, a total of total 56 stations TEP samples and its sinking rate measurements by SETCOL method via water sampling cruise during autumn (2014), summer (2015) and winter (2015) in the Bohai Sea (BS), North Yellow Sea (NYS) and South Yellow Sea (SYS) at three different depths were carried out. Temperature, phytoplankton, chlorophyll-a (Chl-a) and salinity with five nutrients, phosphate (DIP), silicate (DSi), dissolved inorganic nitrate (DIN) (including nitrite, nitrate and ammonium) were also collected and measured for correlation analysis to

visualize the seasonal effects on TEP concentrations (CTEP) and its sinking. Average of total CTEP (2.13 μg Xeq L−1) was higher in NYS (3.32 μg Xeq L−1) costal currents with highest average CTEP during winter (6.17 μg Xeq L−1) specially in NYS (7.00 μg Xeq L−1) through coastal current mixing zone. Average of total sinking rates (1.03 mD−1) was higher in SYS (1.09 mD−1) through mid-water layer than other seas, especially in autumn (1.13 mD−1) with higher seasonal average sinking rates at summer (1.04 mD−1). Carbon associated with TEP (TEP-C) was averagely distributed (1.47 μg C L−1) at subsurface layer of study areas. Seasonal highest distribution of TEP-C was 4.44 μg C L−1 during winter, mostly in NYS. Dominant phytoplankton species Paralia sulcata, Thalassisira excentrica and Rhizosolenia styliformis maintained average correspondences with CTEP which may indicate the influences of them on TEP concentration. Congregating oceanic stations in other groups, coastal stations were averagely clustered together in multivariate analysis. Average canonical correspondence analysis showed close relation of CTEP with Chl-a during autumn and with nutrient during winter.

Jaffe, A.L., Castelle, C.J., Banfield, J.F., Dupont, C.L., 2018. Lateral gene transfer shapes the distribution of RuBisCO among candidate Phyla Radiation bacteria and DPANN archaea. Molecular Biology and Evolution 36, 435-446.

https://dx.doi.org/10.1093/molbev/msy234

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for carboxylase activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a CO2-incorporating pathway that consumes nucleotides. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin–Benson–Bassham cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.

Jahanbani Veshareh, M., Ganji Azad, E., Deihimi, T., Niazi, A., Ayatollahi, S., 2019. Isolation and screening of Bacillus subtilis MJ01 for MEOR application: biosurfactant characterization, production optimization and wetting effect on carbonate surfaces. Journal of Petroleum Exploration and Production Technology 9, 233-245.

https://doi.org/10.1007/s13202-018-0457-0

The bacterial strain MJ01 was isolated from stock tank water of one of the Iranian south oil field production facilities. The 16S rRNA gene of isolate, MJ01, showed 99% similarity to Bacillus subtilis. The results revealed that biosurfactant produced by this strain was lipopeptide-like surfactin based on FTIR analysis. Critical micelle concentration of produced surfactin in distilled water was 0.06 g/l. Wettability study showed that at zero salinity surfactin can change original oil-wet state to water-wet state, but in seawater salinity it cannot modify the wettability significantly. To utilize this

biosurfactant in ex situ MEOR process, economical and reservoir engineering technical parameters were considered to introduce a new optimization strategy using the response surface methodology. Comparing the result of this optimization strategy with the previous optimization research works was shown that significant save in use of nutrients is possible by using this medium. Furthermore, using this method leads to less formation damage due to the incompatibility of injecting fluid and formation brine, and less formation damage due to the bioplugging.

James, H.F., Willmes, M., Boel, C.A., Courtaud, P., Chancerel, A., Ciesielski, E., Desideri, J., Bridy, A., Wood, R., Moffat, I., Fallon, S., McMorrow, L., Armstrong, R.A., Williams, I.S., Kinsley, L., Aubert, M., Eggins, S., Frieman, C.J., Grün, R., 2019. Who's been using my burial mound? Radiocarbon dating and isotopic tracing of human diet and mobility at the collective burial site, Le Tumulus des Sables, southwest France. Journal of Archaeological Science: Reports 24, 955-966.


The burial mound of Le Tumulus des Sables, southwest France, contains archaeological artefacts spanning from the Neolithic to the Iron Age. Human remains have been found throughout the burial mound, however their highly fragmented state complicates the association between the burial mound structure and the archaeological material. Radiocarbon dating and isotopic analyses of human teeth have been used to investigate the chronology, diet and mobility of the occupants. Radiocarbon dating shows that the site was used for burials from the Neolithic to Iron Age, consistent with the range of archaeological artefacts recovered. δ13C and δ15N values (from dentine collagen) suggest a predominately terrestrial diet for the population, unchanging through time. 87Sr/86Sr (on enamel and dentine) and δ18O (on enamel) values are consistent with occupation of the surrounding region, with one individual having a δ18O value consistent with a childhood spent elsewhere, in a colder climate region. These results showcase the complex reuse of this burial mound by a mostly local population over a period of about 2000 years.

Jan, S., Ahmad, P., 2019. Ecometabolomics. Metabolic Fluxes versus Environmental Stoichiometry. Academic Press.

https://www.sciencedirect.com/book/9780128148723/ecometabolomics

Ecometabolomics: Metabolic Fluxes versus Environmental Stoichiometry focuses on the interaction between plants—particularly plants that have vigorous secondary metabolites—and the environment. The book offers a comprehensive overview of the responses of the metabolome of organisms to biotic and abiotic environmental changes. It includes an introduction to metabolomics, summaries of metabolomic techniques and applications, studies of stress in plants, and insights into challenges. This is a must-have reference for plant biologists, plant biochemists, plant ecologists and phytochemists researching the interface between plants and the environment using metabolomics.

Key Features:

Provides an in-depth overview of the basics of the discipline, including non-targeted analysis and quantification of plant metabolites

Outlines the applications of various analytical techniques in comprehending the total metabolome of the organism

Covers both NMR and MS-based approaches

Chapter 1 - Introducing MetabolomicsChapter 2 - An Integrated Approach to Plant Biology via Multi-Analogous MethodsChapter 3 - Metabolomics Studies of Stress in PlantsChapter 4 - Climatic Change and Metabolome FluxesChapter 5 - Instrumentation Applied to Metabolomic AnalysisChapter 6 - Ecological Metabolomics: Challenges and Perspectives

Jaouen, K., Richards, M.P., Le Cabec, A., Welker, F., Rendu, W., Hublin, J.-J., Soressi, M., Talamo, S., 2019. Exceptionally high δ15N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores. Proceedings of the National Academy of Sciences 116, 4928-4933.


Significance: Identifying past hominin diets is a key to understanding adaptation and biological evolution. Bone collagen isotope studies have added much to the discussion of Neandertal subsistence strategies, providing direct measures of diet. Neandertals consistently show very elevated nitrogen isotope values. These values have been seen as the signature of a top-level carnivore diet, but this interpretation was recently challenged by a number of additional theories. We here apply compound-specific isotope analysis of carbon and nitrogen in bone collagen single amino acids of two Neandertals. These Neandertals had the highest nitrogen isotope ratios of bulk collagen measured so far, and our study confirms that these values can be most parsimoniously explained by a carnivorous diet.

Abstract: Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ15N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.

Jeleń, H.H., Majcher, M., Szwengiel, A., 2019. Key odorants in peated malt whisky and its differentiation from other whisky types using profiling of flavor and volatile compounds. LWT Food Science and Technology 107, 56-63.


Key odorants of peated single malt whisky were identified using gas chromatography – olfactometry (GC-O). Twenty compounds were identified with FD (Flavor Dilution) values ranging from 8 to 2048 and 8 of them were volatile phenols. The compounds with the highest FD were 2-methoxyphenol

(guaiacol), 4-ethyl-2-methoxyphenol (4-ethylguaiacol), 4-methylphenol, 4-vinyl-2-methoxyphenol (4-vinylguaiacol) and 4-ethyl-2-methylphenol (FD ranging from 512 to 2048). Then odorants were used successfully to distinguish peated single malts from 3 other whisky types (mild single malts, blended and American whiskies) based on PCA followed by LDA applied to GCxGC-ToFMS data of volatiles extracted using SPME. 36 whiskies representing all groups were used for the differentiation experiments. Finally, 61 volatile compounds based on Fisher ratios were selected to fully discriminate between 4 whisky types based on profile of volatiles obtained in SPME-GCxGC-ToF analysis. Cross-validation confirmed the suitability of PCA and LDA models for the discrimination of different whisky types.

Ji, C., Wu, Z., Fang, C., Yi, H., Xia, G., 2019. High temperature, high reducibility and low productivity of the paleoceanographic environment in the P/T, Tethys. Acta Geologica Sinica - English Edition 93, 248-249.

https://doi.org/10.1111/1755-6724.13787

No abstract

Jiang, B., Zhang, R., Yang, N., Zhang, L., Sun, Y., 2019. Asphaltene aggregation and assembly behaviors in organic solvents with water and inhibitor. Energy & Fuels 33, 1955-1968.


crude oil production, processing, and transport. A deeper understanding of the behaviors of asphaltenes is needed to design remediation treatments to minimize costs during production. In this study, the aggregation and assembly behaviors of asphaltene model compound C5PeC11 under different conditions were studied and visualized through molecular dynamic simulations. C5PeC11 aggregates were formed as a result of the competition between the solvation of C5PeC11 in solvents and the self-association of C5PeC11 molecules. One-dimensional bent linear assembly of C5PeC11 aggregates was observed upon the addition of n-heptane to toluene. Although the water content was low, the addition of water molecules resulted in enhanced C5PeC11 aggregation and considerably different C5PeC11 aggregate assembly behaviors. C5PeC11 aggregates formed a cluster in a parallel horizontal connection manner with the hydrocarbon tails located outside and polar groups located inside. The network formed via the hydrogen bonding between C5PeC11 and water as well as between water molecules provided new binding interactions for C5PeC11 aggregates. Water molecules were indispensable for the formation and retention of a C5PeC11 aggregate cluster. Dodecylbenzene sulfonic acid (DBSA) and water competed with each other to influence asphaltene associations when they were both present in the system. Both the hydrogen bonding between C5PeC11 and water and hydrogen bonding between water molecules contributing to the development of the network were hindered by DBSA. DBSA molecules succeeded in stabilizing C5PeC11 even in the presence of water molecules.

Jiang, C., Zhang, S., Reyes, J., 2019. Black shale xenolith in a Jurassic−Cretaceous kimberlite and organic-rich Upper Ordovician shale on Baffin Island, Canada: A comparison of their organic matter. Marine and Petroleum Geology 103, 202-215.


Rock-Eval pyrolysis and molecular organic geochemical analyses as well as organic petrographic observations were carried out on a rare black shale xenolith core drilled from a Late Jurassic-Early

Cretaceous kimberlite on the Hall Peninsula in southern Baffin Island, Canada. The results are compared with those of outcrop shale samples from the Upper Ordovician Amadjuak Formation, the only organic-rich shale deposit discovered so far in the region. The shale xenolith is found to be organic-rich and thermally mature at the stage of peak oil generation, and contain type II organic matter similar to that of the immature Amadjuak shale. Discounting the differing thermal maturation effect, similar depositional environments and original organic inputs are suggested for both the shale xenolith and the Upper Ordovician shale based on their bulk, molecular and isotopic signatures as well as organic maceral assemblages. The present study cannot exclude the possibility of the shale xenolith being originated from an organic-rich Lower Silurian deposit, as suggested by previous ReOs isotope dating study. It is clear, however, that depending on their areal distribution and thickness, the lithostratigraphic unit from which the organic-rich black shale xenolith is derived would make an excellent petroleum source rock in the study area.

Jiang, H., Frie, A.L., Lavi, A., Chen, J., Zhang, H., Bahreini, R., Lin, Y.-H., 2019. Brown carbon formation from nighttime chemistry of unsaturated heterocyclic volatile organic compounds. Environmental Science & Technology Letters 6, 184-190.

https://doi.org/10.1021/acs.estlett.9b00017

Nighttime atmospheric processing enhances the formation of brown carbon aerosol (BrC) in biomass burning plumes. Heterocyclic compounds, a group of volatile organic compounds (VOCs) abundant in biomass burning smoke, are possible BrC sources. Here, we investigated the nitrate radical (NO3)-initiated oxidation of three unsaturated heterocyclic compounds (pyrrole, furan, and thiophene) as a source of BrC. The imaginary component of the refractive index at 375 nm (k375), the single scattering albedo at 375 nm (SSA375) and average mass absorption coefficients ({MAC}290-700nm) of the resulting secondary organic aerosol (SOA) are reported. Compared to furan and thiophene, NO3 oxidation of pyrrole has the highest SOA yield. Pyrrole SOA (k375=0.015±0.003, SSA=0.86±0.01, {MAC}290-

700nm=3400±700 cm2 g-1) is also more absorbing than furan SOA ({MAC}290-700nm=1,100±200 cm2 g-1) and thiophene SOA (k=0.003 ± 0.002, SSA=0.98±0.01, {MAC}290-700nm=3,000±500 cm2 g-1). Compared to other SOA systems, MACs reported in this study are higher than those from biogenic precursors, and similar to high-NOx anthropogenic SOA. Characterization of SOA molecular composition using high-resolution mass spectrometric measurements revealed unsaturated heterocyclic nitro products or organonitrates as possible chromophores in BrC from all three precursors. These findings reveal nighttime oxidation of fire-sourced heterocyclic compounds, particularly pyrrole, as a plausible source of BrC.

Jiang, H., Wei, L., Fan, X., Xu, J., Shyy, W., Zhao, T., 2019. A novel energy storage system incorporating electrically rechargeable liquid fuels as the storage medium. Science Bulletin 64, 270-280.


We propose a novel concept of energy storage that incorporates electrically rechargeable liquid fuels made of electroactive species, known as e-fuels, as the storage medium. This e-fuel energy storage system comprises an e-fuel charger and an e-fuel cell. The e-fuel charger electrically charges e-fuels, while the e-fuel cell subsequently generates electricity using charged e-fuels whenever and wherever on demand. The e-fuel energy storage system possesses all the advantages of conventional hydrogen storage systems, but unlike hydrogen, liquid e-fuels are as easy and safe to store and transport as gasoline. The potential e-fuel candidates have been identified to include inorganic electroactive materials, organic electroactive materials, and suspension of solid electroactive materials. In this

work, we demonstrate an example e-fuel energy storage system for large-scale energy storage using inorganic e-fuels composed of V2+/V3+ and VO2+/VO2+ redox couples, and compare the performance of the e-fuel energy storage system with that of existing technologies. Results show that our e-fuel charger achieves a charge efficiency of as high as ∼94%, while the e-fuel cell is capable of delivering a peak power density of 3.4 W cm−2, which is 1.7 times higher than that of hydrogen fuel cells. More excitingly, the e-fuel energy storage system exhibits a round-trip efficiency of 80.0% and an electrolyte utilization of 83.0% at an ultra-high discharge current density of 1,000 mA cm−2, which are 19.9% and 67.3% higher than those of conventional vanadium redox flow batteries. This unprecedented performance allows a 27.0% reduction in the capital cost of the e-fuel energy storage system compared with that of vanadium redox flow batteries.

Jiang, M.-z., Qiu, Z.-j., Zhang, G.-w., Gao, S.-y., You, X.-y., Ma, Y.-f., 2019. Mucilaginibacter xinganensis sp. nov., a phenanthrene-degrading bacterium isolated from wetland soil. Antonie van Leeuwenhoek 112, 641-649.

https://doi.org/10.1007/s10482-018-1194-6

An aerobic, Gram-stain negative, rod-shaped and non-motile strain, BJC16-A31T, was isolated from the wetland soil sample taken from Daxing’anling, Heilongjiang, People’s Republic of China. Strain BJC16-A31T was found to be oxidase- and catalase-positive, and produced light orange colonies on modified R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BJC16-A31T is closely related to Mucilaginibacter gotjawali SA3-7T with 96.54% sequence similarity and it formed a separate lineage in the genus Mucilaginibacter. Strain BJC16-A31T contained menaquinone-7 (MK-7) as the predominant isoprenoid quinine. Anteiso-C15:0, C16:0 and anteiso-C15:0 were the major fatty acids. The major polar lipids were phosphatidylethanolamine, six unidentified polar lipid, two unidentified aminophospholipids and one unidentified aminolipid. The genome is composed of a circular 5,301,339 bp chromosome with average G + C percentage of 42.25%. The Average Nucleotide Identity (ANI) between strain BJC16-A31T and M. gotjawali SA3-7T was 77.51%. Combined phenotypic, chemotaxonomic, phylogenetic and genomic characteristics support the conclusion that strain BJC16-A31T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter xinganensis sp. nov. is proposed. The type strain is BJC16-A31T (= CGMCC 1.12728T = NBRC 110384T).

Jiang, M., 2019. Facile approach for calculation of second dimensional retention indices in comprehensive two dimensional gas chromatography with single injection. Analytical Chemistry 91, 4085-4091.


In the present work, a novel and simple approach to generate isovolatility curves for alkane series was established, which serves to calculate the second dimension (2D) retention indices (2I) for peaks in comprehensive two-dimensional gas chromatography (GC×GC). The approach is applicable to routine GC×GC results without requiring multiple injections of alkanes or requiring internal and external standards under different oven temperature conditions which might be normally required in other approaches. A proposed relationship between 2I values and first dimension (1D) and 2D retention times (1tR and 2tR) of compounds can be simplified to an equation with four constants. Values of the four constants can be obtained by fitting the proposed equation with experimental 1tR and 2tR data of standard compounds obtained from a single injection of a standard mixture or by using data of known compounds in an analyzed sample. The effect of selected compound sets on calculation of the four constants and derivation of 2I using the established approach was investigated. The approach was

evaluated by comparison with the traditional method based on multiple injections in calculating 2I values of compounds in a frankincense sample. With a suitable set of chosen standard compounds well-spread over the first and second dimension (2D) space, the potential of the present concept allows simple and reliable calculation of 2I. This approach should facilitate application of 2I for compound identification in GC×GC, which is somewhat underutilized largely due to the tedious and time-consuming approach presently used in construction of isovolatility curves, based on multiple injections.

Jiang, X., Liu, L., Sun, H., Huang, S., Geng, M., Chen, S., Li, N., Shen, P., 2019. Differential distribution of high-quality lacustrine source rocks controlled by climate and tectonics: a case study from Bozhong sag Acta Petrolei Sinica 40, 165-175.

http://www.syxb-cps.com.cn/EN/abstract/abstract5626.shtml

Based on the geochemistry data, well logging and sedimentary facies in Bozhong sag, an analysis was performed on high-quality lacustrine source rocks. In combination with regional seismic interpretation, this paper describes the distribution of high-quality source rocks in Bozhong sag, and then discusses the differences of source rocks under the effect of climate and tectonics. The results show that the high-quality source rocks formed in the saline environment controlled by climate and the rapid subsidence environment controlled by tectonics present different enrichment characteristics. The distribution area of high-quality source rocks in the Member 1 of Shahejie Formation under the main control of the salinized environment accounts for 81.9 % of the depression area, showing a broad distribution; in Member 3 of Shahejie Formation and Member 3 of Dongying Formation under the control of tectonic subsidence, a significant positive correlation exists between the depression subsidence rate and the distribution area of high-quality source rocks in the depression. The redox interface of the lake controls the enrichment of high-quality source rocks in the longitudinal direction. Under the control of saline environment and rapid tectonic subsidence formed by climate, the development conditions of high-quality source rocks in Bozhong sag and adjacent areas can be divided into three categories dominated by salinized water, tectonic subsidence, and jointly by salinized water and tectonic subsidence, respectively. In the case of humid climate and low sedimentation rate, high-quality source rocks are not developed.

Jin, Q., Hou, Q., Cheng, F., Wang, S., Zhang, R., Wang, F., 2019. Evaluation method of effective source rock in mature exploration area: a case study of Liaodong Bay. Acta Petrolei Sinica 40, 257-267.


There are contradictions between the discovered oil and gas reserves and the predicted resources in mature exploration area. It may be because the effective source rocks (including deeply buried source rocks)and their hydrocarbon generation potential are not properly evaluated. Different from the previous evaluations focusing on the minimum of TOC in effective source rocks, a new evaluation method of the resource rocks in Liaodong Bay is proposed in this study. In this area, using geochemical and geophysical methods, the stratified evaluation and hydrocarbon generation simulation experiments are conducted on five sets of source rocks in each depression, so as to calculate out the oil and gas generation intensity. Then, the hydrocarbon generation model, porosity variation model and oil saturation in the source rock burial process are applied to calculate out the oil and gas expulsion rate, and the oil and gas expulsion efficiency is corrected according to the different assemblages of source rock and sandstone, so as to obtain the oil and gas expulsion intensity. Finally, the correlation analysis is made between hydrocarbon generation intensity, expulsion intensity and oil and gas field reserves; on this basis, this study determines the nature and distribution of effective

source rocks and the control laws of oil and gas accumulation. This study shows that in Liaodong Bay, the source rocks with the oil generation intensity greater than 25×104t/km2, i.e., the oil expulsion intensity greater than 15×104t/km2, can accumulate and be developed into the oil field with reserves greater than 500×104t, which are deemed as effective source rocks. Among these, the source rocks with the oil generation intensity greater than 200×104t/km2, i.e., the oil expulsion intensity greater than 125×104t/km2, can accumulate to form the oil field with reserves greater than 5 000×104t, which are considered as high-quality source rocks. If the oil generation intensity is less than 25×104t/km2 and the oil expulsion intensity is less than 15×104t/km2, the source rocks are defined as non-effective source rocks, where no oil fields have been discovered. The evaluation method using hydrocarbon generation intensity and expulsion intensity for effective source rocks is favorable for further fine oil and gas exploration in mature exploration areas of East China.

Jones, D.J.R., McCarthy, D.J., Dodd, T.J.H., 2019. Tectonostratigraphy and the petroleum systems in the Northern sector of the North Falkland Basin, South Atlantic. Marine and Petroleum Geology 103, 150-162.


The North Falkland Basin represents one of the frontier areas for hydrocarbon exploration in the South Atlantic. This study presents the results of new subsurface mapping using 2D seismic data in the north of the Falkland Islands offshore area, which has delineated a series of discrete grabens northwards of the main North Falkland Basin, referred collectively to as the Northern sector of the North Falkland Basin (NNFB). Six regionally significant seismic reflectors are interpreted within this data, dividing the sedimentary fill into six tectonostratigraphic packages, including: early syn-rift; late syn-rift; transitional unit; early post-rift; middle to late post-rift; and a sag unit. Structural interpretation of the 2D seismic data has led to the definition of four north-south orientated depocentres, namely: (1) the Eastern Graben, largest of the depocentres; 20 km wide by 45 km long, reaching depths of 3 km; (2) the Eastern Graben Splay, a smaller depocentre; 10 km wide by 20 km long, reaching depths of 2–2.5 km; (3) the Western Graben Splay, the smallest depocentre; 5 km in width and 20 km long, with a basin depth of 2 km and (4) the newly defined Phyllis Graben, which is 13 km wide and 30 km long, with a basin depth of 3 km. A network of NW-SE and NE-SW trending faults controls the development of these grabens, separated by a Western, Eastern and Intra-Basin high. These grabens represent a northern continuation of the Northern Falkland Basin to the south. Hydrocarbon discoveries to the south of this study area (e.g. Sea Lion, Casper, Beverley, Zebedee, Isobel Deep, and Liz) confirm a working petroleum system adjacent to the Northern sector. This study has identified a number of seismic anomalies, including amplitude brightening events, which potentially correspond to an extension of this petroleum system, indicating active migration pathways. The main targets, in terms of hydrocarbon interest in the northern sector, are likely to be stratigraphically trapped hydrocarbon accumulations, contained within vertically-amalgamated turbidite fan sandstone reservoirs, deposited within the early post-rift. A second, yet to be tested, syn-rift play, in which the trapping geometries are structural and the reservoirs are fluvial sandstones is also identified.

Juhls, B., Overduin, P.P., Hölemann, J., Hieronymi, M., Matsuoka, A., Heim, B., Fischer, J., 2019. Dissolved organic matter at the fluvial-marine transition in the Laptev Sea using in situ data and ocean color remote sensing. Biogeosciences Discussions 2019, 1-37.


River water is the main source of dissolved organic carbon (DOC) in the Arctic Ocean. DOC plays an important role in the Arctic carbon cycle and its export from land to sea is expected to increase as ongoing climate change accelerates permafrost thaw. However, transport pathways and transformation of DOC in the land-to-ocean transition are mostly unknown. We collected DOC and aCDOM(λ) samples from 11 expeditions to river, coastal and offshore waters and present a new DOC-aCDOM(λ) model for the fluvial-marine transition zone in the Laptev Sea The aCDOM(λ) characteristics revealed that the DOM in samples of this dataset are primarily of terrigenous origin. Observed changes in aCDOM and its spectral slopes indicate that DOM is modified by microbial- and photo-degradation. Ocean Color Remote Sensing (OCRS) provides the absorption coefficient of colored dissolved organic matter (aCDOM(λ)sat) at λ = 440 or 443 nm, which can be used to estimate DOC concentration at high temporal and spatial resolution over large regions. We tested the statistical performance of five OCRS algorithms and evaluated the plausibility of the spatial distribution of derived aCDOM(λ)sat. The ONNS algorithm showed the best performance compared to in situ aCDOM(440) (r2 = 0.72). Additionally, we found ONNS-derived aCDOM(440), in contrast to other algorithms, to be partly independent of sediment concentration, making ONNS the most suitable aCDOM(λ)sat algorithm for the Laptev Sea region. The DOC-aCDOM(λ) model was applied to ONNS-derived aCDOM(440) and retrieved DOC concentration maps showed moderate agreement to in situ data (r2 = 0.53). The in situ and satellite-retrieved data were offset by up to several days, which may partly explain the weak correlation for this dynamic region. Satellite-derived surface water DOC concentration maps from MERIS satellite data demonstrate rapid removal of DOC within short time periods in coastal waters of the Laptev Sea, which is likely caused by physical mixing and different types of degradation processes. Using samples from all occurring water types leads to a more robust DOC-aCDOM(λ) model for the retrievals of DOC in Arctic shelf and river waters.

Jurikova, H., Liebetrau, V., Raddatz, J., Fietzke, J., Trotter, J., Rocholl, A., Krause, S., McCulloch, M., Rüggeberg, A., Eisenhauer, A., 2019. Boron isotope composition of the cold-water coral Lophelia pertusa along the Norwegian margin: Zooming into a potential pH-proxy by combining bulk and high-resolution approaches. Chemical Geology 513, 143-152.


High-latitude cold-water coral reefs are particularly vulnerable to climate change due to enhanced CO2 uptake in these regions. To evaluate their physiological functioning and potential application as pH archives, we retrieved both recent and fossil samples of Lophelia pertusa along the Norwegian margin from Oslofjord (59°N), over to Trondheimsfjord, Sula and Lopphavet (70.6°N). Boron isotope analyses (δ11B) were undertaken using solution-based and laser ablation multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS; LA-ICP-MS), and secondary ion mass spectrometry (SIMS). Epi-fluorescence microscopy was employed to provide a rapid pre-screening routine for structure-specific subsampling in the coral skeleton. This integrated approach enabled us to assess heterogeneities within single specimens, as well as to investigate the role of local environmental influences including recent and past variations. All three mass spectrometry methods show substantial differences in the δ11B of the theca wall (TW) and the centres of calcification (COC's). Micro-bulk subsamples milled from the theca wall of modern specimens originating from different habitats but with comparable seawater pH (8–8.16) gave consistent δ11B values averaging 26.7 (±0.2‰, 2σ, n = 4), while COC subsamples systematically deviated towards lower B/Ca (by ~40%) and depleted δ11B values (minimum 22.7 ± 0.3‰, 2σ), implying a difference of at least 4‰ between TW and COC. SIMS and LA-ICP-MS measurements identified much larger internal heterogeneities with maximum variation of ~10‰ between the distinct skeletal structures; minimal SIMS δ11B values of ~17.3 ± 1.2‰ (2σ) were associated with the pure COC material. Our findings may be interpreted in terms of the occurrence of two main, but likely different, biomineralisation

mechanisms in L. pertusa, with the COC's generally exhibiting minimal pH up-regulation, potentially supporting the use of bicarbonate in the early stages of biomineralisation. Furthermore, we highlight the potential utility of L. pertusa for palaeo-proxy studies if targeting the compositionally homogenous TW zones devoid of COC admixtures, which appear to provide highly reproducible measurements.

Kang, S., Yan, H., Zhu, Y., Liu, X., Lv, H.-P., Zhang, Y., Dai, W.-D., Guo, L., Tan, J.-F., Peng, Q.-H., Lin, Z., 2019. Identification and quantification of key odorants in the World’s four most famous black teas. Food Research International 121, 73-83.


Keemun, Assam, Darjeeling and Ceylon black teas are honored as the world's four most famous black teas, and their excellent aroma qualities are well received by people around the world. In this study, aroma components in these four types of teas were analyzed by comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOFMS) and gas chromatography-olfactometry (GC-O) technologies. A total of 40 aroma-active compounds were ultimately identified, especially benzeneacetaldehyde, geraniol, (Z)-3-hexen-1-yl hexanoate, trans-β-ionone, cis-linalool oxide (pyranoid), hotrienol, and methyl salicylate presented the strongest aroma strengths with pleasant scents in all tested teas. The quantification results indicated that 19 compounds including (Z)-3-hexenol, 1-octen-3-ol, linalool, phenylethyl alcohol, hexanal, benzeneacetaldehyde, limonene, heptanoic acid, (Z)-3-hexen-1-ol, acetate, benzyl alcohol, trans-linalool oxide (furanoid), hotrienol, 1-octen-3-one, 2-nonanone, (E)-2-octenal, nonanal, β-myrcene, 2-pentylfuran, and methylpyrazine were identified as the key compounds with odor activity values (OAVs) higher than 1.0 in the world's four most famous black teas. Notably, the comparison of GC-O and OAV calculation results showed that methyl salicylate (Ceylon), (E)-2-octenal (Assam), benzeneacetaldehyde (Keemun) and linalool and trans-linalool oxide (furanoid) (Darjeeling) might be the most definitive odorants in the corresponding tea categories.



Fire condensates from vegetation and household burnings occur ubiquitously in the environment. Until now, however, it was difficult to estimate their origin and any relation to pyrogenic carbon deposited as charcoal. Our aim here was: (i) to differentiate the chemical composition of fire condensates from charcoal particles, and (ii) to relate this to fuel origins from grass, softwood or hardwood. We analysed δ13C and δ15N isotope composition, lignin-derived phenols, benzene polycarboxylic acids (BPCA) and polycyclic aromatic hydrocarbons (PAH), in lab-produced charcoals and condensates at combustion temperatures of 300, 350, 400, 450, 500 and 600 °C. We found that the BPCA and PAH composition of condensates differed significantly from that of charcoals. Condensates exhibited larger portions of benzene penta- to hexacarboxylic acids (B5CA to B6CA), phenanthrene (p < 0.01) and four-ring PAH (fluoranthene, pyrene, chrysene and benz[a]anthracene, p < 0.01). PAH ratios of indeno[1,2,3-cd]pyrene to benzo[ghi]perylene (IP/(IP + B[ghi]P) and fluoranthene to pyrene (Flua/(Flua + Py) were diagnostic for condensates, but independent from fuel type. Composition of the 1,2-, 1,7- and 2,6|3,5 dimethylphenanthrenes (DMP) was fuel specific, with the ratio of the (1,7 + 2,6|3,5)/(1,2 + 1,7 + 2,6|3,5) isomers separating hardwood (0.2–0.6), from grass (0.6–0.9), and softwood (<0.9), thus enabling the identification of both condensate and charcoal fuel sources.

Kara-Gülbay, R., Korkmaz, S., Erdoğan, M.S., Kadınkız, G., 2019. Biomarker geochemistry of crude oils and Neogene bituminous shales in the Yeniköy area, Ereğli-Ulukișla Basin, Central Anatolia, Turkey. Journal of Petroleum Geology 42, 173-191.


In the Ereğli‐Ulukıșla Basin, southern Turkey, crude oil shows have been observed in the subsurface in the shale‐dominated non‐marine Upper Miocene – Pliocene succession. Based on analyses of samples from four boreholes, the shales’ organic matter content, thermal maturity and depositional characteristics are discussed in this study. Geochemical correlations are established between shale extracts and a crude oil sampled from the shale succession. The shales have moderate to high hydrogen index (HI) and very low oxygen index (OI) values. Pyrolysis data show that the shales contain both Types I and II kerogen, and n‐alkane and biomarker distributions indicate that organic matter is dominated by algal material. Very high C26/C25 and C24/C23, and low C22/C21 tricyclic terpane ratios and C31 R/C30 hopane, C29/(C28+C29) MA and DBT/P ratios in shale extracts indicate that deposition occurred in a lacustrine setting. High gammacerane and C35 homohopane concentrations and low diasterane/sterane ratios with a very low Pr/Ph ratio suggest that both the shales and the source rocks for the oil were deposited in a highly anoxic environment in which the water column may have been thermally stratified.

Although the shales analysed have very low Tmax values, the production index is quite high which suggests that the shales are early‐mature to mature. Biomarker ratios including C32 22S/(22R+22S) homohopanes, C29 20S/(20R+20S) and ββ(ββ+αα) steranes, moretane/hopane, TA(I)/TA(I+II) and MPI‐3 all suggest that the shales are within the oil window. Heavy components of free hydrocarbons (S1) within the shales may have been recorded as part of the Rock‐Eval S2 peak resulting in the low Tmax values.

The oil and shale extracts analysed are similar according to their sterane and triterpane distributions, suggesting that the oil was generated by the shales. However burial depths of the Upper Miocene – Pliocene shale succession are not sufficient for thermal maturation to have occurred. It is inferred that intense volcanism during the Pliocene – Pleistocene may have played an important role in local maturation of the shale succession.

Kashkooli, A.B., van der Krol, A., Rabe, P., Dickschat, J.S., Bouwmeester, H., 2019. Substrate promiscuity of enzymes from the sesquiterpene biosynthetic pathways from Artemisia annua and Tanacetum parthenium allows for novel combinatorial sesquiterpene production. Metabolic Engineering 54, 12-23.


The therapeutic properties of complex terpenes often depend on the stereochemistry of their functional groups. However, stereospecific chemical synthesis of terpenes is challenging. To overcome this challenge, metabolic engineering can be employed using enzymes with suitable stereospecific catalytic activity. Here we used a combinatorial metabolic engineering approach to explore the stereospecific modification activity of the Artemisia annua artemisinic aldehyde ∆11(13) double bond reductase2 (AaDBR2) on products of the feverfew sesquiterpene biosynthesis pathway (GAS, GAO, COS and PTS). This allowed us to produce dihydrocostunolide and dihydroparthenolide. For dihydroparthenolide we demonstrate that the preferred order of biosynthesis of dihydroparthenolide is by reduction of the exocyclic methylene of parthenolide, rather than through C4-C5 epoxidation of dihydrocostunolide. Moreover, we demonstrate a promiscuous activity

of feverfew CYP71CB1 on dihydrocostunolide and dihydroparthenolide for the production of 3β-hydroxy-dihydrocostunolide and 3β-hydroxy-dihydroparthenolide, respectively. Combined, these results offer new opportunities for engineering novel sesquiterpene lactones with potentially improved medicinal value.

Kayukova, G.P., Kosachev, I.P., Mikhailova, A.N., Vakhin, A.V., Isakov, D.R., 2019. Hydrothermal transformation of heavy oil and organic matter from carbonate rocks of oil fields of Tatarstan. Petroleum Science and Technology 37, 528-534.

https://doi.org/10.1080/10916466.2018.1550494

In laboratory model experiments were identified features of hydrothermal transformation of heavy oil and organic matter productivity of carbonate rocks from Bashkirian stage of deposits of the Middle-Carboniferous of Tatarstan territories. Experiments were conducted at temperature of 360?°C in hydrogen environment in presence of aqueous phase. The impact of hydrothermal factors on rocks leads to decrease in content of insoluble OM - kerogen and increase content of free hydrocarbons. With increase in content of saturated and aromatic hydrocarbons, content of resin-asphaltene components decreases. Changes in composition lead to significant reduction in density of heavy oil from 0.9254 to 0.8273?g/cm3.

Kebukawa, Y., Ito, M., Zolensky, M.E., Greenwood, R.C., Rahman, Z., Suga, H., Nakato, A., Chan, Q.H.S., Fries, M., Takeichi, Y., Takahashi, Y., Mase, K., Kobayashi, K., 2019. A novel organic-rich meteoritic clast from the outer solar system. Scientific Reports 9, Article 3169.

https://doi.org/10.1038/s41598-019-39357-1

The Zag meteorite which is a thermally-metamorphosed H ordinary chondrite contains a primitive xenolithic clast that was accreted to the parent asteroid after metamorphism. The cm-sized clast contains abundant large organic grains or aggregates up to 20 μm in phyllosilicate-rich matrix. Here we report organic and isotope analyses of a large (~10 μm) OM aggregate in the Zag clast. The X-ray micro-spectroscopic technique revealed that the OM aggregate has sp2 dominated hydrocarbon networks with a lower abundance of heteroatoms than in IOM from primitive (CI,CM,CR) carbonaceous chondrites, and thus it is distinguished from most of the OM in carbonaceous meteorites. The OM aggregate has high D/H and 15N/14N ratios (δD = 2,370 ± 74‰ and δ15N = 696 ± 100‰), suggesting that it originated in a very cold environment such as the interstellar medium or outer region of the solar nebula, while the OM is embedded in carbonate-bearing matrix resulting from aqueous activities. Thus, the high D/H ratio must have been preserved during the extensive late-stage aqueous processing. It indicates that both the OM precursors and the water had high D/H ratios. Combined with 16O-poor nature of the clast, the OM aggregate and the clast are unique among known chondrite groups. We further propose that the clast possibly originated from D/P type asteroids or trans-Neptunian Objects.

Kenig, F., Chou, L., Wardrop, D.J., 2019. Comment on “Evaluation of the tenax trap in the sample analysis at Mars instrument suite on the curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater” by Miller et al. (2015). Journal of Geophysical Research: Planets 124, 644-647.

https://doi.org/10.1029/2018JE005606

Plain Language Summary: Miller et al. [2015, https://doi.org/10.1002/2015JE004825] described the result of experiments testing the potential of Tenax TA, a polymer used on Sample Analysis at Mars (SAM), as a source of chlorinated benzene. Miller et al. [2015] conclude that the amount of chlorobenzene produced is low and that Tenax TA cannot be the source of the chlorobenzene observed on Mars by SAM. Miller et al. [2015] did not provide the identification of two unknown compounds produced during these pyrolysis experiments, though their abundance is orders of magnitude higher than that of chlorobenzene. Here, we tentatively identify these compounds based on the mass spectra provided by Miller et al. [2015], the most abundant of which is a chlorinated monomer of Tenax TA. This chlorinated monomer is likely to accumulate in the hydrocarbon Tenax trap and in the transfer line between the trap and the mass spectrometer. Further breakdown of these compounds could lead the high background of chlorobenzene observed on Mars.

Original Article: Miller, K. E., Kotrc, B., Summons, R. E., Belmahdi, I., Buch, A., Eigenbrode, J. L., Freissinet, C., Glavin, D. P., & Szopa, C. ( 2015). Evaluation of the Tenax trap in the sample analysis at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater. Journal of Geophysical Research: Planets, 120, 1446– 1459.

Reply to comment: Summons, R.E., Miller, K.E., Kotrc, B., Belmahadi, I., Buch, A., Eigenbrode, J.L., Freissinet, C., Glavin, D.P., Szopa, C., 2019. Reply to Comment by F. Kenig, L. Chou, and D. J. Wardrop on “Evaluation of the Tenax trap in the sample analysis at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater” by Miller et al., 2015. Journal of Geophysical Research: Planets 124, 648-650.



Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Network analyses revealed co-occurrence patterns among eukaryotes of different trophic levels as well as between bacteria and eukaryotes, hinting at many possibilities for microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.

Khatibi, S., Ostadhassan, M., Hackley, P., Tuschel, D., Abarghani, A., Bubach, B., 2019. Understanding organic matter heterogeneity and maturation rate by Raman spectroscopy. International Journal of Coal Geology 206, 46-64.


Solid organic matter (OM) in sedimentary rocks produces petroleum and solid bitumen when it undergoes thermal maturation. The solid OM is a ‘geomacromolecule’, usually representing a mixture of various organisms with distinct biogenic origins, and can have high heterogeneity in composition. Programmed pyrolysis is a common method to reveal bulk geochemical characteristics of the dominant OM, while detailed organic petrography is required to reveal information about the biogenic origin of contributing macerals. Despite the advantages of programmed pyrolysis, it cannot provide information about the heterogeneity of chemical compositions present in the individual OM types. Therefore, other analytical techniques such as Raman spectroscopy are necessary.

In this study, we compared geochemical characteristics and Raman spectra of two sets of naturally and artificially matured Bakken source rock samples. A continuous Raman spectral map on solid bitumen particles was created from the artificially matured hydrous pyrolysis residues, in particular, to show the systematic chemical modifications in microscale. Spectroscopic data was plotted for both sets against thermal maturity to compare maturation rate/path for these two separate groups. The outcome showed that artificial maturation through hydrous pyrolysis does not follow the same trend as naturally-matured samples although having similar solid bitumen reflectance values (%SBRo).

Furthermore, Raman spectroscopy of solid bitumen from artificially matured samples indicated the heterogeneity of OM decreases as maturity increases. This may represent an alteration in chemical structure towards more uniform compounds at higher maturity. This study may emphasize the necessity of using analytical methods such as Raman spectroscopy along with conventional geochemical methods to better reveal the underlying chemical structure of OM. Finally, observation by Raman spectroscopy of chemical alteration of OM during artificial maturation may assist in the proposal of improved pyrolysis protocols to better resemble natural geologic processes.

Khattak, H.K., Bianucci, P., Slepkov, A.D., 2019. Linking plasma formation in grapes to microwave resonances of aqueous dimers. Proceedings of the National Academy of Sciences 116, 4000-4005.

http://www.pnas.org/content/early/2019/02/13/1818350116.abstract

Significance: In a popular parlor trick, plasma is created by irradiating grape hemispheres in a household microwave oven. This work ties the source of the plasma to microwave photonic hotspots at the junction of aqueous dielectric spherical dimers. We use a combination of thermal-imaging techniques and computer simulations to show that grape-sized fruit and hydrogel beads form resonant cavities that concentrate electromagnetic fields to extreme subwavelength regions. This is enabled by the large dielectric susceptibility of water at microwave frequencies. Furthermore, the absorptive properties of water are key to washing out complex internal modes and for allowing the evanescent hotspot build-up. Our approach to microwave resonances in high-dielectric materials opens a sandbox for nanocluster photonics research.

Abstract: The sparking of cut grape hemispheres in a household microwave oven has been a poorly explained Internet parlor trick for over two decades. By expanding this phenomenon to whole spherical dimers of various grape-sized fruit and hydrogel water beads, we demonstrate that the formation of plasma is due to electromagnetic hotspots arising from the cooperative interaction of Mie resonances in the individual spheres. The large dielectric constant of water at the relevant gigahertz frequencies can be used to form systems that mimic surface plasmon resonances that are typically reserved for nanoscale metallic objects. The absorptive properties of water furthermore act to homogenize higher-mode profiles and to preferentially select evanescent field concentrations such as the axial hotspot. Thus, beyond providing an explanation for a popular-science phenomenon, we

outline a method to experimentally model subwavelength field patterns using thermal imaging in macroscopic dielectric systems.

Kim, J., Chang, W., 2019. Modified soil respiration model (URESP) extended to sub-zero temperatures for biostimulated petroleum hydrocarbon-contaminated sub-Arctic soils. Science of The Total Environment 667, 400-411.


It has been increasingly reported that aerobic soil respiration activity (CO2 production and O2 consumption) is measurable in frozen cold-climate soils. This study modifies the Generalized Respiration (GRESP) model, a function of soil temperature (T) and unfrozen water content (M), to cover the frozen, partially frozen and unfrozen phases of successfully bioremediated, petroleum hydrocarbon-contaminated, sandy sub-Arctic soils. The Michaelis-Menten equation was modified to express the observable change in unfrozen water content near 0 °C, which is related to soil respiration activity during soil phase changes and at temperatures below the effective endpoint of detectable unfrozen water at −2 °C. The modified Michaelis-Menten equation was further combined with a Q10 temperature term, and was then incorporated into the GRESP equation to produce a new URESP model for the engineered soil bioremediation system at sub-zero temperatures. The URESP model was applied to published input data measured from the biostimulated site soils of a pilot-scale soil tank experiment conducted between −5 and 15 °C. The model fit well with the experimental data for CO2 production (R2 = 0.96) and O2 consumption (R2 = 0.92). A numerical soil thermal model (TEMP/W model) of the thawing biotreated soils in the tank was also used in this study to produce valid alternative (predictive) input T and M data for the URESP model. The URESP-derived respiration quotients (RQ; 0.695 to 0.698), or the ratios of CO2 production to O2 consumption, aligned with the experimental RQ values from the soil tank experiment (0.69) and fell within the theoretical RQ range for aerobic hydrocarbon degradation (0.63–0.80). The URESP model combined with the TEMP/W simulation approximated changes in soil respiration during thawing and characterized the computed soil respiration outputs as related to hydrocarbon utilization, based on their RQ values.


https://doi.org/10.1029/2018JG004561

Abstract : Natural attenuation is very often the remediation method of necessity, rather than choice, for beach environments impacted by offshore exploration/drilling accidents. Robust methods that can be efficiently utilized in difficult to access and ecologically sensitive areas are needed for the long‐term monitoring of such degradation processes. A prime candidate for such a monitoring tool is the spectral induced polarization (SIP) method, a geophysical technique successfully used for characterization and monitoring of hydrocarbon degradation in freshwater environments. In this laboratory experiment the SIP method successfully monitored the natural degradation of beach sediments impacted by the Deepwater Horizon oil spill. Using the SIP, we were able to differentiate between biotic (e.g., microbial driven) and abiotic (e.g., dilution) degradation processes and infer degradation rates. To our knowledge this is the first effort to use the SIP method as a monitoring aid in high salinity environments.

Plain Language Summary: Offshore drilling/exploration accidents can result in the contamination of remote and ecologically sensitive areas. In most cases the only realistic remediation choice is natural

degradation. In this paper we discuss the use of a noninvasive geophysical method, termed spectral induced polarization, as a monitoring tool of oil contamination degradation in brackish environments. The presented laboratory works supports the suitability of the method for monitoring not only the progress of degradation but also any microbial related degradation processes.

King, A.J., Russell, S.S., Schofield, P.F., Humphreys-Williams, E.R., Strekopytov, S., Abernethy, F.A.J., Verchovsky, A.B., Grady, M.M., 2019. The alteration history of the Jbilet Winselwan CM carbonaceous chondrite: An analog for C-type asteroid sample return. Meteoritics & Planetary Science 54, 521-543.

https://doi.org/10.1111/maps.13224

Jbilet Winselwan is one of the largest CM carbonaceous chondrites available for study. Its light, major, and trace elemental compositions are within the range of other CM chondrites. Chondrules are surrounded by dusty rims and set within a matrix of phyllosilicates, oxides, and sulfides. Calcium‐ and aluminum‐rich inclusions (CAIs) are present at ≤1 vol% and at least one contains melilite. Jbilet Winselwan is a breccia containing diverse lithologies that experienced varying degrees of aqueous alteration. In most lithologies, the chondrules and CAIs are partially altered and the metal abundance is low (<1 vol%), consistent with petrologic subtypes 2.7–2.4 on the Rubin et al. (2007) scale. However, chondrules and CAIs in some lithologies are completely altered suggesting more extensive hydration to petrologic subtypes ≤2.3. Following hydration, some lithologies suffered thermal metamorphism at 400–500 °C. Bulk X‐ray diffraction shows that Jbilet Winselwan consists of a highly disordered and/or very fine‐grained phase (73 vol%), which we infer was originally phyllosilicates prior to dehydration during a thermal metamorphic event(s). Some aliquots of Jbilet Winselwan also show significant depletions in volatile elements such as He and Cd. The heating was probably short‐lived and caused by impacts. Jbilet Winselwan samples a mixture of hydrated and dehydrated materials from a primitive water‐rich asteroid. It may therefore be a good analog for the types of materials that will be encountered by the Hayabusa‐2 and OSIRIS‐REx asteroid sample‐return missions.

Kioka, A., Tsuji, T., Otsuka, H., Ashi, J., 2019. Methane concentration in mud conduits of submarine mud volcanoes: A coupled geochemical and geophysical approach. Geochemistry, Geophysics, Geosystems 20, 792-813.

https://doi.org/10.1029/2018GC007890

Mud volcanoes are among the largest geological sources releasing methane gas. Numerous studies have revealed their origins and compositions released from submarine mud volcanoes. However, quantification of the amount of gas inside submarine mud volcanoes has been challenging due to the difficulty of in situ measurements, which has hampered better evaluation for their contribution to the global methane budget. Here we provide a coupled geochemical and geophysical model that bridges bulk methane concentrations and seismic wave velocities in the mud conduit of submarine mud volcano. This model is applicable to most submarine mud volcanoes and is able to estimate methane concentration at the upper several hundreds of meters in the mud conduits using downhole logging data or seismic data. Our calculation for submarine mud volcanoes in the Eastern Mediterranean and the Nankai plate subduction zones shows that the weight fractions of gaseous and dissolved methane in total weight of sediment are 1,000-3,500 ppm within their mud conduits, which are much higher than previously expected from pore-water evidence from conventional shallow subsurface sampling. Although more definitive calculations cannot be made until the model parameters are better constrained, our approach provides an opportunity for re-estimating the global methane budget in

submarine mud volcanoes, shedding new light upon the impact of submarine mud volcanism on carbon cycle.

Kobs Nawotniak, S.E., Miller, M.J., Stevens, A.H., Marquez, J.J., Payler, S.J., Brady, A.L., Hughes, S.S., Haberle, C.W., Sehlke, A., Beaton, K.H., Chappell, S.P., Elphic, R.C., Lim, D.S.S., 2019. Opportunities and challenges of promoting scientific dialog throughout execution of future science-driven extravehicular activity. Astrobiology 19, 426-439.

https://doi.org/10.1089/ast.2018.1901

Science-driven, human spaceflight missions of the future will rely on regular and interactive communication between Earth- and space-based teams during activity in which astronauts work directly on Mars or other planetary surfaces (extravehicular activity, EVA). The Biologic Analog Science Associated with Lava Terrains (BASALT) project conducted simulated human missions to Mars, complete with realistic one-way light time (OWLT) communication latency. We discuss the modes of communication used by the Mars- and Earth-based teams, including text, audio, video, and still imagery. Real-time communication between astronauts in the field (extravehicular, EV) and astronauts in a communication relay station (intravehicular, IV) was broadcast over OWLT, providing important contextual information to the Science Backroom Team (SBT) in Mission Control. Collaborative communication between the Earth- and Mars-based teams, however, requires active communication across latency via the Mission Log. We provide descriptive statistics of text communication between IV and SBT in a high-fidelity, scientifically driven analog for human space exploration. Over an EVA, the SBT sent an average of ∼23 text messages containing recommendations, requests, and answers to questions, while the science-focused IV crew member (IV2) sent an average of ∼38 text messages. Though patterns varied, communication between the IV and SBT teams tended to be highest during ∼50–150 min into the EVA, corresponding to the candidate sample search and presampling instrument survey phases, and then decreased dramatically after minute ∼200 during the sample collection phase. Generally, the IV2 and SBT used ∼4.6 min to craft a reply to a direct question or comment, regardless of message length or OWLT, offering a valuable glimpse into actual time-to-reply. We discuss IV2-SBT communication within the context of case examples from an EVA during which communication failures affected operations in the field. Finally, we offer recommendations for communication practices for use in future analogs and, perhaps, science-driven human spaceflight.

Korte, A.R., Morris, N.J., Vertes, A., 2019. High throughput complementary analysis and quantitation of metabolites by MALDI- and silicon nanopost array-laser desorption/ionization-mass spectrometry. Analytical Chemistry 91, 3951-3958.


Silicon nanopost array (NAPA) structures have been shown to be effective substrates for laser desorption/ionization-mass spectrometry (LDI-MS) and have been used to analyze a variety of samples including peptides, metabolites, drugs, explosives, and intact cells, as well as to image lipids and metabolites in tissue sections. However, no direct comparison has yet been conducted between NAPA-MS and the most commonly used LDI-MS technique, matrix-assisted laser desorption/ionization (MALDI)-MS. In this work, we compare the utility of NAPA-MS to that of MALDI-MS using two common matrices for the analysis of metabolites in cellular extracts and human urine. Considerable complementarity of molecular coverage was observed between the two techniques. Of 178 total metabolites assigned from cellular extracts, 68 were uniquely detected by NAPA-MS and 62 were uniquely detected by MALDI-MS. NAPA-MS was found to provide

enhanced coverage of low-molecular weight compounds such as amino acids, whereas MALDI afforded better detection of larger, labile compounds including nucleotides. In the case of urine, a sample largely devoid of higher-mass labile compounds, 88 compounds were uniquely detected by NAPA-MS and 13 by MALDI-MS. NAPA-MS also favored more extensive alkali metal cation adduction relative to MALDI-MS, with the [M + 2Na/K – H]+ species accounting for as much as 97% of the total metabolite ion signal in positive mode. The capability of NAPA-MS for targeted quantitation of endogenous metabolites in urine via addition of isotopically labeled standards was also examined. Both NAPA-MS and MALDI-MS provided quantitative results in good agreement with one another and the concentrations reported in the literature, as well as good sample-to-sample reproducibility (RSD < 10%).

Kreitsmann, T., Külaviir, M., Lepland, A., Paiste, K., Paiste, P., Prave, A.R., Sepp, H., Romashkin, A.E., Rychanchik, D.V., Kirsimäe, K., 2019. Hydrothermal dedolomitisation of carbonate rocks of the Paleoproterozoic Zaonega Formation, NW Russia — Implications for the preservation of primary C isotope signals. Chemical Geology 512, 43-57.


The Paleoproterozoic Zaonega Formation in Karelia, NW Russia, has played a key role in understanding the environmental conditions postdating the Great Oxidation and Lomagundi-Jatuli Events. Its carbonate- and organic-rich rocks (shungite) define the postulated Shunga Event representing an accumulation of very organic-rich sediments at c. 2 Ga and are central in ideas about changing ocean-atmosphere composition in the wake of those worldwide biogeochemical phenomena. Our work focussed on a key interval of carbonate rocks in the upper part of the Formation to: (i) obtain new high-resolution carbon, oxygen and strontium isotope data complemented by detailed petrography and mineralogical characterisation and (ii) expand upon previous studies by using our data to constrain geochemical modelling and show in greater detail how magmatic hydrothermal fluids induced dedolomitisation and altered geochemical signals. Our findings show that the δ13Ccarb of calcite-rich intervals are the most altered, with values between −16.9 to 0.6‰, whereas the dolomite-dominated parts retain the best-preserved (i.e. most original) values. Those define a trend of steadily increasing δ13Ccarb, from −6 to +0.5‰, which we interpret as a return to normal marine conditions and carbonate-carbon values following the Lomagundi-Jatuli Event.

Kreuter, L.J., Weinfurtner, A., Ziegler, A., Weigl, J., Hoffmann, J., Morgner, N., Müller, V., Huber, H., 2019. Purification of a crenarchaeal ATP synthase in the light of the unique bioenergetics of Ignicoccus species. ournal of Bacteriology 201, e00510-00518.

http://jb.asm.org/content/201/7/e00510-18.abstract

Abstract: In this study, the ATP synthase of Ignicoccus hospitalis was purified, characterized, and structurally compared to the respective enzymes of the other Ignicoccus species, to shed light on energy conservation in this unique group of archaea. The crenarchaeal genus Ignicoccus comprises three described species, i.e., I. hospitalis and Ignicoccus islandicus from hot marine sediments near Iceland and Ignicoccus pacificus from a hydrothermal vent system in the Pacific Ocean. This genus is unique among all archaea due to the unusual cell envelope, consisting of two membranes that enclose a large intermembrane compartment (IMC). I. hospitalis is the best studied member of this genus, mainly because it is the only known host for the potentially parasitic archaeon Nanoarchaeum equitans. I. hospitalis grows chemolithoautotrophically, and its sole energy-yielding reaction is the reduction of elemental sulfur with molecular hydrogen, forming large amounts of hydrogen sulfide. This reaction generates an electrochemical gradient, which is used by the ATP synthase, located in

the outer cellular membrane, to generate ATP inside the IMC. The genome of I. hospitalis encodes nine subunits of an A-type ATP synthase, which we could identify in the purified complex. Although the maximal in vitro activity of the I. hospitalis enzyme was measured around pH 6, the optimal stability of the A1AO complex seemed to be at pH 9. Interestingly, the soluble A1 subcomplexes of the different Ignicoccus species exhibited significant differences in their apparent molecular masses in native electrophoresis, although their behaviors in gel filtration and chromatography-mass spectrometry were very similar.

Importance: The Crenarchaeota represent one of the major phyla within the Archaea domain. This study describes the successful purification of a crenarchaeal ATP synthase. To date, all information about A-type ATP synthases is from euryarchaeal enzymes. The fact that it has not been possible to purify this enzyme complex from a member of the Crenarchaeota until now points to significant differences in stability, possibly caused by structural alterations. Furthermore, the study subject I. hospitalis has a particular importance among crenarchaeotes, since it is the only known host of N. equitans. The energy metabolism in this system is still poorly understood, and our results can help elucidate the unique relationship between these two microbes.

Krim, N., Tribovillard, N., Riboulleau, A., Bout-Roumazeilles, V., Bonnel, C., Imbert, P., Aubourg, C., Hoareau, G., Fasentieux, B., 2019. Reconstruction of palaeoenvironmental conditions of the Vaca Muerta formation in the southern part of the Neuquén Basin (Tithonian-Valanginian): Evidences of initial short-lived development of anoxia. Marine and Petroleum Geology 103, 176-201.


The Vaca Muerta Formation is a famous source rock being largely present in Argentina. The formation was examined in the southern part of the Neuquén Basin through clay-mineral assemblage composition, as well as organic and inorganic geochemical characteristics. In total, 259 samples were analyzed on both sides of the Huincul Arch (major E-W structure that divided the southern part of the basin into two depocentres). South to this structure (Picún Leufú area), the total organic carbon content (TOC) can reach 20% but is generally ranging from 0.1 to 6%. To the north (Covunco area), average TOC does not exceed 0.5%. Clay-mineral assemblages indicate an evolution of the sources of clastic supply through time in response to evolving weathering/erosion at the regional scale. Redox-sensitive trace-element distribution shows that the particulate iron shuttle process operated, with an initially-euxinic depositional environment that evolved rapidly to oxygenated seawater and suboxic sediments. Our results suggest an episodically restricted circulation pattern that occurred at the beginning of the deposition of the Vaca Muerta Formation (highest TOC content).



Pore structures in the shale matrix are an essential factor affecting the storage capacity of gas of shale beds as well as production performance. Twenty organic-rich shale samples at different depths were collected from Barakar Formation of Mand-Raigarh basin, to examine the pore structure and their fractal characteristic. Fractal dimension was calculated by following FHH theory to investigate the complexity of pore surfaces, storage mechanism and the pore network system. The complex pore system influenced by thermal cracking of organic matter, pore dissolution during geochemical weathering and tectonics of the basins having surface area 5.56–23.94 m2/g (avg. 14.21 m2/g).

Whereas, the pore volume determined using the BJH model varying from 0.035 to 0.076 cc/g (avg. 0.053 cc/g). FTIR spectrum demonstrated that significant presence of aliphatic side chains and aromatic carbon structures existing in studied shale influencing the pore volume. It is summarized that pores and matrix of shale are built by complex mixtures of organic and inorganic content. Further, the pores are categorized into organic pores evolved during thermal cracking, inter-granular, intra-granular and inter-crystalline due to the large content of altered clays and minerals showing fissile nature. The SEM-EDX derived facies indicating the involvement of different chemical constituents following the trend of alteration as well as carbon enrichment. The D1 and D2 values obtained through FHH model range from 1.17 to 2.45 and 2.54–2.70, the fractal values particularly D2 are ∼3 demonstrating the pore surfaces and structure of studied shales beds are complex and heterogeneous. This study helps to enhance the exploration and advancement in the shale gas resources from Ib-River of Mand-Raigarh Basin, India.

Kunoh, T., Kusano, Y., Takeda, M., Nakanishi, M., Matsumoto, S., Suzuki, I., Takano, M., Kunoh, H., Takada, J., 2019. Formation of gold particles via thiol groups on glycoconjugates comprising the sheath skeleton of Leptothrix. Geomicrobiology Journal 36, 251-260.

https://doi.org/10.1080/01490451.2018.1550127

Leptothrix, iron-oxidizing bacterium, produces microtubular sheaths that surround the catenulate cells. Organic nanofibrils excreted from the cell surfaces interweave and coalesce to form immature sheaths, which attract aqueous-phase inorganics to eventually form mature organic?inorganic sheaths. Such inorganic encrustation of the sheaths results from interactions between functional groups in the sheath skeleton and inorganics. Based on our previous findings that Leptothrix sheath skeleton sorbed 47 inorganics (Au was one of the most abundant adsorbates), we examined the sorption status of Au cations on cell-enclosing sheaths and their protein-free remnants and found that nano to sub-micron Au particles (AuNPs and AuSMPs, respectively) formed on the sheath-forming polymer consisting of a glycoconjugate (an amphoteric glycan modified with cysteine, glycine, and 3-hydroxypropionic acid). When the purified polymer was incubated in HAuCl4 solution, AuNPs and AuSMPs formed on the polymer surfaces. Both particles formed also on cell-enclosing sheaths and protein-free sheath remnants incubated in HAuCl4 solution. When SH groups in the cell-enclosing sheaths were masked with a fluorescent protein, Au particles did not form after incubation in HAuCl4 solution. Results implicate that SH groups are at least partially involved in the reduction of Au cations to metallic Au and eventual formation of Au particles.

Küppers, M., 2019. The mystery of Ceres' activity. Journal of Geophysical Research: Planets 124, 205-208.

https://doi.org/10.1029/2018JE005910

Abstract: In recent years, the dwarf planet Ceres has been found to release water vapor. Detailed investigation of the surface and subsurface by NASA's Dawn mission reveal localized patches of surface ice and an ice abundance of around 10% in the shallow subsurface, within a meter below the surface. Landis et al. (2019, https://doi.org/10.1029/2018JE005780) quantify the expected sublimation from the surface and subsurface ice reservoirs at Ceres, and the expected evaporation rates are factors of several lower than the observed ones. Although consideration of additional processes may possibly reduce the discrepancy, the origin of Ceres' exosphere is not yet clear.

Plain Language Summary: The dwarf planet Ceres, the largest object in the asteroid belt, is known to contain large amounts of water ice, and water vapor was detected around it. Possible sources of the

water are surface exposure of ice through impacts and subsequent sublimation when heated by sunlight, or volcanic activity. It turns out that with either process it is difficult to create sufficient water vapor to explain the observations. This means that the geological processes on Ceres are not fully understood.

Kushkevych, I., Dordević, D., Vítězová, M., 2019. Toxicity of hydrogen sulfide toward sulfate-reducing bacteria Desulfovibrio piger Vib-7. Archives of Microbiology 201, 389-397.

https://doi.org/10.1007/s00203-019-01625-z

Sulfate-reducing bacteria (SRB) belonging to the intestinal microbiota are the main producers of hydrogen sulfide and their increasing amount due to the accumulation of this compound in the bowel are involved in the initiation and maintenance of inflammatory bowel disease. The purpose of this experiment is to study the relative toxicity of hydrogen sulfide and survival of Desulfovibrio piger Vib-7 through monitoring: sulfate reduction parameters (sulfate consumption, hydrogen sulfide production, lactate consumption and acetate production) and kinetic parameters of these processes. The research is highlighting the survival of intestinal SRB, D. piger Vib-7 under the influence of different hydrogen sulfide concentrations (1–7 mM). The highest toxicity of H2S was measured in the presence of concentrations higher than 6 mM, where growing was stopped, though metabolic activities were not 100% inhibited. These findings are confirmed by cross correlation and principal component analysis that clearly supported the above mentioned results. The kinetic parameters of bacterial growth and sulfate reduction were inhibited proportionally with increasing H2S concentration. The presence of 5 mM H2S resulted in two times longer lag phase and generation time was eight times longer. Maximum rate of growth and hydrogen production was stopped under 4 mM, emphasizing the H2S toxicity concentrations to be < 4 mM, even for sulfide producing bacteria such as Desulfovibrio. The results are confirming H2S concentrations toxicity toward Desulfovibrio, especially the study novelty should be emphasized where it was found that the exact H2S limits (> 4 mM) toward this bacterial strain inhabiting humans and animals intestine.

Kuwayama, T., Charrier-Klobas, J.G., Chen, Y., Vizenor, N.M., Blake, D.R., Pongetti, T., Conley, S.A., Sander, S.P., Croes, B., Herner, J.D., 2019. Source apportionment of ambient methane enhancements in Los Angeles, California, to evaluate emission inventory estimates. Environmental Science & Technology 53, 2961-2970.


Rapid increase in atmospheric methane (CH4) mixing ratios over the past century is attributable to the intensification of human activities. Information on spatially explicit source contributions is needed to develop efficient and cost-effective CH4 emission reduction and mitigation strategies to addresses near-term climate change. This study collected long-term ambient CH4 measurements at Mount Wilson Observatory (MWO) in Los Angeles, California, to estimate the annual CH4 emissions from the portion of Los Angeles County that is within the South Coast Air Basin (SCLA). The measurement-based CH4 emission estimates for SCLA ranged from 3.95 to 4.89 million metric tons (MMT) carbon dioxide equivalent (CO2e) per year between 2012 and 2016. Source apportionment of CH4, CO, CO2, and volatile organic compounds (VOCs) measurements were used to evaluate source categories that contributed to ambient CH4 mixing ratio enhancements (ΔCH4) at SCLA between 2014 and 2016. Results suggested ΔCH4 contributions of 56–79% from natural gas sources, 7–31% from landfills, and 4–15% from transportation sources. The SCLA-specific CH4 emission estimate made using a research grade gridded CH4 emission inventory suggested contributions of 47% from natural gas sources and 50% from landfills. Subsequent airborne measurements determined that CH4

emissions from two major CH4 sources in SCLA were significantly smaller in magnitude than previously thought. This study highlights the importance of studying the variabilities of CH4 emissions across California for policy makers and stakeholders alike.

Kuznetsov, O., Agrawal, D., Suresh, R., Feng, X., Behles, J., Khabashesku, V., 2019. Experimental evaluation of colloidal nanosilica for improving bitumen recovery from mined oil-sand ore. SPE Reservoir Evaluation & Engineering 22, 50-60.

https://doi.org/10.2118/179567-PA

Oil-sand ore flotation is a primary method of bitumen recovery from mined Athabasca tar sands. In bitumen flotation, suspended biwettable ore fines, such as clays, tend to migrate to oil/water interfaces, creating a slime coating on liberated bitumen droplets. Slime coating significantly reduces the efficiency of the flotation process and overall oil recovery. Ultradispersed hydrophilic silica nanoparticles were found to stabilize biwettable ore fines in an aqueous phase by adsorbing onto fines surfaces, even at concentrations as low as 50 ppm. As a result, fine solids move away from oil/water interfaces, reducing the slime coating and increasing bitumen recovery during flotation of low-grade ore by more than 5%. The addition of nanoparticles has no negative effect on froth quality or oil, water, and solid separation in naphthenic and paraffinic froth-treatment processes. The study demonstrated that colloidal nanoparticles affect many stages of the bitumen-extraction process—from bitumen separation to clay-wetability alteration.

Lakhova, A., Soldatova, R., Petrov, S., Nosova, A., Safiulina, A., 2019. Transformation of heavy oil in hydrothermal impact. Petroleum Science and Technology 37, 611-616.

https://doi.org/10.1080/10916466.2018.1560319

The results of experiments on the transformation of heavy oil in a steam-laden environment, at temperatures and pressures ensuring the presence of water in a superheated steam state, as well as in the subcritical and supercritical states are presented. It is shown that supercritical water provides the largest formation of light fractions having a boiling point of 350?°C: their content has increased by 2.5 times. Subcritical water, in contrast to water in the supercritical state, ensures the formation of light fractions at 73% rel. and reduces the content of asphaltenes by 53% rel. compared with the initial oil.



A comprehensive filter-based particulate matter polycyclic aromatic hydrocarbon (PAH) source apportionment study was conducted at the Wood Buffalo Environmental Association Bertha Ganter-Fort McKay (BGFM) community monitoring station from 2014 to 2015 to quantify ambient concentrations and identify major sources. The BGFM station is located in close proximity to several surface oil sands production facilities and was previously found to be impacted by their air emissions. 24-hour integrated PM2.5 and PM10–2.5 samples were collected on a 1-in-3-day schedule yielding 108 complete organic/inorganic filter sets for source apportionment modeling. During the study period PM2.5 averaged 8.6 ± 11.8 μg m−3 (mean ± standard deviation), and PM10–2.5 averaged 8.5 ± 9.5 μg m−3.

Wind regression analysis indicated that the oil sands production facilities were significant sources of PM2.5 mass and black carbon (BC), and that wildland fires were a significant source of the highest PM2.5 (>10 μg m−3) and BC events. A six-factor positive matrix factorization (PMF) model solution explained 95% of the measured PM2.5 and 78% of the measured ΣPAH. Five sources significantly contributed to PM2.5 including: Biomass Combustion (3.57 μg m−3; 40%); Fugitive Dust (1.86 μg m−3; 28%); Upgrader Stack Emissions (1.44 μg m−3; 21%); Petrogenic PAH (1.20 μg m−3; 18%); and Transported Aerosol (0.43 μg m−3 and 6%). However, the analysis indicated that only the pyrogenic PAH source factor significantly contributed (78%) to the measured ΣPAH. A five-factor PMF model dominated by fugitive dust sources explained 98% of PM10–2.5 mass and 86% of the ΣPAH. The predominant sources of PM10–2.5 mass were (i) Haul Road Dust (4.82 μg m−3; 53%), (ii) Mixed Fugitive Dust (2.89 μg m−3; 32%), (iii) Fugitive Oil Sand (0.88 μg m−3; 10%), Mobile Sources (0.23 μg m−3; 2%), and Organic Aerosol (0.06 μg m−3; 1%). Only the Organic Aerosol source significantly contributed (86%) to the measured ΣPAH.



Carbon is found in nature in a huge variety of allotropic forms and recent research in materials science has encouraged the development of technological materials based on nanocarbon. Carbon atoms with sp2 or sp3 hybridization can be thought of as building blocks. Following a bottom-up approach, we show how graphene and diamond molecules are built up and how their properties vary with size, reaching an upper limit with bulk graphite and diamond. Carbon atoms with sp2 hybridization give rise to an impressive number of different materials, such as carbon nanotubes, graphene nanoribbons, porous carbon and fullerene. As in any crystalline phase, the crystal structures of natural carbon allotropes (i.e. graphite and diamond) contain various types of imperfections. These so-called lattice defects are classified by their dimensions into 0D (point), 1D (line), 2D (planar) and 3D (volume) defects. Lattice defects control the physical properties of crystals and are often a fingerprint of the geological environment in which they formed and were modified. Direct observations of lattice defects are commonly accomplished by transmission electron microscopy. We present and discuss the ideal and real structures of carbon allotropes, the energetics of lattice defects and their significance in understanding geological processes and conditions.



There is a disputable theory that hydrocarbon can be injected into the reservoir, and migrate downward in an oil reservoir with an upper oil source, which is still questioned now. However, although some examples are previously found, questions still remain about the theory, regarding oil sources, oil migration pathways, and migration forces that related to downward hydrocarbon migration. For this reason, the Chezhen Graben in the Bohai Bay Basin is selected to study all the problems above. Geo-chemical evidence show that lower Es3 source rock (T6 in seismic profiles) has a close genetic relationship with the underlying Es4 (T7 in seismic profiles) and Ordovician oil. Therefore, the “upper source-lower reservoir” type can be formed inside the lower gentle slopes and sag zones, and inside the Cambrian and Permian reservoirs. The fluid inclusion experiment shows that the lower ES3 source rock underwent 3 over-pressure evolution stages. Meanwhile, there is a

huge pressure difference between the lower ES3 source rock and underlying ES4 reservoirs, which is the migration force of downward migration. In the lower areas of gentle slopes and sags, the early-generated and early-ended faults are terminated at the source rock of Es3 Member, and can be re-opened under the over-pressure influence of the source rock and regional tensile stress. Then they become the pathways of the so-called downward migration. The distance of downward migration can be calculated through the accumulation dynamic, which is obtained by hydrocarbon pressure subtracting the reservoir hydrostatic pressure, pressure attenuation, and displacement pressure. The research result on downward migration process is of great significance to broaden the hydrocarbon exploration fields.

Largen, A.H., Gudde, L.R., Franke, J.D., Hulce, M., 2019. Sterol synthesis is essential for viability in the planctomycete bacterium Gemmata obscuriglobus. FEMS Microbiology Letters 366, Article fnz019.

https://dx.doi.org/10.1093/femsle/fnz019

Oxidosqualene cyclases (OSCs) are remarkable enzymes that catalyze the production of the first sterol, lanosterol, in sterol biosynthetic pathways. These reactions are present in a limited number of bacterial species unlike eukaryotic species where sterol synthesis is ubiquitous. The biological role(s) of OSCs, and the sterols produced by the different sterol biosynthetic pathways in bacteria, are not clearly understood. Here, we show that inhibition of the Gemmata obscuriglobus OSC enzyme resulted in the inability of cells to form colonies on solid medium and resulted in cell death within 24 hr of inactivation for planktonic cells. The inclusion of lanosterol in cell culture medium was able to rescue the cell lethality associated with the OSC inhibitors. We purified active, recombinant bacterial OSC to high levels (>3 mg L−1 of culture) and demonstrated that the purified enzyme is active and inhibited by common OSC inhibitors. Comparable inhibitor concentrations were used in in vivo lethality experiments and in vitro enzymatic assays. Together, these results show that OSC, and the sterols produced by this enzyme, are essential for G. obscuriglobus viability.

Lasher, G.E., Axford, Y., 2019. Medieval warmth confirmed at the Norse Eastern Settlement in Greenland. Geology 47, 267-270.


Recent work has documented glacier advances in West Greenland coincident with the Medieval Climate Anomaly (MCA) and warmth across much of northern Europe. The North Atlantic Oscillation (NAO) has been invoked to explain antiphasing of temperatures between these North Atlantic regions. Historical and model observations suggest negative correlation between the mode of NAO and both temperature and δ18O values of precipitation over much of Greenland. We test for a hypothesized positive NAO mode and associated cool conditions during the MCA in South Greenland within the Norse Eastern Settlement by reconstructing δ18O values of precipitation at subcentennial resolution over the past 3000 yr using aquatic insect subfossils preserved in lake sediments. More positive δ18O values are found between 900 and 1400 CE, indicating a period of warmth in South Greenland superimposed on late Holocene insolation-forced Neoglacial cooling, and thus not supporting a positive NAO anomaly during the MCA. Highly variable δ18O values record an unstable climate at the end of the MCA, preceding Norse abandonment of Greenland. The spatial pattern of paleoclimate in this region supports proposals that North Atlantic subpolar ocean currents modulated South Greenland’s climate over the past 3000 yr, particularly during the MCA. Terrestrial climate in the Labrador Sea and Baffin Bay regions may be spatially heterogeneous on centennial time scales due in part to the influence of the subpolar gyre.

Lasich, M., Tumba, K., 2019. Single-site Langmuir-type adsorption in structure-I clathrate hydrates: A molecular simulation study using a general self-consistent force field. Fluid Phase Equilibria 489, 111-116.


This work reports on an investigation into the utility of a single-site approach to adsorption in structure-I clathrate hydrates through the consideration of a set of known clathrate hydrate-forming gases: carbon monoxide, methane, ethane, ethene, and hydrogen sulphide. Clathrate hydrates are an ice-like non-stoichiometric material consisting of a gas species that has been enclathrated by a hydrogen-bonded water lattice. The structure-I structure itself is a known solution to the Kelvin problem–i.e. a foam of approximately equal-volume bubbles with minimal inter-bubble surface area–and it has been previously demonstrated computationally for methane considered as a single pseudo-atom, that a single Langmuir-type site may suffice, since the cavities within the hydrate lattice do in fact have roughly equal volume. This study considers a broader range of structure-I clathrate hydrates using an explicit-atom approach, and demonstrates some of the limitations of this simplification.

Lee, C., Love, G.D., Hopkins, M.J., Kröger, B., Franeck, F., Finnegan, S., 2019. Lipid biomarker and stable isotopic profiles through Early-Middle Ordovician carbonates from Spitsbergen, Norway. Organic Geochemistry 131, 5-18.


One of the most dramatic episodes of sustained diversification of marine ecosystems in Earth history took place during the Early to Middle Ordovician Period. Changes in climate, oceanographic conditions, and trophic structure are hypothesised to have been major drivers of these biotic events, but relatively little is known about the composition and stability of marine microbial communities controlling biogeochemical cycles at the base of the food chain. This study examines well-preserved, carbonate-rich strata spanning the Tremadocian through Upper Dapingian stages from the Oslobreen Group in Spitsbergen, Norway. Abundant bacterial lipid markers (elevated hopane/sterane ratios, average = 4.8; maximum of 13.1), detection of Chlorobi markers in organic-rich strata, and bulk nitrogen isotopes (δ15Ntotal) averaging 0 to −1‰ for the open marine facies, suggest episodes of water column redox-stratification and that primary production was likely limited by fixed nitrogen availability in the photic zone. Near absence of the C30 sterane marine algal biomarker, 24-n-propylcholestane (24-npc), in most samples supports and extends the previously observed hiatus of 24-npc in Early Paleozoic (Late Cambrian to Early Silurian) marine environments. Very high abundances of 3β-methylhopanes (average = 9.9%; maximum of 16.8%), extends this biomarker characteristic to Early Ordovician strata for the first time and may reflect enhanced and sustained marine methane cycling during this interval of fluctuating climatic and low sulfate marine conditions. Olenid trilobite fossils are prominent in strata deposited during an interval of marine transgression with biomarker evidence for episodic euxinia/anoxia extending into the photic zone of the water column.

Lee, J., Kim, K.-I., Min, K.-B., Rutqvist, J., 2019. TOUGH-UDEC: A simulator for coupled multiphase fluid flows, heat transfers and discontinuous deformations in fractured porous media. Computers & Geosciences 126, 120-130.


A numerical simulator entitled TOUGH-UDEC is introduced for the analysis of coupled thermal-hydraulic-mechanical processes in fractured porous media. Two existing well-established codes, TOUGH2 and UDEC, are coupled to model multiphase fluid flows, heat transfers, and discontinuous deformations in fractured porous media by means of discrete fracture representation. TOUGH2 is widely used for the modeling of heat transfers and multiphase multicomponent fluid flows, and UDEC is a well-known distinct element code for rock mechanics. The two codes are solved sequentially, with coupling parameters passed to each equation at specific intervals. After solving thermal-hydraulic equations within the TOUGH2 code, pressure and temperature information is imported into the UDEC model. After solving the mechanical equation within the UDEC code the calculated fracture apertures are converted to the equivalent permeability and porosity values for a TOUGH2 flow analysis. The solution is calculated by iteratively following an explicit sequence for numerical efficiency. Verifications are presented to demonstrate the capabilities of the coupled TOUGH-UDEC simulator. Three application examples of (1) shear dilation due to increased pore pressure, (2) thermal stress and (3) CO2 injection, show that the new simulator can be an effective tool for geoengineering applications involving shear activation of fractures and faults.

Lee, J.H., Jeong, M.S., Lee, K.S., 2019. Incorporation of multi-phase solubility and molecular diffusion in a geochemical evaluation of the CO2 huff-n-puff process in liquid-rich shale reservoirs. Fuel 247, 77-86.


Despite the development of horizontal well and hydraulic fracturing technologies, natural depletion is limited in low productivity, and thereby considerable hydrocarbon remains in low permeable shale reservoirs. Recent researches proved that the deployment of CO2 huff-puff process could extract the remained hydrocarbon. They quantified various mechanisms behind the process and proposed the potential for CO2 sequestration in the shale formation. However, thorough understanding of fluid transport in the CO2 huff-n-puff process has not been completed due to complexity in tight shale formations. They had a lack to analyze potential factors affecting fluid flow in the system of oil/CO2/brine/shale formation: 1) aqueous solubility; 2) molecular diffusion in aqueous and oleic phases; and 3) geochemistry. Therefore, this study diagnoses the potential factors affecting fluid flow during CO2 huff-n-puff process in the shale oil reservoirs. Then, their effects are quantified by analyzing shale oil recovery and CO2 storage capacity. Since a fraction of injected CO2 dissolves in water and oil during the CO2 huff-n-puff process, transportability is acquired by molecular diffusion in aqueous and oleic phases. In addition, dissolution of CO2 changes the pH of in-situ brine, which is a sensitive factor in geochemistry, and thereby would change physical properties of formation. Implementing these mechanisms, this study simulates the CO2 huff-n-puff process in shale oil reservoirs. It is observed that effects of aqueous solubility and geochemistry decrease oil production by 3.2% and 6%, respectively. Approximately, up to 9.5% of CO2 to be injected is sequestrated in depleted shale formation via solubility mechanism. Molecular diffusion in oleic phase increases the oil production by 2%, but that in aqueous phase is negligible. For the accurate estimation of oil production and CO2 storage capacity in the simulation of CO2 huff-n-puff process for shale oil reservoir, the comprehensive model should consider potential factors such as aqueous solubility, molecular diffusion, and geochemical reactions. Because the potential factors have been neglected in the works of other types of shale reservoirs, the proposed approaches expect to expand our understanding in the CO2 injection to tight and shale gas/oil reservoirs.

Lee, J.K., Lee, G.-D., Lee, S., Yoon, E., Anderson, H.L., Briggs, G.A.D., Warner, J.H., 2019. Atomic scale imaging of reversible ring cyclization in graphene nanoconstrictions. ACS Nano 13, 2379-2388.

https://doi.org/10.1021/acsnano.8b09211

We present an atomic level study of reversible cyclization processes in suspended nanoconstricted regions of graphene that form linear carbon chains (LCCs). Before the nanoconstricted region reaches a single linear carbon chain (SLCC), we observe that a double linear carbon chain (DLCC) structure often reverts back to a ribbon of sp2 hybridized oligoacene rings, in a process akin to the Bergman rearrangement. When the length of the DLCC system only consists of ∼5 atoms in each LCC, full recyclization occurs for all atoms present, but for longer DLCCs we find that only single sections of the chain are modified in their bonding hybridization and no full ring closure occurs along the entire DLCCs. This process is observed in real time using aberration-corrected transmission electron microscopy and simulated using density functional theory and tight binding molecular dynamics calculations. These results show that DLCCs are highly sensitive to the adsorption of local gas molecules or surface diffusion impurities and undergo structural modifications.

Legendre, M., Alempic, J.-M., Philippe, N., Lartigue, A., Jeudy, S., Poirot, O., Ta, N.T., Nin, S., Couté, Y., Abergel, C., Claverie, J.-M., 2019. Pandoravirus celtis illustrates the microevolution processes at work in the giant Pandoraviridae genomes. Frontiers in Microbiology 10, 430. doi: 410.3389/fmicb.2019.00430.


With genomes of up to 2.7 Mb propagated in µm-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including 3 others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96 % identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs (ORFans), with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.

Lei, Y., Shen, J., Algeo, T.J., Servais, T., Feng, Q., Yu, J., 2019. Phytoplankton (acritarch) community changes during the Permian-Triassic transition in South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 84-94.


The Permian-Triassic boundary (PTB) at ~252 Ma coincided with the largest mass extinction of the Phanerozoic. Previous research on diversity and abundance changes during this event has focused

mainly on the terrestrial vertebrate and marine invertebrate records, with little attention to date given to the phytoplankton that form the base of the marine trophic web. Although the fossil record of Permian-Triassic phytoplankton is relatively poor owing to preservational factors, sufficient material is now available to evaluate secular changes in acritarch communities through the mass extinction interval. In this contribution, we evaluate diversity and abundance changes among 8 genera and 25 species of acritarchs, including large-spherical, small-spherical, long-spined, and short-spined forms ranging from the Upper Permian Clarkina yini to the Lower Triassic Isarcicella isarcica zones in eight sections representing different sedimentary facies of the South China Craton. Acritarchs declined sharply from the latest Permian (C. meishanensis Zone) to the earliest Triassic (I. staeschei Zone), with extinctions and abundance changes concentrated at two horizons, the first in the latest Permian C. meishanensis Zone (Bed 25 at Meishan D) and the second in the earliest Triassic I. staeschei Zone (Bed 28 at Meishan D), mirroring the pattern of mortality among marine invertebrates. Differences in the nature and intensity of these two extinction episodes (the second having a relatively larger effect on acritarch community composition) suggest that these events may have resulted from different types of environmental perturbations.

Lemieux, A.J., Hamilton, S.M., Clark, I.D., 2018. Allochthonous sources of iodine and organic carbon in an eastern Ontario aquifer. Canadian Journal of Earth Sciences 56, 209-222.


Regional geochemical characterization of groundwaters in a bedrock aquifer in the Ottawa – St. Lawrence Lowlands of eastern Ontario has identified an iodine (I) anomaly, with values regularly exceeding 150 μg/L and a maximum observed concentration of 10 812 μg/L. The spatial distribution, enrichment mechanisms, and sources of I and organic matter were investigated using geochemical and isotopic data. High-I groundwaters (>150 μg/L) are prevalent in Na–Cl-type groundwaters at low bedrock elevations in areas overlain by thick layers of glacial sediments. I is thought to be linked to massive muds in the glacial sediments overlying the aquifer, deposited during the postglacial incursion of the Champlain Sea 12–10 ka BP. Principal component analysis of I and 18 other chemical parameters revealed correlations among I, salinity, and indicators of microbial oxidation of organic matter, suggesting that the intrusion of saline pore waters affected by decomposition of organic matter such as marine phytoplankton in the massive muds is the dominant process controlling I enrichment in groundwater. 129I/127I ratios in the pre-modern waters vary between near-marine values of 460 × 10−14 and 5 × 10−14, demonstrating that older allochthonous I derived from the surrounding Paleozoic sedimentary terrain also contributed to the I pool in the Champlain Sea basin. 14C ages and δ13C signatures for dissolved organic carbon in groundwater and disseminated organic carbon within the glaciomarine muds highlight an allochthonous source of terrestrial organic carbon predating the Champlain Sea incursion, likely transported via glacial meltwaters in tandem with I to the Champlain Sea basin.

Léon, A., Cariou, R., Hutinet, S., Hurel, J., Guitton, Y., Tixier, C., Munschy, C., Antignac, J.-P., Dervilly-Pinel, G., Le Bizec, B., 2019. HaloSeeker 1.0: A user-friendly software to highlight halogenated chemicals in nontargeted high-resolution mass spectrometry data sets. Analytical Chemistry 91, 3500–3507.


n the present work, we address the issue of nontargeted screening of organohalogenated chemicals in complex matrixes. A global strategy aiming to seek halogenated signatures in full-scan high-resolution mass spectrometry (HRMS) fingerprints was developed. The resulting all-in-one user-

friendly application, HaloSeeker 1.0, was developed to promote the accessibility of associated in-house bioinformatics tools to a large audience. The ergonomic web user interface avoids any interactions with the coding component while allowing interactions with the data, including peak detection (features), deconvolution, and comprehensive accompanying manual review for chemical formula assignment. HaloSeeker 1.0 was successfully applied to a marine sediment HRMS data set acquired on a liquid chromatography–heated electrospray ionization [LC–HESI(−)] Orbitrap instrument (R = 140 000 at m/z 200). Among the 4532 detected features, 827 were paired and filtered in 165 polyhalogenated clusters. HaloSeeker was also compared to three similar tools and showed the best performances. HaloSeeker’s ability to filter and investigate halogenated signals was demonstrated and illustrated by a potential homologue series with C12HxBryClzO2 as a putative general formula.

Leroy, F., Gogo, S., Guimbaud, C., Bernard-Jannin, L., Yin, X., Belot, G., Wang, S., Laggoun-Défarge, F., 2019. CO2 and CH4 budgets and global warming potential modifications in Sphagnum-dominated peat mesocosms invaded by Molinia caerulea. Biogeosciences Discussions 2019, 1-17.


Plant communities play a key role in regulating greenhouse gas (GHG) emissions in peatland ecosystems and therefore in their ability to act as carbon (C) sinks. However, in response to global change, a shift from Sphagnum to vascular plant-dominated peatlands may occur, with a potential alteration in their C-sink function. To investigate how the main GHG fluxes (CO2 and CH4) are affected by a plant community change (shift from dominance of Sphagnum mosses to vascular plants, i.e. Molinia caerulea), a mesocosm experiment was set up. Gross primary production (GPP), ecosystem respiration (ER) and CH4 emission models were used to estimate the annual C balance and global warming potential under both vegetation covers. While the ER and CH4 emission models estimated an output of, respectively, 376 ± 108 and 7 ± 4 gC m−2 y−1 in Sphagnum mesocosms, this reached 1018 ± 362 and 33 ± 8 gC m−2 y−1 in mesocosms with Sphagnum rubellum and Molinia caerulea. Annual modelled GPP was estimated at −414 ± 122 and −1273 ± 482 gC m−2 y−1 in Sphagnum and Sphagnum + Molinia plots, respectively, leading to an annual CO2 and CH4 budget of −30 gC m−2 y−1 in Sphagnum plots and of −223 gC m−2 y−1 in Sphagnum + Molinia ones (i.e., a C-sink). Even if, CH4 emissions accounted for a small part of the gaseous C efflux (ca. 3 %), their global warming potential value makes both plant communities have a climate warming effect. The shift of vegetation from Sphagnum mosses to Molinia caerulea seems beneficial for C sequestration at a gaseous level. However, roots and litters of Molinia caerulea could provide substrates for C emissions that were not taken into account in the short measurement period studied here.

Levy-Booth, D.J., Giesbrecht, I.J.W., Kellogg, C.T.E., Heger, T.J., D’Amore, D.V., Keeling, P.J., Hallam, S.J., Mohn, W.W., 2019. Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil. The ISME Journal 13, 950-963.

https://doi.org/10.1038/s41396-018-0334-3

The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4

flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate–soil feedbacks in the PCTR.

Li, D., Li, R., Tan, C., Zhao, D., Xue, T., Zhao, B., Khaled, A., Liu, F., Xu, F., 2019. Origin of silica, paleoenvironment, and organic matter enrichment in the Lower Paleozoic Niutitang and Longmaxi formations of the northwestern Upper Yangtze Plate: Significance for hydrocarbon exploration. Marine and Petroleum Geology 103, 404-421.


Lower Paleozoic shale is an important source rock and reservoir for gas in the northwestern Upper Yangtze Plate. The paleoenvironment, and its impact on organic matter enrichment of the shale, plays a vital role in the exploration and development of the resource. Based on the analysis of the results of total organic carbon (TOC), maceral examination, bitumen reflectance (Rb), major elements, trace elements, rare earth elements (REEs), and X-ray diffraction (XRD) of shale samples from the Niutitang and Longmaxi formations, the origin of silica, the paleoenvironment, and the mode of organic matter enrichment of the shale were examined. The shales of the Niutitang and Longmaxi formations have high TOC abundance, with Type I organic matter and high maturity. Quartz and clay minerals dominate the mineral constituents, leading to characterization as siliceous shale. The average SiO2 content of the shale in the Niutitang and Longmaxi formations is above 70 wt%. Al2O3 and TFe2O3 (total iron) are the next-most abundant major elements, with average values of 12.80 wt% and 1.95 wt% in the Niutitang Formation, and average values of 11.44 wt% and 4.09 wt% in the Longmaxi Formation. Compared with the Upper Continental Crust (UCC), V, Mo and U are the most enriched elements. The average ∑LREE/∑HREE of the shale samples is very low, and the Chondrite-normalized REE distribution pattern shows sloping LREE trends and flat HREE trends towards the right. The total rare earth elements of the shale vary within the range of 147.85–219.60 ppm and 159.90–222.02 ppm in both the Niutitang and Longmaxi formations, suggesting that the shale has not been subject to obvious hydrothermal fluid activities. The correlation diagrams of SiO2–Al2O3, SiO2-TOC and Siexcess-TOC, the diagrams of hydrothermal origins, and the elemental parameters indicate that the silica of the shales from the Niutitang and Longmaxi formations are mainly of biogenic origins, with a lesser contribution from terrigenous detrital sources. The ratios of MnO2/TiO2 and Al2O3/(Al2O3+TFe2O3) of the shale samples all show limited variability, illustrating that the shales are mainly deposited on the continental margin. The average chemical alteration index (CIA) values of the Niutitang and Longmaxi formations are 71.25 and 72.77 with little variation, and the average Sr/Cu ratios are 4.38 and 2.22, reflecting a warm and humid paleoclimate for both formations. The average Ni/Co, Th/U, and δU readings of the shale samples of the formations are 10.91, 0.97 and 1.51, and 12.69, 0.43 and 1.75, indicating that the redox conditions during the sedimentation of the formations were anoxic. The positive correlations between TOC and paleoenvironmental proxies reveal a warm and humid climate, and that anoxia had a positive effect on organic matter enrichment. These conditions have laid a geological foundation for the enrichment of shale gas, and that the Upper Yangtze Plate is favorable for future shale gas exploration.



Genetic type, source, charging history and reasons for secondary biogenic transformation of tight sandstone gas in the Linxing area in China's Ordos Basin have been studied through a combined analysis of gas compositions, isotopes of alkane and carbon dioxide, fluid inclusions and basin simulation. Tight sandstone gas in this area is predominated by methane, and the dryness coefficient is between 0.864 and 0.997 (average = 0.969). The δ13C1 values of methane and ethane in this area range from −44.5‰ to −33.2‰ (average = −39.4‰) and from −27.5‰ to −24.4‰ (average = −25.9‰), respectively. The non-hydrocarbon gases are nitrogen, followed by carbon dioxide and argon, and δ13C of carbon dioxide ranges from −14.6‰ to 8.6‰. The homogenization temperatures of gas and gas-liquid inclusions in P2s and C3t in Linxing range from 80 °C to 170 °C, which are concentrated at 120–130 °C. The identification of gas origin indicates that tight sandstone gas is coal-type gas, which is mainly due to thermal evolution, followed by the mixing of secondary biogenic gas. Geological conditions and gas geochemical characteristics suggest that tight sandstone gas was produced by coal seam and carbonaceous shale in Upper Paleozoic in the Linxing area. The homogenization temperature of inclusion reflects the continuous accumulation process of tight sandstone gas, and the Cretaceous was the main period for gas charging. The monoclinal structure, maturity of source rocks and activity of underground water in this area are the important factors for secondary biogenic gas formation.



A method for selective methylation of sulfides (particularly aliphatic sulfides) but not thiophenes in petroleum has been developed for positive-ion electrospray ionization (ESI) mass spectrometry. The new method uses only CH3I without AgBF4 to produce methyl sulfonium ions of sulfides for molecular composition analysis. It provides simplicity and saves time compared to a previously developed methylation method using CH3I/AgBF4 to methylate all sulfur compounds into ionic species analyzable by positive-ion ESI. The composition of sulfides by this method agrees with that of the sulfide fraction obtained from CH3I/AgBF4 methylation/demethylation. Hence, the separation of sulfides from thiophenes through elaborate procedures is eliminated. The new method was validated by model compounds and has been successfully applied to the analysis of sulfides in diesel, vacuum gas oil, crude oil, and atmospheric pressure distillation residue. When combined with the previously developed CH3I/AgBF4 method, the new method may have the potential to differentiate reactive sulfur, such as sulfides, from nonreactive sulfur, such as thiophenes. This could provide a means to develop correlations between sulfur types and corrosion, and possibly for other studies.

Li, H., Yu, J., McElwain, J.C., Yiotis, C., Chen, Z.-Q., 2019. Reconstruction of atmospheric CO2 concentration during the late Changhsingian based on fossil conifers from the Dalong Formation in South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 37-48.


A single species of fossil conifer with well-preserved cuticles from multiple layers of the Dalong Formation in two sections in Duanshan Town, Guizhou Province, Southwest China has been used to reconstruct palaeo-atmospheric pCO2. The age of these layers can be dated back to the late Changhsingian (latest Permian), corresponding to the Clarkina changxingensis and Clarkina yini conodont Zones. Two calibration approaches were employed in this study. Using the stomatal ratio method, the pCO2 curves of the two sections showed matching trends, with levels decreasing in the middle of the profiles, and similar ranges at ca. 340–510 ppm and ca. 300–440 ppm. Similar values (ca. 360–520 ppm), yet with wider error ranges, were obtained when the mechanistic model proposed by Franks et al. in 2014 was applied to one of the sections. Our values are lower than the mean pCO2 values from coeval palaeosols, but partly overlap with them when error ranges are taken into consideration, thus more independent studies are needed to evaluate the discrepancies between the two proxy methods. The low atmospheric CO2 concentrations in this study suggest a cool climate rather than extensive glaciation for the brief period of late Changhsingian, which is supported by the oxygen isotope record of conodont apatite and a major restructuring of Late Permian flora and fauna.

Li, J., Zhang, J., Yadav, M.P., Li, X., 2019. Biodegradability and biodegradation pathway of di-(2-ethylhexyl) phthalate by Burkholderia pyrrocinia B1213. Chemosphere 225, 443-450.


This study was conducted to investigate the biodegradation of di-(2-ethylhexyl) phthalate (DEHP) by Burkholderia pyrrocinia B1213. The results showed that DEHP at concentration of 500 mg/L in a mineral salt medium containing 1.0% yeast extract can be almost completely degraded (98.05%) by strain B1213. The optimal condition for DEHP degradation was pH 7.0, temperature 30 °C. Moreover, B1213 shows better degradation effect on long-chain PAEs, such as DEHP, which provides a great potential for its use in bioremediation of soils contaminated with PAEs. The kinetic studies showed that DEHP depletion curves fit well to the modified Gompertz model. The mono(2-ethylhexyl) phthalate (MEHP), mono-dibutyl phthalate (MBP), phthalic acid (PA) and 4-oxo-hexanoic acid were identified as the metabolites of DEHP by HPLC-ESI-QTOFMS. The detection of MBP and 4-oxo-hexanoic acid as intermediates prompted us to propose a novel and more complete DEHP biodegradation pathway compared to the classic pathway: DEHP is first degraded to MEHP by esterases, which is then converted to MBP through β-oxidation. Then MBP is degraded to PA by esterases, which is then converted to protocatechuate (PCA) under aerobic conditions rapidly. PCA is ultimately cleaved to generate CO2 and H2O via 4-oxo-hexanoic acid.

Li, J.S., Barber, C.C., Zhang, W., 2019. Natural products from anaerobes. Journal of Industrial Microbiology & Biotechnology 46, 375-383.

https://doi.org/10.1007/s10295-018-2086-5

Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.

Li, L., Yao, S., Xue, B., Cheng, L., Yan, R., 2019. Methane levels in five shallow lakes in China: Effect of lake paludification. Quaternary International 503, 128-135.


Understanding methane dynamics in lakes is relevant for assessing the natural source of greenhouse gases. Paludification is one of the most common phenomena of lake degeneration, which would have significant influence on CH4 dynamics. However, the actual variety of CH4 dynamics by lake paludification is not yet clear. We investigated CH4 concentrations and production potentials in five shallow lakes located in the east China. The CH4 concentrations and production potentials were significantly higher (approximately 5–10 times) in the lakes with greater paludification degrees and had no significant difference among other lakes with low and similar paludification indexes. High CH4 levels in the paludificated lakes can be associated with the increase of sediment organic matter content and decrease of water depth due to the accelerated sedimentation and outspread of macrophytes during the lake paludification. Similarly, organic matter supply might be a limitation for CH4 production in the lakes with low paludification degrees. These results indicate that lake paludification is probably a main reason for the significant CH4 differences among the studied lakes. This study draws attention to lakes with paludification tendency when making CH4 emission budgets in shallow lakes.

Li, M., Chen, Z., Ma, X., Cao, T., Qian, M., Jiang, Q., Tao, G., Li, Z., Song, G., 2019. Shale oil resource potential and oil mobility characteristics of the Eocene-Oligocene Shahejie Formation, Jiyang Super-Depression, Bohai Bay Basin of China. International Journal of Coal Geology 204, 130-143.


Oil mobility in liquid-rich shale is crucial for economic success of resource development. The characteristics of the host rock and the properties of oil fluids are two primary factors controlling fluid mobility. Organic geochemistry data allows examination of both resource potential and oil mobility. We propose data-driven empirical models in this paper to describe hydrocarbon resource potential with respect to oil mobility. The proposed methods were applied to a dataset collected from the Eocene-Oligocene Es3 and Es4 source rock units in four recent shale oil exploration wells in the Jiyang Super-Depression of the Bohai Bay Basin. The dataset, results from standard programmed pyrolysis of whole rock samples as well as solvent extracted replicates of 139 core samples, was studied to examine the source rock characteristics and shale oil resource potential. Bulk geochemical characteristics and thermal decomposition trends allow for sub-division of the samples into two groups; a) samples with high initial hydrogen index (>800 mg HC/g TOC) and average present day TOC of 4.07% from LY1 and NY1 wells in a distal facies; and b) samples with slightly lower initial hydrogen index (about 700 mg HC/g TOC) and average TOC of 3.11% from FY1 and L69 wells in a transitional facies. Three different categories of oil resource with respect to oil mobility can be defined: adsorbed, restricted and movable based on organic geochemical characteristics and their variations in the stratigraphic intervals represented by the samples in the four wells. We show that expulsion efficiency is a good indicator of hydrocarbon retention in source rock reservoir and that the two wells in the distal facies have higher total resource potentials with abundant movable oil resource than the two wells in the transitional facies. The total oil potential is separated into three types of oil resource to show oil mobility, thus providing more information for business decision.

Li, M., Hinnov, L., Kump, L., 2019. Acycle: Time-series analysis software for paleoclimate research and education. Computers & Geosciences 127, 12-22.


Recognition and interpretation of paleoclimate signals in sedimentary proxy datasets are time consuming and subjective. Acycle is a comprehensive and easy-to-use software package for time series analysis in paleoclimate research and education. It is designed to speed paleoclimate time series analysis, especially cyclostratigraphy, and to provide objective methods for estimating astrochronology. Acycle provides for detrending with multiple options to track and remove secular trends. A selection of power spectral analysis methodologies is offered for the detection of periodic signals. Many of the functions are specific to cyclostratigraphy and astrochronology that are not found in standard statistical packages. A specialized function is provided to assess the astronomical (Milankovitch) forcing of paleoclimate series and search for the most likely sedimentation rate by evaluating the correlation coefficient between power spectra of an astronomical solution and sedimentary proxy data. Sedimentary noise modeling (for past sea-level changes) is also provided in Acycle . As an example, Acycle is applied to a sedimentary proxy series from the cyclostratigraphy of the Paleocene-Eocene thermal maximum (PETM) in Core BH9/05 from the Paleogene Central Basin, Svalbard. Acycle detects significant astronomical forcing in the proxy series and relatively stable sedimentation rates during and after the PETM. Acycle runs in the MATLAB environment or as stand-alone software on Windows and Macintosh OS X, and is open-source software.

Li, M., Huang, C., Ogg, J., Zhang, Y., Hinnov, L., Wu, H., Chen, Z.-Q., Zou, Z., 2019. Paleoclimate proxies for cyclostratigraphy: Comparative analysis using a Lower Triassic marine section in South China. Earth-Science Reviews 189, 125-146.


Multiple proxies for paleoclimatic and paleoenvironmental change within sedimentary sequences have been developed; but understanding their relationships and their relative strengths or weaknesses are required to access a wealth of untapped paleoclimate information. We propose two main criteria for multiple proxy datasets to estimate their individual signal-to-noise levels and to decipher the relationship between multiple proxies. First, for proxies affected by similar processes, then their time-dependent changes should be similar. Second, a paleoclimate proxy that is more sensitive to an external forcing, such as astronomical forcing, is more useful than those that do not have such a response. We introduce two methods to evaluate these criteria: (1) hierarchical cluster analysis (HCA) probes the relationships among multiple proxies based on similarities of their oscillation patterns, and (2) power decomposition analysis (PDA) tests proxy sensitivity to external climate forcing.

We evaluate 16 high-resolution paleoclimate proxies in detail for their applications in paleoclimatology from the marine Lower Triassic Daye Formation at the Daxiakou section in the Three Gorges region of South China, which has carbonate-claystone cycles deposited on an outer ramp. The proxies are spectral gamma ray (gamma-ray intensity, potassium, uranium, thorium, thorium/uranium and thorium/potassium), rock color lightness (L*), redness (a*) and yellowness (b*), magnetic susceptibility (measured in both laboratory and outcrop), anhysteretic remanent magnetization (ARM), lithologic rank, simplified lithologic rank and non-carbonate fraction, carbonate thickness and couplet thickness. Hierarchical cluster analysis (HCA) gathers these proxies into groups likely affected by the same process. The ARM and thorium/uranium proxies seem to reflect the hinterland-weathering process during the Early Triassic. Gamma-ray, potassium, uranium, thorium, magnetic susceptibility and non-carbonate fraction proxies refer to terrestrial input. The L*, a* and lithologic rank proxies indicate the productivity, the redox state and the relative sea level, respectively at this section. This case study contributes to the understanding of the sensitivity of these types of proxies within marine strata for deep-time paleoclimate and astronomical-tuned time scales.



Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and absorbance spectroscopy were utilized to investigate the molecular composition of marine dissolved organic matter (DOM) from the upper 2000 m water column at the Mariana Trench. Molecular indices, calculated based on the relative abundance of 4699 formulas assigned from FT-ICR MS data, showed depth stratification. The degradation index (IDEG) varied from 0.610 to 0.663 (0.645 ± 0.014) in the surface layer to 0.668–0.754 (0.722 ± 0.021) in the deep ocean (below 500 m), indicating that the DOM in the deep layer was more refractory than that of the surface layer. This was confirmed by an increase of modified aromaticity index (AImod) from 0.196 to 0.207 (0.200 ± 0.003) in the surface layer to 0.213–0.225 (0.220 ± 0.003) at depth. Multivariate analysis based on both bulk molecular parameters and relative abundance of individual formulas showed that the molecular composition of DOM was highly stratified and could be well separated into three groups: the upper layer (5–75 m), the middle layer (200 m) and the deep layer (500–2000 m). In addition, surface-enriched and deep-enriched formulas were identified based on Spearman correlation between relative abundance of individual formulas and depth. The surface-enriched formulas were characterized by higher H/C and lower AImod, while deep-enriched formulas showed lower H/C and higher AImod. Variations in AImod and H/C for these formulas indicated that extracellular release (mainly from primary production) and photochemical processes strongly affected the DOM composition in euphotic zone, while microbial processes likely exerted a tremendous influence on the DOM composition at all depths. Moreover, strong correlations between spectroscopic indices (a325, S275–295 and S280–400) and FT- ICR MS derived proxies indicated these two approaches can be integrated to provide valuable information on the molecular characterization of open ocean DOM.

Li, S., Li, Y., Yang, L., Chen, Y., Shao, Y., Sun, J., Xu, R., 2019. Prediction of phase equilibrium of methane hydrate below 272.2 K based on different equations of state. Fluid Phase Equilibria 490, 61-67.


By revealing that a key parameter D in Chen-Guo model is related to the temperature T, a new temperature-dependent parameter D(T) trained by the reported experimental data is proposed with Chen-Guo model to improve the prediction accuracy of phase equilibrium conditions of methane hydrate in the range of 145.75 K- 272.2 K. Four equations of state (EOS) such as Redlich-Kwong (RK), Soave- Redlich-Kwong (SRK), Peng-Robinson (PR) and Patel-Teja (PT) are chosen to calculate the gas fugacity respectively and the corresponding prediction accuracy is evaluated by the average absolute deviation percentage (AADP). The process of training D(T) based on the Chen-Guo model employed with SRK EOS is described in detail first, and the prediction results show that the corresponding prediction accuracy is greatly improved, whose AADP decreases from 10.83% to 3.31%. In order to verify that training D(T) is an effective way to improve the prediction accuracy, the same procedure is also used to the Chen-Guo models employed with RK, PR and PT EOS respectively, and the corresponding AADP decreases from ∼11% to ∼3%. In addition, the prediction accuracy according to the proposed D(T) is also evaluated by other temperatures different from the data used for training D(T) to verify its feasibility and effectiveness.

Li, X., Liu, P., Liu, R., 2019. Methane adsorption characteristics of shale from different basins and its geological significance. Petroleum Science and Technology 37, 261-267.

https://doi.org/10.1080/10916466.2018.1539749

The CH4 adsorption characteristics of shale from different basins was studied based on determination of mineral compositions, Rock-eval pyrolysis parameters and CH4 gas adsorption isotherms. The results show that TOC contents, contents of quartz and maturity stage of shale can influence the CH4 adsorption capacity. Whereas, the results show that there exists unobvious relationships between CH4 adsorption capacity and the contents of clay and carbonate materials can be obtained in this study.

Li, X., Wu, B., 2019. Understanding to the composition and structure of organic chlorides in petroleum and its distillates. Petroleum Science and Technology 37, 119-126.

https://doi.org/10.1080/10916466.2018.1514407

Understanding the molecular compositions of organic chlorides in petroleum and its distillates plays an important role in realizing molecule management of petroleum refining processes. This paper discussed the various advances on analytical methods of organic chlorides in crude oil and its sub-fractions at the molecular level, summarized the known identified organic chlorides with different chemical structures, and provided suggestion on the promising analytical strategy and approach to organic identification in the future.


https://doi.org/10.1111/1755-6724.13767

The Upper Paleozoic (Carboniferous to Permian) succession in the east margin of the Ordos Basin in the North China Craton has a potential to contain significant hydrocarbon resources, though attention have been mainly attracted for its successful development of coalbed methane (CBM). To improve the previous resource estimates and evaluate the hydrocarbon play possibilities, this study incorporated new discoveries of hydrocarbon units and their stratigraphic relation with source rocks, hydrocarbon migration and trapping configurations. Continuous hydrocarbon accumulation units were identified within the Upper Paleozoic, including the Taiyuan, Shanxi and Xiashihezi formations with great tight gas potential, and the Taiyuan and Shanxi formations also containing shale gas and CBM. Different strata combinations are identified with coal deposition and favour for continuous gas accumulations, including the tidal flat, deltaic and fluvial systems distributed in most of the study areas. Methane was not only generated from the thick coal seams in the Taiyuan and Shanxi formations, but also from shale and dark mudstones. The coal, shale and tight sandstones are proved of remarkable gas content and hydrocarbon indications, and the gas saturation of tight sandstones decreases upward. The stacked deposit combinations vary isochronally in different areas, while the coal seams were developed stably showing good gas sources. Two key stages control the hydrocarbon enrichment, the continuous subsidence from coal forming to Late Triassic and the anomalous paleo-geothermal event happened in Early Cretaceous, as indicated by the fluid inclusions evidence. Extensive areas show good hydrocarbon development potential presently, and more works should be focused on the evaluation and selection of good reservoir combinations.



The Sanhecun sag, located in the south of the Zhanhua depression, has yielded a significant amount of heavy oil in recent years and is becoming a new exploration focus in the Jiyang sub-basin. Surprisingly, oils in the deep Shahejie formation have higher densities and viscosities than those in the shallow Guantao formation. In this study, geochemical and fluid inclusion analyses of oils from different depths were carried out to clarify their source and the cause of the high densities. Oils in the Shahejie formation, with high contents of resins and asphaltenes (47%–56%), are generated from the Es4 carbonate source rocks that were deposited in a hypersaline environment with a relatively high terrigenous organic matter contribution. Maturity parameters and fluid inclusions show that the oils with low saturated hydrocarbon contents and high resin and asphaltene contents were charged to the Shahejie formation from 29 Ma to 27 Ma, when the source rocks were in the early oil generation window. Although subsequent biodegradation further increased oil density, the main control on the high densities of oils in the Shahejie formation is the nature of the source kerogen. Oils in the shallow Guantao formation can be divided into two groups: a group from Es3 source rocks in the Gunan sag and a second from Es3 and Es4 source rocks in the Bonan sag. They were expelled within the oil generation window and charged the reservoirs between 3 Ma and the present-day. Oils in the Guantao formation have undergone light to heavy biodegradation, ranging from PM levels 2 to 5. With the increase of biodegradation level, saturated hydrocarbon contents gradually decrease from 50% to 22%, while the contents of resins and asphaltenes increase from 28% to 43%. Biodegradation is the primary cause of oil densification in the Guantao formation. Although oils in the Guantao Formation suffered more severe biodegradation, they still have higher contents of saturated hydrocarbons than those in the Shahejie Formation. Source type, maturity and biodegradation thus combine, in different ways, to control the density of heavy oils in the Sanhecun sag. This study also indicates that low mature oils from Es4 carbonate source rocks can charge reservoirs in the southern part of Zhanhua depression before late Oligocene uplift, and low mature oil may be a potential future target in this area.


https://doi.org/10.1007/s00253-018-09613-x

PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-

degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.



Influence of wettability to petrophysical responses in low permeability reservoirs is increasingly evident, but research of nuclear magnetic resonance (NMR) technology on wettability calibration in such reservoirs is very limited even though it has been used promisingly. The challenge is that the empirical interpretation model only applies to simple pore structure. It is urgent to develop a relatively simple, quick, and practicable model for wettability evaluation in low permeable reservoirs.

This paper presents an experimental NMR study, integrating with Amott tests, X-ray diffraction, and scanning electron microscope (SEM) measurements, on wettability characterization of five typical core samples from different low-permeability reservoirs. NMR relaxation mechanisms and the effect of the aging were analyzed in detail. The study showed that all the core samples had a shift of T2 (spin-spin relaxation time) spectra between before and after aging. According to the shift characteristics, the core samples were divided into two types. The first type is that the wettability alteration relied on the aging and it displaced crude oil into original water-wet movable pore spaces to restore reservoir wettability. This type of formation is generated in distant-source reservoirs, which mainly involves fluid transport through buoyancy. Another type is that the wettability alteration was attributed to the natural oil-wet property of the rock matrix. This formation is mainly found in inner-source or near-source reservoirs, which may generate abundant oil-wet materials. Thus, the wettability alteration is the result of hydrocarbon accumulation modes. Based on the observations, a potential method for obtaining the wettability index was proposed. The method uses both the ratio of oil-wetted to water-wetted pore surface areas and diffusion-relaxation diagrams. The estimated results corresponded reasonably to the independent Amott tests. This study demonstrates that NMR relaxation is an effective solution to analyze and quantify wettability in low permeability reservoirs.

Liao, D., Lu, B., Chen, Y., 2019. An evaluation method of geological sweet spots of shale gas reservoir: a case study of the Jiaoshiba gas field,Sichuan Basin. Acta Petrolei Sinica 40, 144-151.


"Sweet spot" is an important factor for shale gas evaluation. The previous sweet spot determination method based on a comprehensive analysis on lithology, gas content, physical properties and stress distribution is not capable of classifying the types and properties of sweet spot. Through analyzing the sweet spot parameters of shale gas, the sweet spot is divided into two types, i.e., the geological and engineering sweet spot. Through qualitatively analyzing the influence of geological sweet spot parameters on gas production, the main sweet spot parameters of shale gas were selected using correlation coefficient method to choose. In addition, radar area model and correlation weight model were applied to quantitatively characterize the geological sweet spot parameters of shale gas. Through studying the geological characteristics of Jiaoshiba shale gas field, TOC, kerogen content, gas saturation, total porosity and pore pressure are five main geological sweet spot parameters. Using

these two models, the geological sweet spot is evaluated between 0.3 and 0.7, indicating that Jiaoshiba shale gas field has better geological sweet spot and high gas production capacity.

Lim, D.S.S., Abercromby, A.F.J., Kobs Nawotniak, S.E., Lees, D.S., Miller, M.J., Brady, A.L., Miller, M.J., Mirmalek, Z., Sehlke, A., Payler, S.J., Stevens, A.H., Haberle, C.W., Beaton, K.H., Chappell, S.P., Hughes, S.S., Cockell, C.S., Elphic, R.C., Downs, M.T., Heldmann, J.L., 2019. The BASALT research program: Designing and developing mission elements in support of human scientific exploration of Mars. Astrobiology 19, 245-259.

https://doi.org/10.1089/ast.2018.1869

The articles associated with this Special Collection focus on the NASA BASALT (Biologic Analog Science Associated with Lava Terrains) Research Program, which aims at answering the question, “How do we support and enable scientific exploration during human Mars missions?” To answer this the BASALT team conducted scientific field studies under simulated Mars mission conditions to both broaden our understanding of the habitability potential of basalt-rich terrains on Mars and examine the effects of science on current Mars mission concepts of operations. This article provides an overview of the BASALT research project, from the science, to the operational concepts that were tested and developed, to the technical capabilities that supported all elements of the team's research. Further, this article introduces the 12 articles that are included in this Special Collection.

Lin, H.-T., Repeta, D.J., Xu, L., Rappé, M.S., 2019. Dissolved organic carbon in basalt-hosted deep subseafloor fluids of the Juan de Fuca Ridge flank. Earth and Planetary Science Letters 513, 156-165.


Marine dissolved organic carbon (DOC) is highly depleted in radiocarbon and thus inferred to be largely refractory to removal processes that operate on less than millennial timescales. However, a growing number of reports have shown that a large fraction of marine DOC can be effectively removed during circulation through submarine hydrothermal systems. What is not clear, however, is whether the DOC that remains in hydrothermal fluids is remnant non-reactive DOC from recharged seawater, or DOC that has been largely produced in the subsurface. We collected and characterized warm (∼65°C) hydrothermal fluids from deep (18, 40, 73, 200 m) within the basalt-hosted basement of the Juan de Fuca Ridge flank in the Northeast Pacific Ocean. DOC concentrations in hydrothermal fluids were 9 to 18 μM, much lower than measured in local deep seawater (37.5 μM). DOC Δ14C values of −683‰ to −856‰ were much lower than the Δ14C-dissolved inorganic carbon (DIC) values of −880‰ to −918‰, while DOC δ13C values of −23.6‰ to −27.0‰ were much heavier than that of the particulate organic carbon (POC) pool (∼−34‰), suggesting that biological production in the subsurface is not a primary source of DOC. Rather, our data suggest that isotopically enriched DOC are selectively removed from recharged seawater, leaving DOC that is very isotopically depleted in the basaltic basement fluids. Despite the removal of 50–75% of DOC in the subsurface, nuclear magnetic resonance (NMR) functional group analyses indicate that aromatic compounds were added to basaltic basement fluids during passage through the deep subseafloor and may partly contribute to the depleted 14C DOC in the ridge-flank basement fluids.



Asphaltene-related flow assurance problems are prevalent in oil production processes and are at the heart of issues such as the plugging of pipelines, the damage of rock formations, and the stabilization of viscous water-in-oil emulsions. A comprehensive understanding of the interfacial behavior of asphaltenes, from a physical–chemical perspective, is required for an accurate design of solutions to these challenges. In this work, we elucidate the deposition dynamics of various asphaltene subfractions in a porous media microfluidic model. Extrography fractions from the interlaboratory sample known as PetroPhase 2017 asphaltenes, reported to be a mixture of abundant island and archipelago motifs, and Wyoming deposit C7 asphaltenes, known for being island type dominated, are investigated. The deposition rate increases when the compositional ratio archipelago/island motif increases for PetroPhase 2017 derived fractions, whereas Wyoming deposit asphaltenes appear to exhibit stronger aggregation for fractions whose composition is uniformly island type. In general, the deposition rate is consistent with the amount of precipitated asphaltenes. However, the correlation is not merely a linear one and the pore-scale morphology changes even with similar deposition rates. Estimated diffusivity, the relative ratio of convection and diffusion, and fluid flow profiles are used to explain the dynamic growth of the deposit at the pore scale.

Lindaas, J., Farmer, D.K., Pollack, I.B., Abeleira, A., Flocke, F., Fischer, E.V., 2019. Acyl peroxy nitrates link oil and natural gas emissions to high ozone abundances in the Colorado Front Range during summer 2015. Journal of Geophysical Research: Atmospheres 124, 2336-2350.

https://doi.org/10.1029/2018JD028825

Abstract We present measurements of ozone (O3), acyl peroxy nitrates (APNs), and a suite of O3 precursors made at the Boulder Atmospheric Observatory in Erie, Colorado, during summer 2015. We employ an empirical analysis of the APNs and a previously described positive matrix factorization of the volatile organic compounds (VOCs) to investigate the contribution of different VOC sources to high O3 abundances at Boulder Atmospheric Observatory. Based on the ratio of peroxypropionyl nitrate (PPN) to peroxyacetyl nitrate (PAN), we find that anthropogenic VOC precursors dominate APN production when O3 is most elevated. Propane and larger alkanes, primarily from oil and natural gas emissions in the Colorado Front Range, drive these elevated PPN to PAN ratios during high O3 events. The percentage of OH reactivity associated with oil and gas emissions is also positively correlated with O3 and PPN/PAN. Idealized box model simulations are used to probe the chemical mechanisms potentially responsible for these observations. We find that observed abundances of long-lived oil and natural gas-related VOCs are likely high enough such that the oxidation of these VOCs in a single photochemical day produces sufficient peroxy radicals to contribute to O3 formation in the northern Colorado Front Range. Based on our empirical observations and box model simulations, we conclude that oil and natural gas emissions contribute to O3 production on high O3 days in this region during summer 2015.


https://doi.org/10.1029/2018GL080996

Abstract: High‐latitude permafrost regions store large stocks of soil organic carbon (OC), which are vulnerable to climate warming. Estimates of subsurface carbon stocks do not take into account floodplains as unique landscape units that mediate and influence the delivery of materials into river networks. We estimate floodplain soil OC stocks within the active layer (seasonally thawed layer)

and to a maximum depth of 1 m from a large field data set in the Yukon Flats region of interior Alaska. We compare our estimated stocks to a previously published data set and find that the OC stock estimate using our field data could be as much as 68% higher than the published data set. Radiocarbon measurements indicate that sediment and associated OC can be stored for thousands of years before erosion and transport. Our results indicate the importance of floodplains as areas of underestimated carbon storage, particularly because climate change may modify geomorphic processes in permafrost regions.

Plain Language Summary: Large amounts of organic carbon (OC) are stored in the northern permafrost (perennially frozen) soils. Accurately estimating the amount of carbon is important for understanding the movement of carbon between the land, the ocean, and the atmosphere. Soil OC in northern regions may be released to the atmosphere with future warming and permafrost thaw, further indicating the need to accurately understand how much OC is stored in soils. Floodplains, as sites of sediment and nutrient deposition, store significant amounts of soil OC and to date have not been adequately characterized. We estimate the amount of OC in floodplain soils in the Yukon Flats region in interior Alaska, finding that there may be significantly more soil OC in northern floodplains than previously thought.



Microbially mediated early diagenetic pyrite formation in the immediate vicinity of organic material has been the favored mechanism by which to explain widespread preservation of soft-bodied organisms in late Ediacaran sedimentary successions, but an alternative rapid silicification model has been proposed for macrofossil preservation in sandstones of the Ediacara Member in South Australia. We here provide petrological evidence from Nilpena National Heritage Site and Ediacara Conservation Park to demonstrate the presence of grain-coating iron oxides, framboidal hematite, and clay minerals along Ediacara Member sandstone bedding planes, including fossil-bearing bed soles. Scanning electron microscope (SEM), cathodoluminescence microscopy (CL), and petrographic data reveal that framboids and grain coatings, which we interpret as oxidized pyrite, formed before the precipitation of silica cements. In conjunction with geochemical and taphonomic considerations, our data suggest that anactualistically high concentrations of silica need not be invoked to explain Ediacara Member fossil preservation: We conclude that the pyritic death mask model remains compelling.

Liu, B., Vrabec, M., Markič, M., Püttmann, W., 2019. Reconstruction of paleobotanical and paleoenvironmental changes in the Pliocene Velenje Basin, Slovenia, by molecular and stable isotope analysis of lignites. International Journal of Coal Geology 206, 31-45.


Three different lithotypes (xylitic, gelified and matrix) of Pliocene lignite from the Velenje Basin, Slovenia, were investigated to establish the variations of biomarker compositions in solvent extracts and the stable isotope (carbon and nitrogen) compositions of bulk material. From the biomarker results, the xylitic lithotype almost exclusively originates from gymnosperms (conifers such as Taxodiaceae), as indicated by the very high contents of sesquiterpenoids and diterpenoids but very low abundances of n-alkanes and non-hopanoid triterpenoids. The relative proportion of

gymnosperms to angiosperms in the paleomire is reflected by the ratio of diterpenoids to the sum of diterpenoids and non-hopanoid triterpenoids (Di-/(Di-+Tri-terpenoids)), which is close to 1 (av. 0.99) in the xylitic lithotype. The predominance of diterpenoids from conifers in the xylitic lithotype is associated with high C/N ratios and intermediate total sulfur (TS). The very low abundance of hop-17(21)-ene and the absence of further hopanoids in the xylitic lithotype indicate a restricted influence of bacterial degradation under relatively dry conditions in the paleomire. The matrix lithotype also originated preferentially from gymnosperms under dry depositional conditions, as indicated by the high Di-/(Di-+Tri-terpenoids) ratio (0.95), low amounts of hopanoids and low TS content. The gelified lithotype is characterized by a high content of n-alkanes and wide variation of the Di-/(Di-+Tri-terpenoids) ratio (0.13–0.88), indicating a fluctuating contribution of angiosperms to the plant community in the paleomire during formation of this lithotype. In addition, the high abundance of hop-17(21)-ene and TS in the gelified lithotype compared with the other two lithotypes suggests the effect of bacterial activity under relatively wet/humid conditions during formation of the gelified lithotype, which is also supported by the considerable content of mid-chain n-alkanes.

The high correlation between the δ13C and δ15N values (R2 = 0.68) indicates that the stable carbon and nitrogen isotope composition in the Velenje lignites were probably influenced by the same factors (e.g. precursor plants and/or microbial activity). The stable carbon isotopic values (av. −25.44‰) and nitrogen isotopic values (av. 2.15‰) of the xylitic lithotype are higher than those of the gelified lithotype (av. δ13C = −27.48‰, δ15N = 1.37‰) and the matrix lithotype (av. δ13C = −27.09‰, δ15N = 1.10‰). The relatively high correlation between the diterpenoid content and both δ13Cand δ15N values suggests that the stable carbon and nitrogen isotopic composition of the three lithotypes might reflect the composition of the original plant material in the paleomire. The dominance of conifers as precursor plants in the xylitic lithotype might be the main reason for the higher δ13C values and probably also the higher δ15N values. The relatively higher δ15N values in the xylitic lithotype than in the other types could be explained by the high amount of decay-resistant xylem and low mineral (e.g. clay) content in the xylitic lithotype. The slightly lower δ13Cbut higher δ15N values in the gelified lithotype than in the matrix lithotype can be explained by variation of parent plant materials and the influence of bacterial activity.

Liu, C., Gu, C., Huang, W., Sheng, X., Du, J., Li, Y., 2019. Targeted UPLC-MS/MS high-throughput metabolomics approach to assess the purine and pyrimidine metabolism. Journal of Chromatography B 1113, 98-106.


Purines and pyrimidines, the important components of DNA and RNA, are closely related to metabolic syndrome and disorder, such as renal disease, gout and diabetic nephropathy etc. Given the importance of the biological significance of purines and pyrimidines, it is necessary to further develop a rapid and sensitive method for practical detection of a large-scale analyses. In this study, based on 96-well solid phase extraction plates-ultra performance liquid chromatography-triple quadrupole mass spectrometry (SPE-UPLC-QqQ-MS/MS), a novel approach for simultaneous determination of 23 purines and pyrimidines in biological samples was developed. First, plasma samples were pretreated by SPE using 96-well plates, which lead to an automated, simplified and rapid sample preparation process. In the methodology development, a large-scale test was performed to evaluate the stability and reliability of the approach. Finally, the levels of purines and pyrimidines in the biological samples were analyzed by this strategy. Experimental results showed that lowest limit of quantification (LLOQ) range from 6.678 × 10−2 μg/mL to 4.275 × 10−6 μg/mL; intra- and inter-day precision are <15% for all analytes. The stability and maximal capability of a single analytical batch could be extended to at least 431 injections (about 70 h). Analysis time of a single run was controlled in 10 min. Under the optimized conditions, wide linear ranges and good correlation

coefficients (R2 > 0.99) were acquired. The successful development of this method provides a feasible protocol for a large-scale metabolomics study and it also lays the foundation of quantitative analysis in endogenous analytes.

Liu, C.L., Dong, H.G., Zhan, J., Liu, X., Yang, Y., 2019. Multi-modular engineering for renewable production of isoprene via mevalonate pathway in Escherichia coli. Journal of Applied Microbiology 126, 1128-1139.

https://doi.org/10.1111/jam.14204

Aims: To establish the biotechnology platforms for production of bio‐based chemicals in various micro‐organisms is considered as a promising target to improve renewable production of isoprene.

Methods and Results: In this study, we heterologously expressed the mevalonate (MVA) isoprene biosynthesis pathway, and explored three strategies of increasing isoprene production in Escherichia coli. We first manipulated the expression levels of the MVA pathway genes through changing the gene cassettes and promoters. To introduce cofactor engineering, we then overexpressed NADP‐dependent glyceraldehyde‐3‐phosphate dehydrogenase gene from Clostridium acetobutylicum to supply available NADPH. To reduce the inhibitory by‐product accumulation, we finally knocked out acetate‐producing genes, phosphate acetyl transferase and pyruvate oxidase B in E. coliJM109 (DE3), decreasing acetate accumulation 89% and increasing isoprene production 39%. The strategies described here finally increased the isoprene titre to 92 mg l−1 in two‐gene deletion strain JMAB‐4T7P1Trc, increasing 2·6‐fold comparing to strain JM7T7.

Conclusion: The multimodularly engineering approaches including promoter engineering, cofactor engineering and by‐product reducing could be used to improve isoprene production in E. coli.

Significance and Impact of the Study: The metabolic strategies in this study show us directions for further studies to promote transformation of renewable sources to isoprene.



Here we further demonstrate asphaltene to be the main carrier of Re and Os in crude oil and additionally show that generally the less soluble fractions of asphaltene contain higher concentrations of Re and Os, with the 187Os/188Os and 187Re/188Os values showing different trends between oils. These observations are considered as evidence of the existence of different Re and Os carriers in crude oil. The multiple heteroatomic ligands and porphyrins proposed as Re and Os hosts in crude oil are likely present as free molecules, initially absorbed and occluded in the asphaltene aggregates and co-precipitate with asphaltene in response to the addition of n-alkanes. The ReOs elemental and isotopic systematic behaviour revealed herein are interpreted to be the result of the involvement of Re and Os carriers in the aggregation and precipitation of asphaltene, and the chemical make-up of each particular crude oil.

Asphaltene and maltene separated by a series of different alkanes show that asphaltene yields decrease from n-pentane to n-heptane and then tend to stay stable until n-decane. The 187Os/188Os values of the series of asphaltenes are extremely similar for each oil sample, inhibiting the possibility of determining any Re-Os dates with the asphaltenes of a single crude oil. In contrast, the maltene fractions exhibit Re-Os isotopic variation. Nevertheless, only the maltenes of one oil defined a

reasonable isochron with an age similar to that of source rock. As such, this study highlights the need for a greater understanding in order to determine whether, and in what cases, fractions separated from a single crude oil by different alkanes can provide meaningful Re-Os ages.



Two sets of organic-rich shale are developed in Yanshan area,including Mesoproterozoic Hongshuizhuang Formation and Xiamaling Formation. Because of low exploration level,the exploration potential of these shale gas resource is unknown. Based on the field geological survey in the Huailai county and Kuancheng county of Hebei province and the Ming Tombs area of Beijing,and the observation and experimental test of Mesoproterozoic black shale cores in Wells Jiyuan-1,Jiqian-1 and Jing-101,the geological conditions of shale gas accumulation in black shale of Hongshuizhuang Formation and Xiamaling Formation are studied,including the sedimentary facies distribution,abundance and type of organic matter,thermal maturity,porosity,permeability and rock mineral features. Research result shows that the shale in Hongshuizhuang Formation and Xiamaling Formation is characterized by large thickness,high organic matter content,moderate thermal evolutionary degree,late hydrocarbon generation,little destructive effect from late tectonic activity,and favorable accumulation geological conditions. The shale gas favorable area for Hongshuizhuang Formation is in the stable tectonic zone from Chengde to Kuancheng of Hebei province; and the area for Xiamaling Formation is in the stable tectonic zone from Zhuozhou of Hebei province to Fangshan,Mentougou and Changping of Beijing,as well as in the Lanqiyingzi area of Hebei province.

Liu, L., Ryu, B., Sun, Z., Wu, N., Cao, H., Geng, W., Zhang, X., Jia, Y., Xu, C., Guo, L., Wang, L., 2019. Monitoring and research on environmental impacts related to marine natural gas hydrates: Review and future perspective. Journal of Natural Gas Science and Engineering 65, 82-107.


In response to the accelerating processes of marine natural gas hydrate exploration and gas production from hydrate-bearing sediments, their potential impacts on the environment have been attracting extensive attention from international academia as well as from industry, especially in recent years. Methane seeps related to gas hydrate degradation on the seafloor are ubiquitous on continental slopes in both active and passive continental margins. A previous series of articles suggest that hydrate dissociation (gas release or ebullition at large scale) mainly occurs as a result of faulting or decreased lithostatic pressure triggered by many external driving forces (mainly including tectonic activities, overpressure zone, earthquake and tides), and temperature change. These frequently affect methane inputs into the atmosphere, fueling seafloor oxygen consumption or ocean acidification, and even posing submarine geohazards. Gas hydrate-related areas are usually estimated from indirect biochemical indications (cold-seep communities, element and isotopic anomalies in pore water) and geophysical indications (surface morphology, gas plumes and pathways). Therefore, appropriate application of monitoring and detection methods is of crucial significance for assessing the temporal and spatial variability of related environmental indicators in gas hydrate reservoirs. Monitoring is also as an essential support for harvesting this potential alternative energy in ways that are safer, more economical, and more environmentally friendly. Following the three structural elements of a hydrocarbon seep pumping system (gas/fluid source, fluid migration pathway, and seeping structures

at or near the seafloor), this paper sets forth the significance of indicators for dynamics resulting from the destabilization of reservoirs of natural gas hydrates, reviews the corresponding monitoring or detection methods and integrated monitoring systems; and especially, expatiates the in situ observation networks regarding gas hydrate reservoirs and gas hydrate production tests. In the closing section, we discuss and draw conclusions regarding the challenges for future development of hydrate environmental monitoring and significant environmental issues requiring special attention. We intend this paper to provide references and to set the scene for future research activities about gas hydrates, so as to ignite the interest of more research groups around the world.

Liu, M., Xue, Y., Yang, J., 2019. Rare plankton subcommunities are far more affected by DNA extraction kits than abundant plankton. Frontiers in Microbiology 10, 454. doi: 410.3389/fmicb.2019.00454.


Advances in high-throughput sequencing technologies allow a more complete study of microbial plankton community composition and diversity, especially in the rare microbial biosphere. The DNA extraction of plankton is a key step for such studies; however, little is known about its influences on the abundant or rare microbial biosphere. Our aim was to quantify the influences of different DNA extraction kits on abundant and rare plankton in the surface waters of a reservoir and provide a reference for the comparisons between microbial community studies with different extraction methods. We evaluated the influence of five common commercial kits on DNA quality, microbial community diversity and composition, and the reproducibility of methods using both 16S and 18S rRNA genes amplicon sequencing. Our data showed that results of Fast DNA Spin Kit for Soil (MPF) had higher α diversity for bacteria and high DNA quality, indicating that it is the most suitable approach for bacterioplankton diversity study. However, DNeasy Blood & Tissue Kit (QD) and QIAamp DNA Mini Kit (QQ) methods could produce results that are easier to replicate for bacteria and eukaryotes, respectively, and were more comparable between studies. The use of different DNA extraction kits had larger influence on the rare taxa compared with abundant taxa. Therefore, the comparability between studies that employed different extraction methods can be improved by removing low-abundance or less-representative OTUs. Collectively, this study provides a comprehensive assessment of the biases associated with DNA extraction for plankton communities from a freshwater reservoir. Our results may guide researchers in experimental design choices for DNA-based ecological studies in aquatic ecosystem.

Liu, P., Zhang, T., Sun, S., 2019. A tutorial review of reactive transport modeling and risk assessment for geologic CO2 sequestration. Computers & Geosciences 127, 1-11.


The world's concern about global warming continues to rise, while CO2 sequestration is always considered as an effective measure to reduce the carbon content in the atmosphere to slow down the warming. To meet the technical requirements of this issue challenging us human beings, increasing numbers of researches have been published around this topic, among which reactive modeling is a popular viewpoint. In this paper, mathematical models governing the reactive transport process from fluid dynamics and thermal dynamics have been comprehensively reviewed, and the corresponding numerical methods have been concluded and presented in details. To help readers new in this area to have a basic knowledge of how to conduct a reactive transport modeling, some commonly used simulators are introduced in our paper, with their general simulation logic and authors' comments. Due to the urgent need of CO2 sequestration, risks are often inevitable in the practical application of CO2 injection and trapping process. Varieties of risks are concluded from different viewpoints of

business, technique and social impacts, and we have presented some monitoring methods to handle these risks. It should be pointed out that long-term sequestration is still a difficulty, and the complex environmental conditions including changing temperature, porous structure, and chemical compositions are still hard to specify. Numerically speaking, high order schemes are still in need to meet the stability and convergence requirement, as well as local mass conservation property. No simulator now can handle CO2 sequestration cases in all projects, so that a more common model and solver should still be our future aim.

Liu, Q., Liu, H.-C., Zhou, Y.-G., Xin, Y.-H., 2019. Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Systematic and Applied Microbiology 42, 168-177.


Cryobacterium and Arthrobacter are members of Actinobacteria, and are often found in cold environments. In this study, 48 Cryobacterium strains, including 9 type strains and 39 new isolates collected from glaciers in China were subjected to multilocus sequence analysis (MLSA). Phylogenetic analysis revealed that Cryobacterium comprised four cold-adapted clusters. Also, 19 potential novel Cryobacterium species were found using 0.065 as the cut-off point of genetic distance between the concatenated gene sequences. Additionally, three Cryobacterium strains (TMN-42T, TMN-39-1 and TMB1-8) and two Arthrobacter strains (HLT2-12-2T, TMN-18) isolated from glaciers were subjected to taxonomic analysis. Based on 16S rRNA gene sequences, MLSA data and average nucleotide identity (ANI) values, they represented a novel Cryobacterium species and a novel Arthrobacter species. Specifically, strain TMN-42T was most closely related to the type strains of Cryobacterium arcticum and Cryobacterium psychrotolerans with 83.79% and 77.78% ANI values, respectively. The ANI values between strain HLT2-12-2T and its closely relatives Arthrobacter psychrochitiniphilus GP3T and Arthrobacter alpinus S6-3T were 76.66% and 77.94%, respectively. Therefore, we propose two novel species, Cryobacterium zongtaii sp. nov. (TMN-42T=CGMCC 1.9695T=NBRC 111591T) and Arthrobacter glacialis sp. nov. (HLT2-12-2T=CGMCC 1.10025T=NBRC 113092T).

Liu, Q., Zhu, D., Jin, Z., Meng, Q., Li, S., 2019. Influence of volcanic activities on redox chemistry changes linked to the enhancement of the ancient Sinian source rocks in the Yangtze craton. Precambrian Research 327, 1-13.


Volcanic eruptions and related submarine hydrothermal activities were very extensive during the Precambrian periods in the Yangtze craton in southern China. How these geological events affected redox chemistry changes linked to the enhancement of mudstone/shale hydrocarbon source rocks in ancient strata is an important concern for oil and gas exploration in the Precambrian strata. Samples were collected from two Sinian (Ediacaran) outcrops in the northern Sichuan Basin, the Zhaiziyan and Yanhe outcrops, which revealed Doushantuo Formation (Z1ds) shales approximately 30.5 m in thickness, and shales in the third member of the Deying Formation (Z2dn3) approximately 30.0 m in thickness. TOC contents of the black carbonaceous shales in the Doushantuo Formation of the Zhaiziyan outcrop are mostly greater than 5.0% (up to 12.9%). Positive correlations were observed between TOC contents and trace and rare earth element concentrations in the shales: samples with high concentrations of trace elements such as V, Ni, Cu, Zr, Rb, and Pb and total rare earth element (∑REE) concentrations had relatively high TOC contents. The shales are rich in volcanic ash interlayers and thin siliceous layers and have positive Eu anomalies, indicating that volcanic activities

and related hydrothermal activities significantly impacted the development of black shale source rocks. In the rifting background of the Sinian cratonal marginal, extensive volcanic activities brought rich nutrients to the seawater, which may have promoted the breeding of cyanobacteria and multicellular algae. At the same time, the volcanic activities released large amounts of H2S and SO2, which could cause the seawater to become a euxinic environment in which the bottom seawater was sulfurized and anoxic. Massive amounts of organic matters formed in the surface seawater entered the anoxic bottom seawater and were well preserved in the shale sediments. Therefore, under the influence of volcanic activities, ancient Sinian organic-rich high-quality source rocks were widely developed and had a large hydrocarbon supply potential for the Sinian dolomite reservoirs.

Liu, Q., Zhu, D., Meng, Q., Liu, J., Wu, X., Zhou, B., Fu, Q., Jin, Z., 2019. The scientific connotation of oil and gas formations under deep fluids and organic-inorganic interaction. Science China Earth Sciences 62, 507-528.

https://doi.org/10.1007/s11430-018-9281-2

As a relatively stable craton block in the earth system, the petroliferous basin is influenced by the evolution of the earth system from the early development environment of source rocks, hydrocarbon formation, and reservoir dissolution to hydrocarbon accumulation or destruction. As a link between the internal and external factors of the basin, deep fluids run through the whole process of hydrocarbon formation and accumulation through organic-inorganic interaction. The nutrients carried by deep fluids promote the bloom of hydrocarbon-generating organisms and extra addition of carbon and hydrogen source, which are beneficial to the development of high-quality source rock and enhancement of the hydrocarbon generation potential. The energy carried by the deep fluid promotes the early maturation of the source rock and facilitates the hydrocarbon generation by activation and hydrogenation in high-mature hydrocarbon sources. The dissolution alteration of carbonate rocks and clastic reservoirs by CO2-rich deep fluids improves the deep reservoir space, thus extending the oil and gas reservoir space into greater depth. The extraction of deeply retained crude oil by deep supercritical CO2 and the displacement of CH4 in shale have both improved the hydrocarbon fluidity in deep and tight reservoirs. Simultaneously, the energy and material carried by deep fluids (C, H, and catalytic substances) not only induce inorganic CH4 formation by Fischer-Tropsch (F-T) synthesis and “hydrothermal petroleum” generation from organic matter by thermal activity but also cause the hydrothermal alteration of crude oil from organic sources. Therefore, from the perspective of the interaction of the earth’s sphere, deep fluids not only input a significant amount of exogenous C and H into sedimentary basins but also improve the reservoir space for oil and gas, as well as their enrichment and accumulation efficiencies.



Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 was isolated from oil-contaminated soil in Xinjiang and characterised morphologically, physiologically and phylogenetically. Environmental parameters including PHE concentration, pH, temperature and salinity were optimised, and heavy metal tolerance was investigated. Atypically for a B. fungorum strain, FM-2 utilised PHE (300 mg L-

1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical

emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.

Long, J., Wang, K., Yang, M., Zhong, W., 2019. Rapid crude oil analysis using near-infrared reflectance spectroscopy. Petroleum Science and Technology 37, 354-360.

https://doi.org/10.1080/10916466.2018.1547754

This work describes a new approach to predict the properties of crude oil by using near infrared spectrum with a reflective fiber-optic probe. The absorbance spectra of crude oil samples were pre-processed by the first derivative. The pretreated near-infrared spectrum data were analyzed with principal component analysis to detect eventual outliers in the data set. The spectral data were correlated with crude oil property parameters by partial least squares regression. The comparison results of predicted and measured values for API gravity and sulfur content revealed a better performance for the model.


https://doi.org/10.1007/s10533-019-00559-4

Ancient sedimentary organic matter (kerogen) represents the largest terrestrial organic carbon (OC) reservoir on earth and is vulnerable to remineralization upon exposure to earth’s atmosphere during the oxidative weathering of sedimentary rocks on the continents. Due to the potential for large carbon-cycle implications, the mechanisms and rates involved in kerogen transformation by oxidative weathering are becoming increasingly well-constrained in contemporary models of the global carbon cycle. Past field studies have focused primarily on areas where high erosion rates deliver large amounts of kerogen to earth’s surface, making the relative importance of low-lying landscapes a key unknown in regional or global scale estimates of kerogen recycling. The weathered residuum of organic-rich sedimentary rocks serves as the parent material for many soils. Therefore, some aspects of the chemical structure and biogeochemical cycling of the soil organic matter are likely to be inherited from the bedrock. We used a combination of solid-state 13C nuclear magnetic resonance (NMR) spectroscopy, and carbon isotope techniques to describe molecular and isotopic changes that occur throughout oxidative weathering of marine kerogens, and the subsequent formation of modern soils, in two outcropping Cretaceous mudstones of the Eagle Ford and Pepper Formations in central, Texas. Increasing production of oxygenated functional groups was coupled with reductions in characteristically abundant aliphatic components of marine kerogens along the weathering profiles. Organic matter structural parameters, derived from C–H dephasing NMR experiments, also provide the basis for a novel weathering index that accounts for the degree of post-sedimentary alteration of kerogen samples along the bedrock-soil continuum. An uncertain future marked by climatic shifts in temperature and/or precipitation and increased continental weathering and denudation rates highlights the potential for enhanced vulnerability of kerogen, and the need for molecular and isotopic tools for quantifying mechanisms and rates involved in kerogen weathering.

Lorenzo-Parodi, N., Kaziur, W., Stojanović, N., Jochmann, M.A., Schmidt, T.C., 2019. Solventless microextraction techniques for water analysis. TrAC Trends in Analytical Chemistry 113, 321-331.


Microextraction techniques have been proven to provide similar or better results in terms of sensitivity and reproducibility in comparison to liquid-liquid extraction (LLE) and solid-phase extraction (SPE). Furthermore, the high time efficiency and decreased workload leads to a higher sample throughput. In this review the state of the art of some of these techniques, namely solid-phase microextraction (SPME), stir-bar sorptive extraction (SBSE), solid-phase dynamic extraction (SPDE), in-tube extraction-dynamic headspace (ITEX-DHS) and PAL SPME Arrow is shown. Furthermore, their benefits and drawbacks are discussed, together with their applicability to the analysis of water samples. To that end, the latest publications of microextraction techniques for a selection of regulated compound classes (chlorophenols (CPs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), pesticides, short-chained chlorinated paraffins (SCCPs) and volatile organic compounds (VOCs)) are compared. Finally, a guideline for choosing the best microextraction technique for different analytical needs is described.

Love, S.G., 2018. BASALT: The future of Mars, on Earth today. Astrobiology 19, 243-244.

https://doi.org/10.1089/ast.2018.1863

Someday, human explorers will walk on the planet Mars.

But, as young children and older space exploration enthusiasts often lament, “someday” doesn't seem to be getting much closer.

In one sense, that's a blessing. To carry off a successful Mars expedition, we must solve a daunting array of technical problems, including regenerative life support, improved in-space propulsion, Mars surface power, use of martian resources, and landing of heavy payloads. Seen through the lens of these challenges—many of which will take 10- or 11-digit budgets to overcome—“someday” can seem all too close.

The problems a Mars expedition will face include the limited bandwidth and long latency time of the communication link back to Earth. In modern life, upload and download speeds of megabits per second can seem barely adequate. Our existing communication satellites can manage rates like that. But take a communication satellite to the Moon, and its data rate drops by a factor of 100. Take it to Mars, and the rate drops by a factor of 100 million. Communication between Earth and Mars also means coping with up to 40 min of round-trip speed-of-light latency between asking a simple question and getting an “immediate” answer.

Under those conditions, how can a large team of specialists on Earth best advise a small group of generalists on another planet? How can the home team keep aware of what their distant collaborators are seeing and doing? How can their recommendations arrive “just in time” rather than tens of minutes late? And how can both teams work together to make the best possible scientific decisions?

Some of those problems can be addressed today, on Earth, with a modest budget. Dozens of space exploration “analog” projects have made progress in solving the communication challenges of future exploration. Many “analogs” have included field work, but the science has often played second fiddle to operational and engineering objectives.

Over the past 4 years, the BASALT (Biologic Analog Science Associated with Lava Terrains) team has taken the next great step in analog mission fidelity. BASALT conducted real science investigations, with real sample collection protocols and real consequences if those protocols were broken—all while employing Mars-realistic communication bandwidths and latencies, with

“extravehicular astronauts” in the field and “intravehicular astronauts” communicating with them in real time to help with science questions, navigation, and procedural protocols. In a separate “Mission Control” room, a team of engineers worked with two-way delayed communication streams to monitor and maintain a complex data architecture and a suite of scheduling, mapping, and situational awareness (including augmented reality) tools. “Mission Control” also hosted a science team with broad, deep expertise. The scientists analyzed the flood of voice calls, imagery, and instrument data coming in from the field to make decisions on a tight schedule, so that they could deliver sampling priorities to the field team on time, rather than many minutes too late.

The team members faced variable weather, volcanic fumes, rough and unstable terrain, and heavy loads. They mastered inevitable frustrations with real-time work replanning, delays for weather and equipment failure, and confusion registering field imagery to real landmarks at the site. The work was hard, but the team's efforts have paid dividends. After reading this Special Collection, which presents the scientific, operational, and engineering insights gained by the BASALT team during their intensive field activities and thousands of hours of postmission analysis, we hope you will agree.

For this participant, a planetary scientist and veteran of one space flight, two seasons in Antarctica, a half dozen NASA “analogs”, hundreds of hours in mission control, and a career focused on exploration, BASALT was a chance to work in the amazing future that scientists and engineers are now creating, a future in which the Earth is just one of many worlds for people to explore and understand. “Someday” won't come soon enough for me to fly to Mars myself. But projects like BASALT give a taste of what planetary exploration will become, while doing meaningful science and blazing the trail for the men and women who will make the trip for real. It is hard to imagine more rewarding work. It'd be greedy to ask for more…but I hope they invite me back.



Abstract: The quest to manipulate microbiomes has intensified, but many microbial communities have proven to be recalcitrant to sustained change. Developing model communities amenable to genetic dissection will underpin successful strategies for shaping microbiomes by advancing an understanding of community interactions. We developed a model community with representatives from three dominant rhizosphere taxa, the Firmicutes, Proteobacteria, and Bacteroidetes. We chose Bacillus cereus as a model rhizosphere firmicute and characterized 20 other candidates, including “hitchhikers” that coisolated with B. cereus from the rhizosphere. Pairwise analysis produced a hierarchical interstrain-competition network. We chose two hitchhikers, Pseudomonas koreensis from the top tier of the competition network and Flavobacterium johnsoniae from the bottom of the network, to represent the Proteobacteria and Bacteroidetes, respectively. The model community has several emergent properties, induction of dendritic expansion of B. cereus colonies by either of the other members, and production of more robust biofilms by the three members together than individually. Moreover, P. koreensis produces a novel family of alkaloid antibiotics that inhibit growth of F. johnsoniae, and production is inhibited by B. cereus. We designate this community THOR, because the members are the hitchhikers of the rhizosphere. The genetic, genomic, and biochemical tools available for dissection of THOR provide the means to achieve a new level of understanding of microbial community behavior.

importance: The manipulation and engineering of microbiomes could lead to improved human health, environmental sustainability, and agricultural productivity. However, microbiomes have proven

difficult to alter in predictable ways, and their emergent properties are poorly understood. The history of biology has demonstrated the power of model systems to understand complex problems such as gene expression or development. Therefore, a defined and genetically tractable model community would be useful to dissect microbiome assembly, maintenance, and processes. We have developed a tractable model rhizosphere microbiome, designated THOR, containing Pseudomonas koreensis, Flavobacterium johnsoniae, and Bacillus cereus, which represent three dominant phyla in the rhizosphere, as well as in soil and the mammalian gut. The model community demonstrates emergent properties, and the members are amenable to genetic dissection. We propose that THOR will be a useful model for investigations of community-level interactions.


https://doi.org/10.1038/s41396-018-0336-1

Variation in microbial species diversity has typically been explained as the outcome of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity–environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates the species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in the surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on the relative abundances of phyla and their contributions of species numbers in the global seawater pool—highlighting the important influence of evolutionary constraints on local community diversity.

Lu, Z., Zhao, X., Liu, Z., Liu, Q., 2019. Mutual influences between organic matter and minerals during oil shale pyrolysis. Energy & Fuels 33, 1850-1858.


To better understand the mutual influence between organic matter and minerals during oil shale pyrolysis, Huadian oil shale was treated with HCl-HF acids and eight dominant minerals were added separately into the resulting oil shale for pyrolysis. The pyrolysis experiment was performed on a thermogravimetric analyzer coupled with mass spectroscopy (TG-MS), and the influence was discussed from the viewpoints of mass loss of organic matter and release of light volatile products (CH4, C2H6, C3H8, C4H10, C6H6, C7H8, C6H6O, H2, H2O, CO and CO2). Results indicate that the organic matter or pyrolysis products delay(s) the release of water in clays. All the minerals have little effect on the decomposition of organic matter and CaCO3, kaolinite and TiO2 also have little effect on the volatiles reaction; while K2CO3, Na2CO3, MnCO3, montmorillonite and Fe2O3 influence the volatiles reaction in different ways which were discussed in detail in this work.

Luan, G., Dong, C., Azmy, K., Lin, C., Ma, C., Ren, L., Zhu, Z., 2019. Origin of bedding-parallel fibrous calcite veins in lacustrine black shale: A case study from Dongying Depression, Bohai Bay Basin. Marine and Petroleum Geology 102, 873-885.


The bedding-parallel fibrous calcite veins in black shales are common in sedimentary basins and retain significant information about shale diagenesis and organic matter evolution. However, the origin of the bedding-parallel fibrous calcite veins in black shales is still of great controversy. Carbonaceous black shales of Es4s–Es3x interval are the main source rock in Dongying Depression, Bohai Bay Basin, and fibrous calcite veins parallel to bedding are widely spread in these shales. Petrographic examination, fluid-inclusion microthermometry, and isotopic analyses were conducted to study the timing, diagenetic fluid conditions and formation mechanism of fibrous calcite veins. The bedding-parallel fibrous calcite veins include beef veins and cone-in-cone structures. The beef veins occur as short lenses and are filled with sub-vertical fibrous calcite. They contain a “median line” defined with brown granular calcite, scattered host rock fragment and pyrite framboids. Several adjacent beef veins may combine and grow together as a cone-in-cone structure and black shale laminas involved in it occur as sinusoidal solid inclusions in slices. Primary two-phase inclusions in fibrous calcite have homogenization temperatures (Th) between 86.4 °C and 117.4 °C. The δ13C composition of the micritic calcite in host shale ranges from +3.7‰ to +6.3‰VPDB and that of granular calcite ranges from −0.2‰ to +1.4‰VPDB, but the fibrous calcite has a moderate δ13C values ranging from +1.8‰ to +5.0‰ VPDB. The δ13C compositions of these calcite suggest an evolving carbon source at different burial stages. The fibrous calcite likely precipitated from modified pore water at elevated temperature, which is supported by its low δ18O values (−13.7‰ to −11.4‰ VPDB).

The veins formed over two stage and the fibrous calcite growth was continuous and at least partly driven by the force of crystallization. The bicarbonate responsible for the fibrous calcite was derived from a mixed source including inorganic carbon from previous carbonate dissolution, and organic carbon from both fermentation and thermal decarboxylation.

Lübeck, J.S., Malmquist, L.M.V., Christensen, J.H., 2019. Supercritical fluid chromatography for the analysis of oxygenated polycyclic aromatic compounds in unconventional oils. Journal of Chromatography A 1589, 162-172.


Unconventional oil feeds can be rich in oxygenated organic compounds that will negatively affect the fuel properties if they are not removed during refining. In this study, supercritical fluid chromatography (SFC) was utilised for the combined analysis of polycyclic aromatic hydrocarbons (PAHs) and oxygenated polycyclic aromatic compounds (OPACs). One objective was to chromatographically separate PAHs from OPACs; another to reach a high peak capacity, improved peak shapes and high signal-to-noise ratios (S/N) for OPACs. These objectives were set to establish a non-target analysis method for oxygenated compounds in unconventional oils by SFC hyphenated to a UV detector and a quadrupole time-of-flight mass spectrometer (QTOF-MS) with negative electrospray ionisation (ESI−). Highest peak capacities were observed with a 2-picolylamine column with methanol as modifier, however, a better resolution and S/N were obtained with ethanol and 0.1% formic acid. The elution order for OPACs on all columns followed mainly the polarity of the analytes: furans < aldehydes ≤ ketones < phenols ≤ carboxylic acids. Best separation between PAHs and OPACs was achieved with the ethylene-bridged silica column. The optimised SFC-UV-ESI−-QTOF-MS method was tested on a coal tar middle distillate and a pyrolysis oil where a number of homologous series (e.g. hydroxy-naphthalenes and –benzaldehydes) was tentatively identified.

Lunt, P.H., Fyfe, R.M., Tappin, A.D., 2019. Role of recent climate change on carbon sequestration in peatland systems. Science of The Total Environment 667, 348-358.


This paper provides information on the impact of recent climate change on carbon sequestration in peatland systems in South West England. This is important because peatlands have the potential to sequester and hold large quantities of anthropogenically released CO2. This paper investigates whether there has been a reduction in the strength of carbon sinks in a valley mire and blanket bog, which occur on the limits of the biogeographical envelop for peatlands in Britain. Past rates of carbon accumulation were calculated from peat depth and the sequential analysis of peat age, bulk density and carbon content from cores taken from valley mire and blanket bog. At the valley mire site contemporary net ecosystem carbon balance (NECB) was calculated by measuring inputs to the peat body, via net primary productivity (NPP), of Sphagna. Losses of C from the peat body were calculated by measuring CH4, and aquatic carbon, calculated from catchment export of particulate and dissolved organic carbon. The study found similar mean rates of carbon accumulation since 1850 of 11.26 t ± 0.68 t CO2e ha−1 yr−1 (307 g C m−2 yr−1) in valley mire and 11.77 t ± 0.88 t CO2e ha−1 yr−1 (321 g C m−2 yr−1) in blanket bog. The mean present-day CO2 sequestration rate for Sphagna on valley mire was calculated to be 9.13 t ± 0.98 t CO2e ha−1 yr−1 (249 g C m−2 yr−1). Both past and contemporary rates of CO2 sequestration were found to be at the maxima of those reported for temperate peatlands. NPP was found to vary according to microform with higher rates of carbon sequestration found in lawn and hummock microforms compared with pools. Our work suggests that recent changes in the climate appear to have had limited impact on the strength of peatland carbon sinks in South West England.

Luo, B., Xia, M., Wang, H., Fan, Y., Xu, L., Liu, R., Zhan, W., 2019. Hydrocarbon accumulation conditions of Permian volcanic gas reservoirs in the western Sichuan Basin. Natural Gas Industry 39, 9-16.

http://www.cngascn.com:81/ngi_wk/EN/abstract/abstract18751.shtml

In order to figure out the hydrocarbon accumulation conditions of Permian volcaniclastic gas reservoirs in the western Sichuan Basin, we analyzed the hydrocarbon accumulation characteristics of volcaniclastic gas reservoirs in this area in terms of reservoir, gas source, play and trap. It is indicated that the favorable conditions for the hydrocarbon accumulation of volcaniclastic gas reservoirs in the Jianyang area in the western Sichuan Basin are as follows. First, in the Well Yongtan 1, vocaniclastic lava of effusive facies is dominant, and superimposed with late alteration and dissolution, pore-type reservoirs with devitrified dissolution micropores as the main reservoir space are developed. Second, geochemical analysis and comparison on natural gas reveal that the gas of the volcanic gas reservoirs in the Well Yongtan 1 is mainly derived from the Qiongzhusi Formation of Lower Cambrian. Cambrian quality source rocks of great thickness are developed in Deyang–Anyue rift in the Jianyang area and they provide sufficient gas sources for the formation of gas reservoirs. Third, volcaniclastic reservoirs and Cambrian source rocks constitute a proximal high-efficiency source–reservoir assemblage with reservoir in the upper part and source rock in the lower part, hydrocarbon source faults communicate source rocks with reservoirs effectively, and the direct caprock of Longtan Formation mudstone of Upper Permian and the regional caprock of Triassic gypsum rock are developed. Thus, a good assemblage of source, reservoir and caprock is formed. Fourth, tectonic–lithologic (stratigraphic) composite traps are developed in Chengdu–Jianyang area and their favorable gas bearing area is preliminarily confirmed to be 1300 km2, presenting a great exploration potential of natural gas. In conclusion, the volcaniclastic gas reservoirs in western Sichuan Basin are much different from Zhougongshan basalt gas reservoir in southwestern Sichuan Basin in terms of hydrocarbon accumulation conditions. It is predicted that the distribution area of vocaniclastic rocks in the Zhongjiang–Santai area is over 4000 km2, and their hydrocarbon accumulation conditions of

volcanic gas reservoirs are similar to those in the Jianyang area, so this is a favorable area for exploration breakthrough in the next stage.


https://doi.org/10.1080/10916466.2018.1552968

The wax deposition of crude oil during transportation reduces the inner diameter, blocks the pipeline, and eventually increases the cost of petroleum production. This study reports a paraffin-degrading bacterial strain DG2 isolated from petroleum-contaminated soil. The effect of this strain on the removal of paraffin in crude oil was investigated. DG2, identified as Pseudomonas, produced biosurfactant that reduced the surface tension to 35.7?mN/m?1 and exhibited high emulsification activity. Results of gas chromatography?mass spectrometry analysis of the waxy crude oil treated by DG2 showed decreased heavy hydrocarbon fractions (C25 and C32). The degradation test revealed that DG2 reduced the wax appearance temperature by 4.16?°C and the viscosity by 23% of the waxy crude oil. These findings indicate that paraffin-degradation strain DG2 may be used for effective paraffin biodegradation.

Luo, G., Yang, H., Algeo, T.J., Hallmann, C., Xie, S., 2019. Lipid biomarkers for the reconstruction of deep-time environmental conditions. Earth-Science Reviews 189, 99-124.


Lipids can survive long geological intervals within sediments and provide a unique tool that allows the reconstruction of past organismic diversity and environmental conditions. The lipids discussed in this review include all substances produced by organisms that are insoluble in water but extractable by organic solvents. Lipid biomarkers refer to both functionalized biolipids as well as their hydrocarbon derivatives in geological materials that contain diverse information about biotic sources and environmental conditions. In spite of diagenetic and catagenetic alteration, lipid biomarkers commonly preserve the hydrocarbon structure of their biotic counterparts and have been found in rocks up to 1.6 billion years in age. These features have promoted the use of lipid biomarkers in many fields, including petroleum geology, paleoclimatology, oceanography, meteorology, geobiology and environmental science. Here, we (i) review the use of lipid biomarker records for the reconstruction of environmental conditions in deep time, including climatic conditions (temperature), sedimentary environments (redox, salinity and chemical composition) as well as catastrophic terrestrial events (soil erosion and wildfire), and (ii) generate new insights into environmental perturbations during the Permian-Triassic transition based on investigation of lipid biomarkers. We further propose that the ratio of dibenzothiophene to phenanthrene (DBT/P) in marine carbonates may be a robust proxy for seawater sulfate concentrations in deep time. Our compiled DBT/P records show substantial variations in seawater sulfate levels through Earth history that are consistent with the results of other proxies. We discuss the future outlook for application of lipid biomarker records to deep-time environmental research.



Like microbialites, microbially induced sedimentary structures (MISSs) are commonly observed in siliciclastic and mixed carbonate siliciclastic settings in the Lower Triassic, and are represented by several morphological types including wrinkle structures. However, their origin and their role in the Early Triassic ecosystem recovery is currently a hot topic of debate. Herein we report and describe abundant wrinkle structures from the Smithian Kockatea Shale Formation of Northampton area in the Perth Basin, Western Australia, on the basis of detailed field observations as well as petrographic and SEM examinations of rock thin sections. The surficial morphologies of wrinkles are characterized by closely spaced crests and ridges on the upper bedding surfaces, together with other forms such as pitted bulges and reticulated ridges. Detailed petrologic analysis revealed that the Smithian wrinkle structures from the northern Perth Basin possess a distinct vertical profile: (1) cross-stratified/lamianted sandstone, (2) alternating laminated layers and sandstone, (3) laminated layers, and (4) wrinkled layers, in an ascending order. The wrinkled layers are overlain by thin shale. Laminated layers beneath wrinkled surfaces comprise densely packed, pronounced, wavy laminae. Mica flakes in laminations show a preferred alignment parallel to bedding under SEM imaging, suggesting the binding and trapping of the former presence of a microbial matground. These evidences support that the Early Triassic wrinkle structures from the Smithian Kockatea Formation are biogenic in origin. Close association of both trace and body fossils with the wrinkle structure-bearing layers is interpreted to indicate the presence of a matground ecosystem in which some small gastropods and various trace-making animals lived, possibly taking the habitat as a refuge. The global temporal and spatial occurrences of Early Triassic MISS were tabulated and analyzed, revealing a wide range of palaeoenvironmental distributions and the seemingly selected association between metazoans and certain MISS. As to why only some MISSs have been found together with metazoans remains as an open question. It will require further investigation especially with regard to the specific type of microbes that had built the microbial matground ecosystems and their interplay with the hosted metazoans in the aftermath of the end-Permian mass extinction.

Lyu, Z., Orchard, M.J., Chen, Z.-Q., Wang, X., Zhao, L., Han, C., 2019. Uppermost Permian to Lower Triassic conodont successions from the Enshi area, western Hubei Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 49-64.


We present recent study results of the Lower Triassic conodont succession from the Ganxi and Jianshi areas of Enshi city, western Hubei Province, South China, which were situated on a carbonate ramp at the northeastern margin of the Upper Yangtze Platform. Therein, the uppermost Permian to Lower Triassic succession is well exposed and yielded abundant conodonts. A total of nine conodont zones are differentiated: (1) Clarkina yini Zone, (2) Clarkina meishanensis Zone, (3) Hindeodus changxingensis Zone, (4) Hindeodus parvus Zone, (5) Hindeodus postparvus Zone, (6) Clarkina planata Zone, (7) Neoclarkina aff. discreta Zone, (8) Neospathodus dieneri Zone, and (9) Novispathodus waageni Zone. The Ns. dieneri M1, Ns. dieneri M2, and Ns. dieneri M3 Subzones have also been distinguished within the Ns. dieneri Zone, and the Nv. waageni eowaageni and Nv. waageni waageni Subzones are recognizable within the Nv. waageni Zone in Jianshi. Most of the zones occur in succession, but the C. planata Zone is a local ecozone reflecting deeper water biofacies during H. postparvus Zone time. In the Jianshi section, the Permian–Triassic boundary is placed at Bed 136-2 based on the appearance of Hindeodus parvus immediately above the disappearance of Changhsingian taxa, while the Induan–Olenekian boundary (IOB) is drawn at Bed 225+40cm based on the first appearance of Nv. waageni eowaageni within the upper range of the Ns. dieneri Zone indices. The Enshi conodont zones overall correlate well with those recognized elsewhere in South China and worldwide.

Ma, X., Yang, Y., Zhang, J., Xie, J., 2019. A major discovery in Permian volcanic rock gas reservoir exploration in the Sichuan Basin and its implications Natural Gas Industry 39, 1-8.

http://www.cngascn.com:81/ngi_wk/EN/abstract/abstract18750.shtml

Recently, a high-yield gas flow of 22.5×104 m3/d was achieved in the wildcat well Yongtan 1, deployed by the PetroChina Southwest Oil and Gasfield Company, and an extrusive facies vocaniclastic gas reservoir was first discovered in the Sichuan Basin, which is a major breakthrough in the exploration of volcanic rock gas reservoirs. In order to further evaluate the exploration potential in Permian volcanic rock gas reservoirs in this basin, we systematically reviewed and summarized the exploration process of volcanic rocks in this study area, as well as the characteristics of gas reservoirs of well Yongtan 1, the controlling factors and modes of hydrocarbon accumulation. The following findings were obtained. (1) Over the past five decades of gas exploration of volcanic rocks, the change of exploration thought and progress in seismic prediction contribute to a major discovery in this study area, i.e., the well location deployment of Yongtan 1 was determined in the Jianyan area, where the volcanic anomalies of the Permian developed outbursts are well developed and the gas reservoir conditions are favorable. This also proves that another new gas exploration area in this basin was found. (2) From the data of Yongtan 1, we found high-quality volcanic porous reservoirs with a thickness of over 100 m developed in the Permian strata, the effusive volcanic rock types dominated by breccia and tuffaceous breccia, reservoir space composed of dissolution pores, interbreccia dissolution pores, and other pores, the porosity of which is between 6.68% and 13.22% and 10.26% on average, the permeability between 0.01 and 4.43 mD and 2.35 mD on average. (3) This abnormally high pressure gas reservoir was buried 4 500–6 000 m deep underground with the middle formation pressure being 125.625 MPa and the pressure coefficient being up to 2.22. Methane content in the minor H2S-bearing produced gas flow reached up to 99.03%. (4) Volcanic rocks in the Jianyang–Zhongjiang–Santai area are developed, and they are adjacent to the Cambrian high-quality source rocks in the Deyang–Anyue rifting. The early extensional deep faults play a role in connecting source and storage. There are many sets of caprocks, such as the Upper Permian Longtan Formation and Lower Triassic layered thick paste rocks, providing conditions for forming large-scale tectonic–lithologic composite trap gas reservoirs, and the favorable exploration area reaches up to 6 000 km2. In conclusion, this major discovery not only proves that Permian volcanic rocks in the Sichuan Basin has large potential for oil and gas exploration, but reaffirms the confidence in changing our exploration thought, speeding up new exploration zones and areas, and discovering more and bigger gas fields.

MacDougall, M.J., Brocklehurst, N., Fröbisch, J., 2019. Species richness and disparity of parareptiles across the end-Permian mass extinction. Proceedings of the Royal Society B: Biological Sciences 286, Article 20182572.

https://doi.org/10.1098/rspb.2018.2572

The amniote clade Parareptilia is notable in that members of the clade exhibited a wide array of morphologies, were successful in a variety of ecological niches and survived the end-Permian mass extinction. In order to better understand how mass extinction events can affect clades that survive them, we investigate both the species richness and morphological diversity (disparity) of parareptiles over the course of their history. Furthermore, we examine our observations in the context of other metazoan clades, in order to identify post-extinction survivorship patterns that are present in the clade. The results of our study indicate that there was an early increase in parareptilian disparity, which then fluctuated over the course of the Permian, before it eventually declined sharply towards the end of the Permian and into the Triassic, corresponding with the end-Permian mass extinction

event. Interestingly, this is a different trend to what is observed regarding parareptile richness, that shows an almost continuous increase until its overall peak at the end of the Late Permian. Moreover, richness did not experience the same sharp drop at the end of the Permian, reaching a plateau until the Anisian, before dropping sharply and remaining low, with the clade going extinct at the end of the Triassic. This observed pattern is likely to be due to the fact that, despite the extinction of several morphologically distinct parareptile clades, the procolophonoids, one of the largest parareptilian clades, were diversifying across the Permian–Triassic boundary. With the clade's low levels of disparity and eventually declining species richness, this pattern most resembles a ‘dead clade walking’ pattern.

Mahato, N.K., Sharma, A., Singh, Y., Lal, R., 2019. Comparative metagenomic analyses of a high-altitude Himalayan geothermal spring revealed temperature-constrained habitat-specific microbial community and metabolic dynamics. Archives of Microbiology 201, 377-388.

https://doi.org/10.1007/s00203-018-01616-6

Metagenomic surveys across microbial mat (~ 55 °C) samples of high-altitude (1760 m above sea level) Himalayan geothermal springs have revealed specialized community enriched with niche-specific functions. In this study, we have performed metagenomic sequence-based analyses to get insights into taxonomic composition and functional potential of hyperthermophiles in water (~ 95 °C) and sediment samples (78–98 °C). Community analyses revealed predominance of thermophilic bacterial and archeal genera dwelling in water in contrast to microbial mats (55 °C), namely Methylophilus, Methyloversatilis, Emticicia, Caulobacter, Thermus, Enhydrobacter and Pyrobaculum. Sediment samples having surface temperature (~ 78 °C) were colonized by Pyrobaculum and Chloroflexus while genus Massilia was found to be inhabited in high-temperature sediments (~ 98 °C). Functional analyses of metagenomic sequences revealed genetic enrichment of genes such as type IV secretion system, flagellar assembly and two-component system in contrast to mats. Furthermore, inter-sample comparison of enriched microbial diversity among water, sediment and microbial mats revealed habitat-specific clustering of the samples within same environment highlighting the role of temperature dynamics in modulating community structure across different habitats in same niche. However, function-based analysis demonstrated site-specific clustering among sediment, microbial mat and water samples. Furthermore, a novel thermophilic genotype of the genus Emticicia (designated as strain MM) was reconstructed from metagenome data. This is a correlative study between three major habitats present in geothermal spring environment, i.e., water, sediment and microbial mats revealing greater phylogenetic and functional dispersion emphasizing changing habitat-specific dynamics with temperature.

Mahlstedt, N., Horsfield, B., 2019. Thermovaporisation: A screening tool for the gas-sorptive properties of source rocks. Organic Geochemistry 131, 1-4.


We have developed a new geochemical logging method to evaluate the amount and composition of sorbed gas within source rocks quickly and inexpensively, thereby providing a practical tool for the rapid identification of “sweet spots” or heterogeneities within vertical profiles. Thermovaporisation GC-FID (Tvap) forms the basis of the screening method and can be easily run alongside Rock-Eval pyrolysis in high resolution. A fairly good correlation of S2 normalised Tvap gas yields with the rocks TOC normalised measured Langmuir amounts (nL) assessed using standard petrophysical methods (e.g., excess sorbed methane versus pressure curves) demonstrates that Tvap is capable of defining the basic sorption characteristics of source rocks or gas shales. The Tvap screening tool excels at detecting

zones (organofacies/lithofacies) and related heterogeneities in the sorption behaviour of the respective rocks, but not in directly detecting sorption properties. Nevertheless, adsorptive property profiling is possible for large data sets by including direct integration of Langmuir parameters.

Małachowska, A., Mastalerz, M., Hampton, L., Hupka, J., Drobniak, A., 2019. Origin of bitumen fractions in the Jurassic-early Cretaceous Vaca Muerta Formation in Argentina: insights from organic petrography and geochemical techniques. International Journal of Coal Geology 205, 155-165.


This paper investigates chemical functional groups of the two extracted bitumen fractions in shales of the Jurassic to early Cretaceous Vaca Muerta Formation of the Neuquén Basin in Argentina, South America. The results indicate that Bitumen I is strongly aliphatic and appears to be genetically related to fluorescent amorphous organic matter. In contrast, Bitumen II consists of highly condensed, aromatic hydrocarbons, and has some correspondence to nonfluorescent amorphous organic material. Comparison of Rock-Eval VI pyrolysis data (S1 and S2) with the bitumen yields suggests that Bitumen I relates to S1 but also to S2. In addition, Bitumen I has a positive correlation with light liquid hydrocarbons (C5–C29), but also partially with heavier hydrocarbons (above C30). This suggests that Bitumen I corresponds to the majority of lighter hydrocarbons up to C29 and some portion to heavier hydrocarbons. These results have implications for the assessment of the mobility of generated hydrocarbons and their availability for production.

Malagar, B.R.C., Lijith, K.P., Singh, D.N., 2019. Formation & dissociation of methane gas hydrates in sediments: A critical review. Journal of Natural Gas Science and Engineering 65, 168-184.


Methane Gas Hydrates, MGHs, are perceived as a future source of energy for the sustenance of mankind owing to their abundance, usually found in continental margins and permafrost regions. However, identification of potential MGHs reserves, characterized by their high saturation in sediment pores, Sh, establishing their spatial distribution in hydrate bearing sediemnts, HBS, and their extraction, is extremely challenging. This calls for a proper understanding of the mechanisms and factors, associated with sediments and their matrix characteristics, viz., the pore-diameter, dp, particle diameter, d, specific surface area, SSA, initial water saturation, Sw, salinity of the pore-water, S, mineralogy, porosity, η, and density, ρ and thermodynamic conditions, affecting the formation and dissociation of MGHs in sediments. In this context, several laboratory investigations have been conducted to mimic the natural process of MGHs formation, with an intention to gain an insight into (i) mechanisms involved in formations, (ii) response of HBS during dissociation, and (iii) CH4 gas recovery rate under prevailing thermodynamic conditions. However, such studies have, usually, focused on the simulation of ‘specific reservoir conditions’ (viz., P-T, S, d) and hence acquiring a comprehensive picture about the (i) MGHs formation and dissociation process, and (ii) influence of above-mentioned parameters on these processes, becomes necessary. With this in view, a critical review of the literature pertaining to the synthesis of MGHs has been conducted and it has been demonstrated that in addition to thermodynamic conditions, d, dp, Sw, S, SSA and mineralogy of the sediments have a significant influence on the formation as well as dissociation process. In this context, the discussion, analysis and relationship proposed in this manuscript prima facie will aid in estimating Sh and understanding the mechanisms governing its dependency on sediments and their matrix characteristics.

Malfatti, F., Lee, C., Tinta, T., Pendergraft, M.A., Celussi, M., Zhou, Y., Sultana, C.M., Rotter, A., Axson, J.L., Collins, D.B., Santander, M.V., Anides Morales, A.L., Aluwihare, L.I., Riemer, N., Grassian, V.H., Azam, F., Prather, K.A., 2019. Detection of active microbial enzymes in nascent sea spray aerosol: Implications for atmospheric chemistry and climate. Environmental Science & Technology Letters 6, 171-177.


The oceans cover nearly three-quarters of the Earth’s surface and produce vast quantities of sea spray aerosols (SSA). Studies have shown that due to ocean biology SSA particles are comprised of much more than just sea salt and often include proteins, lipids, sugars, viruses, and bacteria. In this study, we show for the first time that a diverse array of microbial enzymes (protease, lipases, and alkaline phosphatase) are transferred from the ocean into the atmosphere and often become even more active with measured activities in SSA particles that are 1–2 orders of magnitude higher than those in bulk seawater. We hypothesize that these enzymatic reactions are enhanced in the interfacial environment of droplets and aerosols that can dynamically modify surface chemical species and properties. Simulations reveal that enzyme-containing SSA particles can rapidly coagulate with other preexisting aerosols, thus transferring the impact of enzyme reactions to a broad range of marine aerosols. These biotic reaction pathways are expected to profoundly change the composition of marine aerosols, particularly at the interface, and thus will impact cloud properties in marine environments. Future studies are needed to determine how photochemistry, changing ocean conditions in a warming climate, and other external factors will influence the activities of these enzymes and their impact on the composition of the marine atmosphere.

Malizia, A., Monmany-Garzia, A.C., 2019. Terrestrial ecologists should stop ignoring plastic pollution in the Anthropocene time. Science of The Total Environment 668, 1025-1029.


The massive production of plastic started in mid 20th century. Today, only 60 years later and despite its obvious benefits, plastic pollution is ubiquitous, influencing all global environments and the planet's biota, including human-well-being. Plastic pollution may interact with other global change drivers, having large-scale, remote and long-lasting effects. Here we highlight that plastic pollution should be considered a main topic for global change research in the 21st century, especially among terrestrial ecologists at understudied continental regions such as South America.

Mansour, E.M., Al-Sabagh, A.M., Desouky, S.M., Zawawy, F.M., Ramzi, M., 2019. A laboratory investigation of carbon dioxide-enhanced oil recovery by focusing on CO2-oil physical properties. Egyptian Journal of Petroleum 28, 21-26.


Carbon dioxide (CO2) miscible flooding has become an important method in enhanced oil recovery (EOR) for recovering residual oil. In addition it may help in protection of the environment as (CO2) is widely viewed as an important agent in global warming. Knowledge of the interactions between (CO2) and reservoir crude oil is very critical for any (CO2)-enhanced oil recovery (EOR) projects. This paper shows the effect of (CO2) miscible flooding application for Egyptian oil fields by swelling studies. The swelling test is a laboratory simulation of the process of injecting gradually different percentage of (CO2) gas into a reservoir containing under-saturated oil. The gas (injection solvent) can dissolve, causing the reservoir fluid to swell. This paper presents a summary of a wide range of

laboratory tests conducted on ten different crude oils varying from 26.4 to 40.5 API. These were used to invested the use of (CO2) and its effect on parameters such as viscosity, density, gas solubility and swelling factor as a function of pressure at temperature from 620.3 to 706.0 °R.

Markosyan, L., Badalyan, H., Vardanyan, N., Vardanyan, A., 2019. Study of colloidal polysaccharides produced by iron oxidizing bacteria Leptospirillum ferriphilum CC. Geomicrobiology Journal 36, 188-193.

https://doi.org/10.1080/01490451.2018.1534903

Iron and sulfur oxidizing bacteria produce capsular and colloidal extracellular polymeric substances. The properties and functional role of capsular polysaccharides are well studied. However, colloidal polysaccharides produced by iron oxidizing bacteria have not been sufficiently explored. In this paper, the physical and chemical properties of colloidal polysaccharides produced by the iron oxidizing bacterial isolate Leptospirillum ferriphilum CC have been studied. Colloidal polysaccharides were extracted and further investigated by optical polarized microscopy and analytical programs (LobVIEW15 and NOVA) that allowed determining the size, changes in shape, perimeter, degree of hydration, and crystallization of polysaccharides. Computer modeling of the experimental data has revealed that polysaccharides concentration does not contribute to the size of colloids but influence the number of particles.

Marquez, J.J., Miller, M.J., Cohen, T., Deliz, I., Lees, D.S., Zheng, J., Lee, Y.J., Kanefsky, B., Norheim, J., Deans, M., Hillenius, S., 2019. Future needs for science-driven geospatial and temporal extravehicular activity planning and execution. Astrobiology 19, 440-461.

https://doi.org/10.1089/ast.2018.1838

Future human missions to Mars are expected to emphasize scientific exploration. While recent Mars rover missions have addressed a wide range of science objectives, human extravehicular activities (EVAs), including the Apollo missions, have had limited experience with science operations. Current EVAs are carefully choreographed and guided continuously from Earth with negligible delay in communications between crew and flight controllers. Future crews on Mars will be expected to achieve their science objectives while operating and coordinating with a science team back on Earth under communication latency and bandwidth restrictions. The BASALT (Biologic Analog Science Associated with Lava Terrains) research program conducted Mars analog science on Earth to understand the concept of operations and capabilities needed to support these new kinds of EVAs. A suite of software tools (Minerva) was used for planning and executing all BASALT EVAs, supporting text communication across communication latency, and managing the collection of operational and scientific EVA data. This paper describes the support capabilities provided by Minerva to cope with various geospatial and temporal constraints to support the planning and execution phases of the EVAs performed during the BASALT research program. The results of this work provide insights on software needs for future science-driven planetary EVAs.

Marshall, B.D., Bokis, C.P., 2019. A PC-SAFT model for hydrocarbons I: Mapping aromatic π-π interactions onto a dipolar free energy. Fluid Phase Equilibria 489, 83-89.


Aromaticity is an important property of many petroleum derived streams. Traditional thermodynamics tools (e.g., cubic equations of state) do not provide any special treatment to these

aromatic hydrocarbons. A feature which discriminates aromatics from paraffins is that aromatic rings exhibit anisotropic π-π interactions. Accounting for this key difference between aromatic and non-aromatic hydrocarbons in an equation of state will allow for a level of predictability which is not possible with our current tools. By mapping the anisotropy of π-π attractions onto a dipolar free energy, we develop a simple and powerful treatment of aromatic hydrocarbons within the PC-SAFT equation state. We demonstrate that this approach provides a substantial increase in performance over the standard non-polar treatment of aromatic molecules. The methodology developed is used to develop a generalized hydrocarbon model in instalment II of this series.

Martín-Ortiz, A., Ruiz-Matute, A.I., Sanz, M.L., Moreno, F.J., Herrero, M., 2019. Separation of di- and trisaccharide mixtures by comprehensive two-dimensional liquid chromatography. Application to prebiotic oligosaccharides. Analytica Chimica Acta 1060, 125-132.


Carbohydrates are one of the most important ingredients in foods. They are normally present as complex mixtures with different glycosidic linkages, monomeric units and degrees of polymerization. This structural heterogeneity impairs their comprehensive characterization and requires the use of analytical techniques with high resolving power and sensitivity. The use of chromatographic techniques, especially liquid chromatography (LC), has been extremely helpful for the analysis of carbohydrates. However, in many cases, the use of monodimensional LC is not enough to resolve these complex mixtures; then, the use of techniques with a higher resolving power, as multidimensional LC, could be a good alternative. To the best of our knowledge, our findings are pioneer in applying online LC × LC for the analysis of carbohydrate mixtures. For this purpose, different conditions such as stationary phases (BEH amide, C18 and PGC columns) and chromatographic conditions for the separation of di- and trisaccharide mixtures were optimized. The BEH amide × C18 combination was selected for the LC × LC analysis of carbohydrate standards with different degrees of polymerization, linkages and monomeric units. In order to allow their proper UV detection, carbohydrates were previously derivatized using p-aminobenzoic ethyl ester. This method also resulted to be successful for the separation of commercial prebiotic mixtures of galacto-oligosaccharides and gentio-oligosaccharides. This is the first time that LC × LC has been applied for the separation of bioactive carbohydrate mixtures and it could be considered as a powerful analytical technique for the characterization of other oligosaccharide complex mixtures.

Martínez-Mena, M., Almagro, M., García-Franco, N., de Vente, J., García, E., Boix Fayos, C., 2019. Fluvial sedimentary deposits as carbon sinks: organic carbon pools and stabilization mechanisms across a Mediterranean catchment. Biogeosciences 16, 1035-1051.


carbon (OC) stabilization in alluvial sediments in semiarid and subhumid catchments where those mechanisms are quite complex because sediments are often redistributed and exposed to a range of environmental conditions in intermittent and perennial fluvial courses within the same catchment. The main goal of this study was to evaluate the contribution of transport and depositional areas as sources or sinks of CO2 at the catchment scale. We used physical and chemical organic matter fractionation techniques and basal respiration rates in samples representative of the three phases of the erosion process within the catchment: (i) detachment, representing the main sediment sources from forests and agricultural upland soils, as well as fluvial lateral banks; (ii) transport, representing suspended load and bedload in the main channel; and (iii) depositional areas along the channel, downstream in alluvial wedges, and in the reservoir at the outlet of the catchment, representative of

medium- and long-term residence deposits, respectively. Our results show that most of the sediments transported and deposited downstream come from agricultural upland soils and fluvial lateral bank sources, where the physicochemical protection of OC is much lower than that of the forest soils, which are less sensitive to erosion. The protection of OC in forest soils and alluvial wedges (medium-term depositional areas) was mainly driven by physical protection (OC within aggregates), while chemical protection of OC (OC adhesion to soil mineral particles) was observed in the fluvial lateral banks. However, in the remaining sediment sources, in sediments during transport, and after deposition in the reservoir (long-term deposit), both mechanisms are equally relevant. Mineralization of the most labile OC (the intra-aggregate particulate organic matter (Mpom) was predominant during transport. Aggregate formation and OC accumulation, mainly associated with macroaggregates and occluded microaggregates within macroaggregates, were predominant in the upper layer of depositional areas. However, OC was highly protected and stabilized at the deeper layers, mainly in the long-term deposits (reservoir), being even more protected than the OC from the most eroding sources (agricultural soils and fluvial lateral banks). Altogether our results show that both medium- and long-term depositional areas can play an important role in erosive areas within catchments, compensating for OC losses from the eroded sources and functioning as C sinks.

Mason-Jones, K., Banfield, C.C., Dippold, M.A., 2019. Compound-specific 13C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria. Rapid Communications in Mass Spectrometry 33, 795-802.

https://doi.org/10.1002/rcm.8407

Rationale: Many bacteria synthesize carbon (C) and energy storage compounds, including water‐insoluble polyester lipids composed mainly or entirely of poly(3‐hydroxybutyrate) (PHB). Despite the potential significance of C and energy storage for microbial life and C cycling, few measurements of PHB in soil have been reported.

Methods: A new protocol was implemented, based on an earlier sediment extraction and derivatization procedure, with quantification by gas chromatography/mass spectrometry (GC/MS) and 13C‐isotopic analysis by GC/combustion/isotope ratio mass spectrometry (GC/C/IRMS).

Results: The PHB content was 4.3 μg C g−1 in an agricultural soil and 1.2 μg C g−1 in a forest topsoil. This was an order of magnitude more PHB than obtained by the existing extraction method, suggesting that native PHB in soil has been previously underestimated. Addition of glucose increased the PHB content by 135% and 1,215% over 5 days, with the largest increase in the relatively nutrient‐poor forest soil. In the agricultural soil, 68% of the increase was derived from added 13C‐labeled glucose, confirming synthesis of PHB from glucose for the first time in soil.

Conclusions: The presence and responsiveness of PHB in both these contrasting soils show that PHB could provide a useful indicator of bacterial nutritional status and unbalanced growth. Microbial storage could be important to C and nutrient cycling and be a widespread strategy in the life of soil bacteria. The presented method offers new insight into the significance of this compound in soil.

Matava, T., Matt, V., Flannery, J., 2019. New insights on measured and calculated vitrinite reflectance. Basin Research 31, 213-227.

https://doi.org/10.1111/bre.12317

Measurement of dispersed vitrinite reflectance in organic sediments is one of the few regional data sets used for placing bounds on the thermal history of a sedimentary basin. Reflectance data are

important when access to complementary information such as high-quality seismic data is unavailable to place bounds on subsidence history and in locations where uplift is an important part of the basin history. Attributes which make vitrinite reflectance measurements a useful data set are the relative ease of making the measurement, and the availability of archived well cores and cuttings in state, provincial, and federal facilities. In order to fully utilize vitrinite data for estimating the temperature history in a basin, physically based methods are required to calibrate an equivalent reflectance from a modelled temperature history with measured data. The most common method for calculating a numerical vitrinite reflectance from temperature history is the EASY%Ro method which we show systematically underestimates measured data. We present a new calculated reflectance model and an adjustment to EASY%Ro which makes the correlation between measured vitrinite values and calculated vitrinite values a physical relationship and more useful for constraining thermal models. We then show that calibrating the thermal history to vitrinite on a constant age date surface (e.g., top Cretaceous) instead of calibrating the thermal history in depth removes the heating rate component from the reflectance calculation and makes thermal history calibration easier to understand and more directly related to heat flow. Finally, we use bounds on the vitrinite?temperature relationships on a constant age date surface to show that significant uncertainty exists in the vitrinite data reported in most data sets.

McCutcheon, J., Power, I.M., Shuster, J., Harrison, A.L., Dipple, G.M., Southam, G., 2019. Carbon sequestration in biogenic magnesite and other magnesium carbonate minerals. Environmental Science & Technology 53, 3225-3237.


The stability and longevity of carbonate minerals make them an ideal sink for surplus atmospheric carbon dioxide. Biogenic magnesium carbonate mineral precipitation from the magnesium-rich tailings generated by many mining operations could offset net mining greenhouse gas emissions, while simultaneously giving value to mine waste products. In this investigation, cyanobacteria in a wetland bioreactor enabled the precipitation of magnesite (MgCO3), hydromagnesite [Mg5(CO3)4(OH)2·4H2O], and dypingite [Mg5(CO3)4(OH)2·5H2O] from a synthetic wastewater comparable in chemistry to what is produced by acid leaching of ultramafic mine tailings. These precipitates occurred as micrometer-scale mineral grains and microcrystalline carbonate coatings that entombed filamentous cyanobacteria. This provides the first laboratory demonstration of low temperature, biogenic magnesite precipitation for carbon sequestration purposes. These findings demonstrate the importance of extracellular polymeric substances in microbially enabled carbonate mineral nucleation. Fluid composition was monitored to determine carbon sequestration rates. The results demonstrate that up to 238 t of CO2 could be stored per hectare of wetland/year if this method of carbon dioxide sequestration was implemented at an ultramafic mine tailing storage facility. The abundance of tailings available for carbonation and the anticipated global implementation of carbon pricing make this method of mineral carbonation worth further investigation.


https://doi.org/10.1038/s41564-019-0362-4

Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the

metagenome of a circumneutral, suboxic hot spring that contains high levels of sulfate, sulfide, methane, hydrogen and carbon dioxide. One population is closely related to ‘Candidatus Korarchaeum cryptofilum OPF8’, while the more abundant korarchaeote, ‘Candidatus Methanodesulfokores washburnensis’, contains genes that are necessary for anaerobic methane and dissimilatory sulfur metabolisms. Phylogenetic and ancestral reconstruction analyses suggest that methane metabolism originated in the Korarchaeota, whereas genes for dissimilatory sulfite reduction were horizontally transferred to the Korarchaeota from the Firmicutes. Interactions among enzymes involved in both metabolisms could facilitate exergonic, sulfite-dependent, anaerobic oxidation of methane to methanol; alternatively, ‘Ca. M. washburnensis’ could conduct methanogenesis and sulfur reduction independently. Metabolic reconstruction suggests that ‘Ca. M. washburnensis’ is a mixotroph, capable of amino acid uptake, assimilation of methane-derived carbon and/or CO2 fixation by archaeal type III-b RuBisCO for scavenging ribose carbon. Our findings link anaerobic methane metabolism and dissimilatory sulfur reduction within a single deeply rooted archaeal population and have implications for the evolution of these traits throughout the Archaea.

McKenna, A.M., Chacón-Patiño, M.L., Weisbrod, C.R., Blakney, G.T., Rodgers, R.P., 2019. Molecular-level characterization of asphaltenes isolated from distillation cuts. Energy & Fuels 33, 2018-2029.


Asphaltenes challenge nearly all analytical techniques because of their immense polydispersity in molecular composition and structure. This operationally defined fraction of crude oil, insoluble in n-alkanes but soluble in aromatic solvents, is known to concentrate in vacuum residues and is linked to fouling and deposition issues. However, presence and subsequent characterization of asphaltenes are seldom discussed in conventional/unconventional distillate fractions. Here, we isolate asphaltenes from conventional (<593 °C/1099 F) and unconventional (>593 °C) distillation cuts and provide molecular-level characterization by electrospray ionization and atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry as a function of boiling point. Our results indicate that asphaltene molecular composition starts in the vacuum gas oil range and extends into vacuum residues. Moreover, we report that distillable asphaltene composition exists as both highly polar (heteroatom rich), aliphatic (atypical asphaltenes) species as well as condensed aromatic structures (classical asphaltenes). As a function of distillation temperature, asphaltene compounds exhibit structural trends consistent with thermal cracking that starts between 510 and 538 °C, increases between 538 and 593 °C, and is readily observed at temperatures up to 700 °C. Above 600 °C, low molecular weight compounds (expected to boil at much lower temperatures) that are n-heptane insoluble are detected across all heteroatom classes. Results herein suggest that these compounds are formed through structural rearrangement of archipelago asphaltenes because of thermal cracking reactions that occur during distillation and precipitate as asphaltenes. We report the isolation and mass spectral characterization of asphaltenes isolated from distillation cuts and propose that quantification of asphaltenes in distillates is critical to predict and prevent problems related to catalyst deactivation.

McNeill, L.C., Shillington, D.J., Carter, G.D.O., Everest, J.D., Gawthorpe, R.L., Miller, C., Phillips, M.P., Collier, R.E.L., Cvetkoska, A., De Gelder, G., Diz, P., Doan, M.-L., Ford, M., Geraga, M., Gillespie, J., Hemelsdaël, R., Herrero-Bervera, E., Ismaiel, M., Janikian, L., Kouli, K., Le Ber, E., Li, S., Maffione, M., Mahoney, C., Machlus, M.L., Michas, G., Nixon, C.W., Oflaz, S.A., Omale, A.P., Panagiotopoulos, K., Pechlivanidou, S., Sauer, S., Seguin, J., Sergiou, S., Zakharova, N.V., Green, S., 2019. High-resolution record reveals climate-driven environmental and sedimentary changes in an active rift. Scientific Reports 9, Article 3116.

https://doi.org/10.1038/s41598-019-40022-w

Young rifts are shaped by combined tectonic and surface processes and climate, yet few records exist to evaluate the interplay of these processes over an extended period of early rift-basin development. Here, we present the longest and highest resolution record of sediment flux and paleoenvironmental changes when a young rift connects to the global oceans. New results from International Ocean Discovery Program (IODP) Expedition 381 in the Corinth Rift show 10s–100s of kyr cyclic variations in basin paleoenvironment as eustatic sea level fluctuated with respect to sills bounding this semi-isolated basin, and reveal substantial corresponding changes in the volume and character of sediment delivered into the rift. During interglacials, when the basin was marine, sedimentation rates were lower (excepting the Holocene), and bioturbation and organic carbon concentration higher. During glacials, the basin was isolated from the ocean, and sedimentation rates were higher (~2–7 times those in interglacials). We infer that reduced vegetation cover during glacials drove higher sediment flux from the rift flanks. These orbital-timescale changes in rate and type of basin infill will likely influence early rift sedimentary and faulting processes, potentially including syn-rift stratigraphy, sediment burial rates, and organic carbon flux and preservation on deep continental margins worldwide.

Meng, F.-W., Zhang, Z.-l., Yan, X.-q., Ni, P., Liu, W.-H., Fan, F., Xie, G.-W., 2019. Stromatolites in Middle Ordovician carbonate–evaporite sequences and their carbon and sulfur isotopes stratigraphy, Ordos Basin, northwestern China. Carbonates and Evaporites 34, 11-20.

https://doi.org/10.1007/s13146-017-0367-0

At the present day, stromatolites are very rare and limited to high-salinity settings. However, abundant and variable stromatolite fossils occur in thick evaporite sequences, the Middle Ordovician Majiagou Formation of the Ordos Basin, northwestern China. The setting and fossil assemblage imply that the high salinity prevented metazoan grazing and allowed stromatolites to flourish. The carbon isotope curve based on new data (average data range from −4.52 to +0.56‰) from drilling cores in Majiagou Formation is in good agreement with Middle Ordovician (Darriwilian), and supports the Middle Ordovician age inferred from biostratigraphy. Sulfur isotopes values (range from +27.1 to +28.0‰) are higher than those of the Upper Ordovician but much lower than those of the Lower Middle Cambrian; thus, the sulfur values imply that the Majiagou Formation is of Middle Ordovician age. New carbon and sulfur isotope data imply that these strata are of Middle Ordovician age, in good agreement with previous paleontological dating.

Mikhailova, A.N., Kayukova, G.P., Vakhin, A.V., Eskin, A.A., Vandyukova, I.I., 2019. Composition features of hydrocarbons and rocks of Domanic deposits of different oil fields in the Tatarstan territory. Petroleum Science and Technology 37, 374-381.

https://doi.org/10.1080/10916466.2018.1547757

Study was conducted of rocks composition and its extracted moving hydrocarbons from Domanic deposits of Tatarstan, differing in location and occurrence depth from 1379 to 1891 m. The rocks are represented from carbonate-siliceous to pure carbonates with calcite content from 24 to 99%. With increase in calcite content in rocks, the yield of extracts from them decreases. Within Romashkinskoye field, an increase in yield of bitumoids with increase the occurrence depth of the host rocks - from 0.63 to 2.40% was established. Saturated hydrocarbons content of changes from 18 to 39%, of asphaltenes - from 9 to 26%.

Miller, M.J., Miller, M.J., Santiago-Materese, D., Seibert, M.A., Lim, D.S.S., 2019. A flexible telecommunication architecture for human planetary exploration based on the BASALT science-driven Mars analog. Astrobiology 19, 478-496.

https://doi.org/10.1089/ast.2018.1906

There is a synergistic relationship between analog field testing and the deep space telecommunication capabilities necessary for future human exploration. The BASALT (Biologic Analog Science Associated with Lava Terrains) research project developed and implemented a telecommunications architecture that serves as a high-fidelity analog of future telecommunication capabilities for Mars. This paper presents the architecture and its constituent elements. The rationale for the various protocols and radio frequency (RF) link types required to enable an interdisciplinary field mission are discussed, and the performance results from the BASALT field tests are provided. Extravehicular Informatics Backpacks (EVIB) designed for BASALT and tested by human subjects are also discussed, and the proceeding sections show how these prototype extravehicular activity (EVA) information systems can augment future human exploration. The paper concludes with an aggregate analysis of the data product types and data volumes generated, transferred, and utilized by the ground team and explorers over the course of the field deployments.

Minor, E.C., Tennant, C.J., Brown, E.T., 2019. A seasonal to interannual view of inorganic and organic carbon and pH in western Lake Superior. Journal of Geophysical Research: Biogeosciences 124, 405-419.

https://doi.org/10.1029/2018JG004664

Abstract: To investigate the carbon cycle of Lake Superior, Earth's largest freshwater lake by surface area, we performed total organic carbon, dissolved organic carbon, chlorophyll, spectrophotometric pH, total inorganic carbon, and alkalinity measurements on seasonal samples from the western lake. The last three parameters, along with in situ temperature, were used to calculate the partial pressure of carbon dioxide in surface water (pCO2(w)) using the CO2SYS algorithm. There was a strong positive correlation between pH and water temperature and a weaker but significant positive correlation between pH and chlorophyll concentration. Total organic carbon exhibited higher nearshore concentrations (as determined by a negative correlation with total water column depth); such a spatial relationship did not appear in the inorganic carbon parameters (total inorganic carbon, pH, or pCO2(w)). Western Lake Superior exhibited net outgassing in spring, little net gas transfer in summer, and some outgassing in the fall. The pCO2(w) values were negatively correlated with both water temperature and chlorophyll concentration. Seasonal differences in pCO2(w) in Lake Superior appeared more strongly driven by biology and terrestrial inputs as compared to direct effects of temperature on CO2 solubility. Interannual data from the long‐term Great Lakes Environmental Database data set indicated that lake alkalinity has been increasing over the past 20 years, and lake surface water pH appeared relatively stable. Modeling pH change over the same time frame in CO2SYS shows that increases in alkalinity and lake surface water temperature counteract the increase in atmospheric carbon dioxide concentration, leading to a relatively constant pH, consistent with observational data.

Plain Language Summary: This study focused upon carbon cycling in western Lake Superior, investigating how biological, chemical, and physical changes interact to determine lake acidity and carbon dioxide content. On seasonal scales, biological and chemical changes play a strong role in carbon dioxide content relative to the effect of temperature on carbon dioxide solubility. Interannual

trends over the past 20 years show that the lake has not significantly changed in its level of acidity but that it has experienced an increase in its ability to neutralize added acid.

Misch, D., Gross, D., Hawranek, G., Horsfield, B., Klaver, J., Mendez-Martin, F., Urai, J.L., Vranjes-Wessely, S., Sachsenhofer, R.F., Schmatz, J., Li, J., Zou, C., 2019. Solid bitumen in shales: Petrographic characteristics and implications for reservoir characterization. International Journal of Coal Geology 205, 14-31.


The presence of solid bitumen strongly affects hydrocarbon storage and expulsion from a source rock as it might either cause blockage of pore throats leading to lower effective gas permeability, or contribute to hydrocarbon storage and provide migration pathways when a continuous network of hydrocarbon-wet organic matter (OM) pores is formed. Furthermore, organic matter transformation reactions are suggested to influence mineral diagenesis as well. In an attempt to characterize different solid bitumen types and transformation stages over a broad maturity interval (0.5–2.7%Ro) and for varying primary kerogen compositions, we reviewed optical and scanning electron microscopy (SEM) data of 35 solid bitumen-rich shale samples with a Cambrian to Triassic age. We were able to identify in-situ pre-oil solid bitumen, as well as remobilized post-oil solid bitumen at various maturity stages from the early oil window onwards. Solid bitumen is the main host for SEM-visible organic matter porosity; onset of porosity development in solid bitumen differs considerably between predominantly oil-prone (e.g., alginites, amorphous OM from algal and bacterial precursors) and gas-prone (vitrinite-rich) kerogen compositions. Furthermore, solid bitumen (pyrobitumen) in rocks with a terrestrially dominated OM composition seems to be considerably less mobile within the source rock compared to pre- and post-oil solid bitumen in oil-prone rocks, and less reactive in terms of porosity generation. In most samples, several solid bitumen populations with varying fluorescence properties and bitumen reflectance were observed, complicating the use of these petrographic maturity indicators. The apparently different solid bitumen populations often form continuous networks at the SEM-scale. Microstructural features such as irregularly distributed sponge-like porosity or detrital and authigenic mineral inclusions in the sub-micrometer scale were found to have a great influence on texture and reflectance under reflected light microscopy. The formation of authigenic minerals (quartz, various carbonate phases with different Ca/Mg/Fe proportions, magnetite in Cambrian samples) was observed frequently in post-oil solid bitumen of oil-prone rocks, indicating a close genetic relationship between transformation products formed during hydrocarbon generation (e.g., acetate, carbon dioxide and methane) and the dissolution and precipitation of minerals during diagenesis. In some cases, stylolite-like features in the sub-micrometer scale were found, showing that processes well-known from reservoir characterization at core-scale also play a role at the micrometer-scale. Furthermore, the observed strong interaction between organic matter transformation and mineral authigenesis indicates a substantial aqueous component even in pores filled apparently exclusively with solid bitumen.

Moelling, K., Broecker, F., 2019. Viruses and evolution – viruses first? A personal perspective. Frontiers in Microbiology 10, 523. doi: 510.3389/fmicb.2019.00523.


The discovery of exoplanets within putative habitable zones revolutionized astrobiology in recent years. It stimulated interest in the question about the origin of life and its evolution. Here we discuss what the roles of viruses might have been at the beginning of life and during evolution. Viruses are the most abundant biological entities on Earth. They are present everywhere, in our surrounding, the

oceans, the soil and in every living being. They Retroviruses contributed to about half of our genomic sequences and contributed to the evolution of the mammalian placenta. Contemporary viruses reflect evolution ranging from the RNA world to the DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, choloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even in vitro the loss of genes can be recapitulated all the way from coding to non-coding RNA. Furthermore, the giant viruses may indicate that there is no sharp border between living and non-living entities but an evolutionary continuum. Here, it is discussed how viruses can lose and gain genes, and that they are essential drivers of evolution. This discussion may stimulate the thinking about viruses as early possible forms of life. Apart from our view "viruses first", there are others such as "proteins first" and "metabolism first".

Mohagheghian, E., Hassanzadeh, H., Chen, Z., 2019. Estimation of shale apparent permeability for multimechanistic, multicomponent gas production using rate transient analysis. Energy & Fuels 33, 1990-1997.


Gas-producing shale and ultratight reservoirs are playing a key role in the energy industry and the global gas market. Compositional simulation of gas production from shale media in the presence of different mechanisms such as viscous flow, slip flow (Klinkenberg effect), Knudsen diffusion, sorption, pore radius variation, and real gas effect is a computational challenge. In this work, we present a model that takes into account all of the noted mechanisms of gas transport in shale media. It is shown that the compositional effect of gas in shale media can be lumped into a single component by introducing an apparent gas permeability, which can be estimated from the conventional rate transient analysis. The main contribution of this study is a workflow incorporating the relevant physics into a single term (apparent permeability) that will substitute the Darcy permeability. This procedure reduces the simulation runtime substantially and will find applications in reservoir characterization and simulation of production from shale gas reservoirs.

Mohajeri, M., Reza Rasaei, M., Hekmatzadeh, M., 2019. Experimental study on using SiO2 nanoparticles along with surfactant in an EOR process in micromodel. Petroleum Research 4, 59-70.


Surfactant flooding is a common chemical method for enhancing oil recovery. Recently, the simultaneous application of nanoparticles and chemical substances has been considered for improving the efficiency of EOR processes. In the present study, the microscopic and macroscopic efficiency of oil recovery in a linear micromodel in three injection cases of Sodium dodecyl sulfate (SDS) as an anionic surfactant, SiO2 nanoparticles, and simultaneous injection of nanoparticles and surfactant was investigated. In our study, adding the nanoparticles along with SDS (2000 ppm) decreased Interfacial tension by 84%, while the figure was 74% and only 10% when the surfactant and the nanoparticles were used alone, respectively. Seemingly, although the nanoparticles alone could not reduce IFT values, adding them to surfactant solution could strongly decrease the interfacial tension between oil and water, leading to enhancement of oil recovery. However, our findings showed that an optimum

concentration of nanoparticles in surfactant solution must be used. In this regard, in low concentrations of nanoparticles, they were attached to the interface and IFT decreased due to absorption process. Nevertheless, in high concentrations, nanoparticles removed the surfactant from aqueous phase resulting in no free surfactant available in the bulk. Therefore, surfactant effectiveness in reducing IFT and alteration wettability decreased, and as a consequence, oil recovery efficiency dropped compared to lower nanoparticles’ concentrations. Moreover, the results of sessile drop experiments and wettability measurements revealed that coating with either the surfactants or the nanoparticles could partially alter the wettability of surface to water-wet, while coating with the surfactants along with the nanoparticles could make a strongly water-wet surface. Seemingly, investigating the microscopic images of pores and throats showed a strong water-wet condition when the surfactant along with the nanoparticles was used. In addition, the results of flooding tests demonstrated that adding the nanoparticles to surfactant solution could increase the ultimate oil recovery significantly. Moreover, microscopic images confirmed that adding the nanoparticles to the surfactant solution can lead to forming oil-in-water and water-in-oil micro-emulsions due to ultra-low IFT. Obviously, this can result in improving the effectiveness of injection fluid to influence a wider range of porous media.



The discovery of the ability of microorganisms to exchange electrons with inert electrodes has triggered new areas in fundamental and applied research. However, the field is currently limited to several known electrochemically active microorganisms enriched and isolated in research laboratories. An alternative strategy is to enrich such microorganisms in their native environment by allowing them to exchange electrons with polarized solid electrodes. The use of this approach is currently limited because of a lack of available tools. We developed a low-cost, battery-operated potentiostat that is capable of controlling the potential of a working electrode and can be deployed and operated remotely, allowing the enrichment of microorganisms on electrodes in their native environment. The device was tested in four alkaline hot springs in Heart Lake Geyser Basin in Yellowstone National Park (with a temperature ranging from 45 οC to 91 οC and a relatively constant pH of 8.5–8.7). Microbial community analysis showed a change in microbial community structure after 32 days of polarization. The impact of polarization on microbial community was most substantial on the electrodes that generated the highest cathodic and anodic currents, suggesting a direct impact of polarization on electrode microbial community.



Asphaltene deposition is a known problem that causes significant cost increases in the oil industry. Two bio-templated adsorbents, namely the NiO/ZSM-5 and NiO/AlPO-5 nanocomposites, were used as new green adsorbents to remove asphaltene from a model oil solution. Composite adsorbents were characterized by FTIR, BET, TEM and XRD analysis. Batch adsorption experiments were carried out as a function of D/C0 [(g)adsorbent/(mg/l)initial], pH, and temperature (K). Results showed that maximum adsorption is obtained at D/C0 = 0.072[g/(mg/l)] with a pH of 4.8 and a temperature of 298 K for

NiO/ZSM-5 and D/C0 = 0.084[g/(mg/l)] with a pH of 3.4 and a temperature of 298 K for NiO/AlPO-5. In the experimental data, equilibrium adsorption models were introduced and their constants were calculated. The equilibrium adsorption data on NiO/ZSM-5 were well matched to the Freundlich model at 298 K and 325 K, and Temkin model at 342 K and 353 K. For the NiO/AlPO-5 adsorption data, the Temkin model was the best model showing strong adsorption interactions of asphaltene and adsorbent. The adaptive neuro-fuzzy interference system (ANFIS) was also used to model and predict the amount of asphaltene adsorbed by the proposed nanocomposites. ANFIS designed by triangular-shaped membership functions with three nodes and first-order polynomial Sugeno type FIS was the optimal structure and gave R2 = 0.9999 and R2 = 0.9996 for train and test data, respectively. Finally, Monte Carlo algorithm was used for sensitivity analysis on the input variables which is necessary for process optimization. Results demonstrated that D/C0, pH, and temperature have the highest effect on asphaltene removal by nanoparticles.

Moldovan, R.-C., Bodoki, E., Servais, A.-C., Crommen, J., Oprean, R., Fillet, M., 2019. Selectivity evaluation of phenyl based stationary phases for the analysis of amino acid diastereomers by liquid chromatography coupled with mass spectrometry. Journal of Chromatography A 1590, 80-87.


D-amino acids (AA) analysis is becoming more and more relevant for metabolomics, therefore new analytical tools need to be developed. A common approach to achieve AA enantioseparation is chiral derivatization. Among the chiral derivatization reagents, (+) or (-)-1-(9-fluorenyl) ethyl chloroformate ((+) or (-)-FLEC) has proved to be one of the most versatile. Suitable chiral selectivity for FLEC derivatives of amino acids could be obtained in reversed-phase HPLC using nonpolar stationary phases (C4, C8 and C18) and tetrahydrofuran (THF) based mobile phases. This study is meant to provide alternatives to the use of THF as organic modifier by evaluating the selectivity obtained on two phenyl based stationary phases for 19 FLEC-DL-AA pairs of diastereomers using UHPLC-MS. Several mobile phases consisting of ammonium acetate and different common organic solvents (acetonitrile (ACN), methanol (MeOH), 2-propanol (IPA)) were tested using gradient elution. Experimental design was employed for the optimization of the separation conditions. In the optimized conditions, complete chiral separation can be achieved for 18 out of 19 FLEC-DL-AAs in less than 30 min.

Moore, L.R., Bodnar, R.J., 2019. A pedagogical approach to estimating the CO2 budget of magmas. Journal of the Geological Society 176, 398-407.


On a planetary scale, the carbon cycle describes the movement of carbon between the atmosphere and the deep Earth. Carbon species are involved in diverse Earth processes, ranging from sedimentary, metamorphic and igneous petrology to the long-term viability of life at the Earth's surface. Volcanoes, and their associated magmatic systems, represent the interface through which carbon is transferred from the deep Earth to the surface. Thus, quantifying the CO2 budget of volcanic systems is necessary for understanding the deep carbon cycle and, concomitantly, the CO2 budget of the near surface, including the atmosphere. In this review, Kilauea volcano (Hawaii) is used as a case study to illustrate simple calculations that can account for processes that affect the amount and distribution of CO2 in this relatively well-studied volcanic system. These processes include methods to estimate the concentration of CO2 in a melt derived by partial melting of a source material, enrichment of CO2 in the melt during fractional crystallization, exsolution of CO2 from a fluid-saturated melt, trapping and post-entrapment modification of melt inclusions, and outgassing from the volcanic edifice. Our goal

in this review is to provide straightforward example calculations that can be used to derive first-order estimates regarding processes that control the CO2 budgets of magmas and that can be incorporated into global carbon cycle models.

Morono, Y., Wishart, J.R., Ito, M., Ijiri, A., Hoshino, T., Torres, M., Verba, C., Terada, T., Inagaki, F., Colwell, F.S., 2019. Microbial metabolism and community dynamics in hydraulic fracturing fluids recovered from deep hydrocarbon-rich shale. Frontiers in Microbiology 10, 376. doi: 310.3389/fmicb.2019.00376.


Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013, Daley et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with 13C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and 15N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of 13C and 15N incorporation in individual cells, while isotope ratio monitoring – gas chromatography – mass spectrometry (IRM-GC-MS) was used to measure 13CO2, and 13CH4 as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. 13CO2 production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.

Mou, W., Zhang, Z., Li, S., Yan, C., Guo, R., Zhang, J., Li, S., 2019. The application of sterane in the oil-sources correlation of near-source and multi-source: a case study of CH-8 oil reservoir in Central Ordos Basin, China. Petroleum Science and Technology 37, 701-709.

https://doi.org/10.1080/10916466.2018.1564768

CH-8 oil reservoir holds the characteristics of near-source and multi-source in Ordos Basin, China. The sterane is one of the effective biomarkers in the study of oil-source correlation. The research results show that the parent material source and maturity degree of source rocks (CH-7, CH-9 and CH-10) and crude oil (CH-8) are similar. At the same time, the diasterane parameters of DiaC27?α(20S?+?20R), DiaC28?α(20S?+?20R) and DiaC29?α(20S?+?20R) can distinguish the source rocks into 5 types with great result, including CH-7, CH-10, CH9-WQ, CH9-HXK and CH9-SN. In addition, the dominated source of CH-8 crude oil is CH-7 source rock, the CH9-WQ source rock may make a small amount of contribution and the other of source rocks have little contribution to CH-8 crude oil in Shanbei area of Ordos Basin, China.

Munkittrick, T.J.A., Varney, T.L., Pike, K.-A., Grimes, V., 2019. Life histories from the Southside Cemetery, St. John's, Newfoundland: Insights into Royal Naval diet using stable isotopes. Journal of Archaeological Science: Reports 24, 815-828.


While the Southside Cemetery, St. John's, Newfoundland was excavated in 1979, previous historical and morphological investigations had been unable to distinguish between potential associations: Royal Navy, Royal Army, early Newfoundland settlers, and recent Anglican parishioners from the south side of St. John's harbour. Due to the difficulty of discerning between these hypotheses with historical and morphological investigations alone, stable isotope analyses of bone collagen and tooth enamel carbonate (δ13CCOLL, δ13CCARB, δ15NCOLL, and δ18OCARB) were used to examine the diet and geographic origins of skeletal remains (n = 21) from the Southside Cemetery in St. John's, Newfoundland. In order to distinguish between local and likely British origins, data from these individuals were compared to bone collagen and enamel carbonate isotope values of a civilian population from St. Paul's Anglican Church, Harbour Grace, Newfoundland (n = 6), and to published values from Newfoundland and the British Isles. These comparisons, along with a strong historical and archaeological context, suggest that individuals from the Southside Cemetery were associated with the St. John's Naval Hospital's use of the cemetery from ca. 1750–1825. This study then considers these data with previously published data of contemporaneous Royal Naval Hospital cemeteries within their historical contexts to better understand naval rations and movement in the British Atlantic World. This re-examination of the data, with an emphasis on historical and physiological contexts, highlights factors previously undervalued that limit the ability of stable isotope analyses to define the variability of naval rations in the late 18th and early 19th centuries.

Muscente, A.D., Bykova, N., Boag, T.H., Buatois, L.A., Mángano, M.G., Eleish, A., Prabhu, A., Pan, F., Meyer, M.B., Schiffbauer, J.D., Fox, P., Hazen, R.M., Knoll, A.H., 2019. Ediacaran biozones identified with network analysis provide evidence for pulsed extinctions of early complex life. Nature Communications 10, Article 911.

https://doi.org/10.1038/s41467-019-08837-3

Rocks of Ediacaran age (~635–541 Ma) contain the oldest fossils of large, complex organisms and their behaviors. These fossils document developmental and ecological innovations, and suggest that extinctions helped to shape the trajectory of early animal evolution. Conventional methods divide Ediacaran macrofossil localities into taxonomically distinct clusters, which may represent evolutionary, environmental, or preservational variation. Here, we investigate these possibilities with network analysis of body and trace fossil occurrences. By partitioning multipartite networks of taxa, paleoenvironments, and geologic formations into community units, we distinguish between biostratigraphic zones and paleoenvironmentally restricted biotopes, and provide empirically robust and statistically significant evidence for a global, cosmopolitan assemblage unique to terminal Ediacaran strata. The assemblage is taxonomically depauperate but includes fossils of recognizable eumetazoans, which lived between two episodes of biotic turnover. These turnover events were the first major extinctions of complex life and paved the way for the Cambrian radiation of animals.

Muschitiello, F., D’Andrea, W.J., Schmittner, A., Heaton, T.J., Balascio, N.L., deRoberts, N., Caffee, M.W., Woodruff, T.E., Welten, K.C., Skinner, L.C., Simon, M.H., Dokken, T.M., 2019. Deep-water circulation changes lead North Atlantic climate during deglaciation. Nature Communications 10, Article 1272.

https://doi.org/10.1038/s41467-019-09237-3

Constraining the response time of the climate system to changes in North Atlantic Deep Water (NADW) formation is fundamental to improving climate and Atlantic Meridional Overturning Circulation predictability. Here we report a new synchronization of terrestrial, marine, and ice-core records, which allows the first quantitative determination of the response time of North Atlantic climate to changes in high-latitude NADW formation rate during the last deglaciation. Using a continuous record of deep water ventilation from the Nordic Seas, we identify a ∼400-year lead of changes in high-latitude NADW formation ahead of abrupt climate changes recorded in Greenland ice cores at the onset and end of the Younger Dryas stadial, which likely occurred in response to gradual changes in temperature- and wind-driven freshwater transport. We suggest that variations in Nordic Seas deep-water circulation are precursors to abrupt climate changes and that future model studies should address this phasing.

Myers, M.B., Roberts, J.J., White, C., Stalker, L., 2019. An experimental investigation into quantifying CO2 leakage in aqueous environments using chemical tracers. Chemical Geology 511, 91-99.


Chemical tracers can be an effective means of detecting, attributing and quantifying any leaks to the surface from geological CO2 stores. CO2 release experiments have found it difficult to ascertain the fate, or quantify the volume of CO2 without the application of tracers. However, a significant proportion of global CO2 storage capacity is located offshore, and the marine environment poses constraints that could limit the success of using tracers. These constraints include uncertainties in the behaviour of tracers in marine sediments and the water column and sampling challenges. However, to date there have been few experimental investigations to address these uncertainties. Here, we used a benchtop experimental setup to explore how effectively methane, a common constituent of captured CO2 and of reservoir fluids, can aid the quantitation of CO2 leakage in aqueous environments. The experiment simulated gas leakage into sediments that mimic the seabed, and we measured the partitioning of co-released gases under different environmental conditions and injection rates. We find that the style of seepage and the fate of the CO2 are affected by the presence of a sand layer and the injection rate. We discuss the implications for leak monitoring approaches, including how tracers may be used to quantify the leak rates and fate of CO2 in aqueous environments. Our work contributes to ongoing efforts to develop robust offshore monitoring system that will assure operators, regulatory bodies and the public of CO2 storage integrity.

Myshakin, E.M., Singh, H., Sanguinito, S., Bromhal, G., Goodman, A.L., 2019. Flow regimes and storage efficiency of CO2 injected into depleted shale reservoirs. Fuel 246, 169-177.


Depleted shale reservoirs are potentially attractive targets to store carbon dioxide (CO2) as free and adsorbed phases. The time-dependent efficiency factors that depict dynamic storage performance in shale are estimated as a function of key reservoir parameters, shapes of stimulated reservoir volume, and injection scenarios. Efficiency of CO2 storage and flow regimes are determined dynamically as CO2 is injected in a depleted shale formation for a time period of 60 years. The most effective reservoir utilization for carbon storage was achieved during the transition from predominant flow in the stimulated reservoir volume to flow into unfractured zones. That transition occurs within first 15–30 years of injection depending on cases considered. The importance of adsorption as a mechanism of

storage is determined based on sensitivity, which indicates that the amount of CO2 stored by adsorption would be on average ∼26% of the CO2 stored as a free phase.

Nardella, F., Landi, N., Degano, I., Colombo, M., Serradimigni, M., Tozzi, C., Ribechini, E., 2019. Chemical investigations of bitumen from Neolithic archaeological excavations in Italy by GC/MS combined with principal component analysis. Analytical Methods 11, 1449-1459.

http://dx.doi.org/10.1039/C8AY02429D

An analytical protocol involving microwave assisted solvent extraction and fractionation on silica gel columns followed by gas chromatography/mass spectrometry (GC/MS) and principal component analysis (PCA) of the chromatographic data was used for the characterization of bituminous residues sampled from Neolithic flint flakes and potsherds recovered from archaeological excavations in Abruzzo and Apulia (Italy). The analytical protocol was optimized and primarily tested in the study of geological bitumen (used as reference materials) from rocks and sediments of central-southern Italy (Abruzzo, Sicily and Lazio), and subsequently used to characterize the archaeological bitumen. Since bitumen is usually present in very low amounts in archaeological objects, we paid attention to improve the extraction efficiency of terpanes and steranes, the main soluble components of bitumen. The highest efficiency was obtained using microwave assisted extraction with a mixture of n-hexane/dichloromethane/methanol (80 : 15 : 5, v/v/v). Given that the composition of the bitumen varies depending on the area of origin, the results obtained from the archaeological materials allowed us not only to draw hypotheses on the possible function of tools/objects from which the bitumen is sampled, but also to obtain information on its geographical origin. In particular, PCA, used as a tool for an extensive analysis of chromatographic data, enabled us to correlate the quantitative chemical composition and the geographical origin of the samples, and finally to distinguish bitumen originating from the different Italian sites, based on their molecular profiles.

Naullage, P.M., Bertolazzo, A.A., Molinero, V., 2019. How do surfactants control the agglomeration of clathrate hydrates? ACS Central Science 5, 428-439.

https://doi.org/10.1021/acscentsci.8b00755

Clathrate hydrates can spontaneously form under typical conditions found in oil and gas pipelines. The agglomeration of clathrates into large solid masses plugs the pipelines, posing adverse safety, economic, and environmental threats. Surfactants are customarily used to prevent the aggregation of clathrate particles and their coalescence with water droplets. It is generally assumed that a large contact angle between the surfactant-covered clathrate and water is a key predictor of the antiagglomerant performance of the surfactant. Here we use molecular dynamic simulations to investigate the structure and dynamics of surfactant films at the clathrate–oil interface, and their impact on the contact angle and coalescence between water droplets and hydrate particles. In agreement with the experiments, the simulations predict that surfactant-covered clathrate–oil interfaces are oil wet but super-hydrophobic to water. Although the water contact angle determines the driving force for coalescence, we find that a large contact angle is not sufficient to predict good antiagglomerant performance of a surfactant. We conclude that the length of the surfactant molecules, the density of the interfacial film, and the strength of binding of its molecules to the clathrate surface are the main factors in preventing the coalescence and agglomeration of clathrate particles with water droplets in oil. Our analysis provides a molecular foundation to guide the molecular design of effective clathrate antiagglomerants.

Negandhi, K., Edwards, G., Kelleway, J.J., Howard, D., Safari, D., Saintilan, N., 2019. Blue carbon potential of coastal wetland restoration varies with inundation and rainfall. Scientific Reports 9, Article 4368.

https://doi.org/10.1038/s41598-019-40763-8

There is a growing interest in how the management of ‘blue carbon’ sequestered by coastal wetlands can influence global greenhouse gas (GHG) budgets. A promising intervention is through restoring tidal exchange to impounded coastal wetlands for reduced methane (CH4) emissions. We monitored an impounded wetland’s GHG flux (CO2 and CH4) prior to and following tidal reinstatement. We found that biogeochemical responses varied across an elevation gradient. The low elevation zone experienced a greater increase in water level and an associated greater marine transition in the sediment microbial community (16 S rRNA) than the high elevation zone. The low elevation zone’s GHG emissions had a reduced sustained global warming potential of 264 g m−2 yr−1 CO2-e over 100 years, and it increased to 351 g m−2 yr−1 with the removal of extreme rain events. However, emission benefits were achieved through a reduction in CO2 emissions, not CH4 emissions. Overall, the wetland shifted from a prior CH4 sink (−0.07 to −1.74 g C m−2 yr−1) to a variable sink or source depending on the elevation site and rainfall. This highlights the need to consider a wetland’s initial GHG emissions, elevation and future rainfall trends when assessing the efficacy of tidal reinstatement for GHG emission control.

Nie, H., Wang, H., He, Z., Wang, R., Zhang, P., Peng, Y., 2019. Formation mechanism,distribution and exploration prospect of normal pressure shale gas reservoir: a case study of Wufeng Formation-Longmaxi Formation in Sichuan Basin and its periphery. Acta Petrolei Sinica 40, 131-143,164.


Normal pressure shale gas reservoirs have low pressure coefficient and gas content as well as small stratum energy, characterized by mid-low abundance, mid-low grade, large amount of resource and large scale of reserves. Normal pressure shale gas reservoirs are widely distributed in South China with favorable geological settings and accumulation conditions, but their types, formation mechanism and enrichment regularities are still unknown. According to the shale gas exploration and development practice as well as geological analyses, this study explores the types, formation mechanism, distribution characteristics and enrichment laws of normal pressure shale gas reservoir, and proposes the exploration prospect and technical strategies of normal pressure shale gas reservoirs. This research suggests that there are four main types of normal pressure shale gas reservoirs, i.e., absent/thinning type of high-quality shales, early escaping type, fault failure type and residual syncline type. The distribution and enrichment of normal pressure shale gas reservoirs are obviously controlled by geological tectonism. Through comprehensively analyzing the types, formation mechanism and features of normal pressure shale gas reservoirs, it is suggested that the residual syncline type is the most favorable exploration target. Geological evaluation should focus on the areas close to basin, far from regional deep fault, showing late uplift, large area of residual syncline, and early sealing of fractures. The exploration and development target should preferentially be adjacent to the center of syncline with stable structure, high pressure coefficient and moderate burial depth. As for technical countermeasures, it is recommended to use the drilling fluid with low mud density and the fracturing with small number of segments and multi-perforation clusters, large displacement, medium liquid volume and high sand volume to achieve cost-effective volume transformation. The research results can provide a reference for the geological evaluation and exploration practice of normal pressure shale gas reservoirs.

Niu, X., Yang, X., Yan, D., Zhuang, X., Wang, B., Huo, S., Xu, X., 2019. Development background of Mesozoic high-quality source rocks: Evidence from microfossils in North Carnarvon Basin, Australia. Petroleum Research 4, 71-83.


Based on numerous microfossils in Mesozoic of North Carnarvon Basin in Australia, the Mesozoic paleoclimate and paleoenvironment were analyzed, the paleogeographic background and development model of Mesozoic high-quality source rocks were investigated and discussed. Variation of microfossil species and their relative contents in Mesozoic different intervals indicates changes of paleoclimate and paleoenvironment. The paleoclimate shows a cycle variation of arid–humid–arid–humid, the regression occurred in the Early Triassic–Late Triassic and the transgression occurred in the Late Triassic–Late Cretaceous. Four sedimentary facieses including delta facies, littoral facies, restricted sea facies and open sea facies were developed in the Mesozoic. The open sea was mainly developed in the Early Triassic, the delta was distributed in the Middle–Late Triassic, the restricted sea was especially well developed in the Jurassic, and the restricted sea and open sea were mainly distributed in the Cretaceous. Characteristics of microfossil assemblage in these four sedimentary facies are dramatically different. From the delta facies, littoral facies, restricted sea facies to open sea facies, content of pollen gradually decreases, but content of the dinoflagellate + acritarch gradually increases. The delta facies and littoral facies are dominated by the pollen. In the restricted sea facies, content of the pollen is equivalent to that of the dinoflagellate + acritarch. The open sea facies is dominated by the dinoflagellate and acritarch. Supply of sediment and formation of organic matter are influenced by the paleoclimate and paleoenvironment, and type of organic matter is controlled by the microfossil assemblage. Based on the palaeogeographic background, paleoclimatic condition and microfossil assemblage, two developmental models of the Mesozoic source rocks such as the development model of terrestrial organic matter under the background of large delta and the development model of mixed organic matter under the background of the restricted sea, were proposed.

Novak, T., Godrijan, J., Pfannkuchen, D.M., Djakovac, T., Medić, N., Ivančić, I., Mlakar, M., Gašparović, B., 2019. Global warming and oligotrophication lead to increased lipid production in marine phytoplankton. Science of The Total Environment 668, 171-183.


Earth temperature is rising and oligotrophication is becoming apparent even in coastal seas. In this changing environment, phytoplankton use carbon and nutrients to form important biomolecules, including lipids. However, the link between lipid production and changing environment is still unexplored. Therefore, we investigated the phytoplankton lipid production in the diatom Chaetoceros pseudocurvisetus cultures under controlled temperatures ranging from 10 to 30 °C and nutrient regimes mimicking oligotrophic and eutrophic conditions. Results were compared to plankton community's lipid production in the northern Adriatic at two stations considered as oligotrophic and mesotrophic during an annual monthly sampling. In order to gain detailed information on the investigated system, we supplemented lipid data with chlorophyll a concentrations, phytoplankton taxonomy, cell abundances and nutrient concentration along with hydrographic parameters. We found enhanced particulate lipid production at higher temperatures, and substantially higher lipid production in oligotrophic conditions. Enhanced lipid production has two opposing roles in carbon sequestration; it can act as a retainer or a sinker. Lipid remodeling, including change in ratio of phospholipids and glycolipids, is more affected by the nutrient status, than the temperature increase. Triacylglycerol accumulation was observed under the nitrogen starvation.


https://doi.org/10.1029/2018GB005922

Abstract The terrestrial carbon sink has increased since the turn of this century at a time of increased fossil fuel burning, yet the mechanisms enhancing this sink are not fully understood. Here we assess the hypothesis that regional increases in nitrogen deposition since the early 2000s has alleviated nitrogen limitation and worked in tandem with enhanced CO2 fertilization to increase ecosystem productivity and carbon sequestration, providing a causal link between the parallel increases in emissions and the global land carbon sink. We use the Community Land Model (CLM4.5-BGC) to estimate the influence of changes in atmospheric CO2, nitrogen deposition, climate, and their interactions to changes in net primary production and net biome production. We focus on two periods, 1901-2016 and 1990-2016, to estimate changes in land carbon fluxes relative to historical and contemporary baselines, respectively. We find that over the historical period, nitrogen deposition (14%) and carbon-nitrogen synergy (14%) were significant contributors to the current terrestrial carbon sink, suggesting that long-term increases in nitrogen deposition led to a substantial increase in CO2 fertilization. However, relative to the contemporary baseline, changes in nitrogen deposition and carbon-nitrogen synergy had no substantial contribution to the 21st century increase in global carbon uptake. Nonetheless, we find that increased nitrogen deposition in East Asia since the early 1990s contributed 50% to the overall increase in net biome production over this region, highlighting the importance of carbon-nitrogen interactions. Therefore, potential large-scale changes in nitrogen deposition could have a significant impact on terrestrial carbon cycling and future climate.



Significance: This study provides evidence of an enormous solar storm around 2,610 B.P. It is only the third such event reliably documented and is comparable with the strongest event detected at AD 774/775. The event of 2,610 years B.P. stands out because of its particular signature in the radionuclide data [i.e., carbon-14 (14C) data alone does not allow for an unequivocal detection of the event]. It illustrates that present efforts to find such events based solely on 14C data likely lead to an underestimated number of such potentially devastating events for our society. In addition to 14C data, high-resolution records of beryllium-10 and chlorine-36 are crucial for reliable estimates of the occurrence rate and the properties of past solar proton events.

Abstract: Recently, it has been confirmed that extreme solar proton events can lead to significantly increased atmospheric production rates of cosmogenic radionuclides. Evidence of such events is recorded in annually resolved natural archives, such as tree rings [carbon-14 (14C)] and ice cores [beryllium-10 (10Be), chlorine-36 (36Cl)]. Here, we show evidence for an extreme solar event around 2,610 years B.P. (∼660 BC) based on high-resolution 10Be data from two Greenland ice cores. Our conclusions are supported by modeled 14C production rates for the same period. Using existing 36Cl ice core data in conjunction with 10Be, we further show that this solar event was characterized by a very hard energy spectrum. These results indicate that the 2,610-years B.P. event was an order of magnitude stronger than any solar event recorded during the instrumental period and comparable with

the solar proton event of AD 774/775, the largest solar event known to date. The results illustrate the importance of multiple ice core radionuclide measurements for the reliable identification of short-term production rate increases and the assessment of their origins.

O’Malley, M.A., Leger, M.M., Wideman, J.G., Ruiz-Trillo, I., 2019. Concepts of the last eukaryotic common ancestor. Nature Ecology & Evolution 3, 338-344.

https://doi.org/10.1038/s41559-019-0796-3

Insight into the last eukaryotic common ancestor (LECA) is central to any phylogeny-based reconstruction of early eukaryotic evolution. Increasing amounts of data enable such reconstructions, without necessarily providing further insight into what LECA actually was. We consider four possible concepts of LECA: an abstract phylogenetic state, a single cell, a population, and a consortium of organisms. We argue that the view most realistically underlying work in the field is that of LECA as a population. Drawing on recent findings of genomically heterogeneous populations in eukaryotes (‘pangenomes’), we examine the evolutionary implications of a pangenomic LECA population. For instance, how does this concept affect standard expectations about the ecology, geography, fitness, and diversification of LECA? Does it affect evolutionary interpretations of LECA’s cellular functions? Finally, we examine whether this novel pangenomic concept of LECA has implications for phylogenetic reconstructions of early eukaryote evolution. Our aim is to add to the conceptual toolkit for developing theories of LECA and interpreting genomic datasets.

O’Mara, N.A., Dunne, J.P., 2019. Hot spots of carbon and alkalinity cycling in the coastal oceans. Scientific Reports 9, Article 4434.

https://doi.org/10.1038/s41598-019-41064-w

Ocean calcium carbonate (CaCO3) production and preservation play a key role in the global carbon cycle. Coastal and continental shelf (neritic) environments account for more than half of global CaCO3 accumulation. Previous neritic CaCO3 budgets have been limited in both spatial resolution and ability to project responses to environmental change. Here, a 1° spatially explicit budget for neritic CaCO3 accumulation is developed. Globally gridded satellite and benthic community area data are used to estimate community CaCO3 production. Accumulation rates (PgC yr−1) of four neritic environments are calculated: coral reefs/banks (0.084), seagrass-dominated embayments (0.043), and carbonate rich (0.037) and poor (0.0002) shelves. This analysis refines previous neritic CaCO3 accumulation estimates (~0.16) and shows almost all coastal carbonate accumulation occurs in the tropics, >50% of coral reef accumulation occurs in the Western Pacific Ocean, and 80% of coral reef, 63% of carbonate shelf, and 58% of bay accumulation occur within three global carbonate hot spots: the Western Pacific Ocean, Eastern Indian Ocean, and Caribbean Sea. These algorithms are amenable for incorporation into Earth System Models that represent open ocean pelagic CaCO3 production and deep-sea preservation and assess impacts and feedbacks of environmental change.

Oksman, M., Juggins, S., Miettinen, A., Witkowski, A., Weckström, K., 2019. The biogeography and ecology of common diatom species in the northern North Atlantic, and their implications for paleoceanographic reconstructions. Marine Micropaleontology 148, 1-28.


Sound knowledge of present-day diatom species and their environments is crucial when attempting to reconstruct past climate and environmental changes based on fossil assemblages. For the North

Atlantic region, the biogeography and ecology of many diatom taxa that are used as indicator-species in paleoceanographic studies are still not well known. Using information contained in large diatom-environment calibration datasets can greatly increase our knowledge on diatom taxa and improve the accuracy of paleoenvironmental reconstructions. A diatom calibration dataset including 183 surface sediment samples from the northern North Atlantic was used to explore the distribution and ecology of 21 common Northern Hemisphere diatom taxa. We define the ecological responses of these species to April sea ice concentrations and August sea surface temperatures (aSSTs) using Huisman-Olff-Fresco (HOF)-response curves, provide distribution maps, temperature optima and ranges, and high-quality light microscope images. Based on the results, we find species clearly associated with cold, warm and temperate waters. All species have a statistically significant relationship with aSST, and 15 species with sea ice. Of these, Actinocyclus curvatulus, Fragilariopsis oceanica and Porosira glacialis are most abundant at high sea ice concentrations, whereas Coscinodiscus radiatus, Shionodiscus oestrupii, Thalassionema nitzschioides, Thalassiosira angulata, Thalassiosira nordenskioeldii and Thalassiosira pacifica are associated with low sea ice concentrations/ice-free conditions. Interestingly, some species frequently used as sea ice indicators, such as Fragilariopsis cylindrus, show similar abundances at high and low sea ice concentrations with no statistically significant relationship to sea ice.

Olalde, I., Mallick, S., Patterson, N., Rohland, N., Villalba-Mouco, V., Silva, M., Dulias, K., Edwards, C.J., Gandini, F., Pala, M., Soares, P., Ferrando-Bernal, M., Adamski, N., Broomandkhoshbacht, N., Cheronet, O., Culleton, B.J., Fernandes, D., Lawson, A.M., Mah, M., Oppenheimer, J., Stewardson, K., Zhang, Z., Jiménez Arenas, J.M., Toro Moyano, I.J., Salazar-García, D.C., Castanyer, P., Santos, M., Tremoleda, J., Lozano, M., García Borja, P., Fernández-Eraso, J., Mujika-Alustiza, J.A., Barroso, C., Bermúdez, F.J., Viguera Mínguez, E., Burch, J., Coromina, N., Vivó, D., Cebrià, A., Fullola, J.M., García-Puchol, O., Morales, J.I., Oms, F.X., Majó, T., Vergès, J.M., Díaz-Carvajal, A., Ollich-Castanyer, I., López-Cachero, F.J., Silva, A.M., Alonso-Fernández, C., Delibes de Castro, G., Jiménez Echevarría, J., Moreno-Márquez, A., Pascual Berlanga, G., Ramos-García, P., Ramos-Muñoz, J., Vijande Vila, E., Aguilella Arzo, G., Esparza Arroyo, Á., Lillios, K.T., Mack, J., Velasco-Vázquez, J., Waterman, A., Benítez de Lugo Enrich, L., Benito Sánchez, M., Agustí, B., Codina, F., de Prado, G., Estalrrich, A., Fernández Flores, Á., Finlayson, C., Finlayson, G., Finlayson, S., Giles-Guzmán, F., Rosas, A., Barciela González, V., García Atiénzar, G., Hernández Pérez, M.S., Llanos, A., Carrión Marco, Y., Collado Beneyto, I., López-Serrano, D., Sanz Tormo, M., Valera, A.C., Blasco, C., Liesau, C., Ríos, P., Daura, J., de Pedro Michó, M.J., Diez-Castillo, A.A., Flores Fernández, R., Francès Farré, J., Garrido-Pena, R., Gonçalves, V.S., Guerra-Doce, E., Herrero-Corral, A.M., Juan-Cabanilles, J., López-Reyes, D., McClure, S.B., Merino Pérez, M., Oliver Foix, A., Sanz Borràs, M., Sousa, A.C., Vidal Encinas, J.M., Kennett, D.J., Richards, M.B., Werner Alt, K., Haak, W., Pinhasi, R., Lalueza-Fox, C., Reich, D., 2019. The genomic history of the Iberian Peninsula over the past 8000 years. Science 363, 1230-1234.


Abstract: We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we

document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

Editor's summary: Genomics of the Iberian Peninsula. Ancient DNA studies have begun to help us understand the genetic history and movements of people across the globe. Focusing on the Iberian Peninsula, Olalde et al. report genome-wide data from 271 ancient individuals from Iberia (see the Perspective by Vander Linden). The findings provide a comprehensive genetic time transect of the region. Linguistics analysis and genetic analysis of archaeological human remains dating from about 7000 years ago to the present elucidate the genetic impact of prehistoric and historic migrations from Europe and North Africa.

Oliveira, M., Almeida, M., 2019. The why and how of micro(nano)plastic research. TrAC Trends in Analytical Chemistry 114, 196-201.


The presence of small plastic particles in the environment, reported for the first time in the 1970's, has only recently been recognized as a global issue. Although environmental awareness continues to grow, so does its consumption and associated risks. The number of studies reporting the presence of microplastics, has grown exponentially as did the concern over plastic degradation into smaller particles like nanoplastics, a potentially more pernicious form of plastic pollution. The reported effects of micro(nano)plastics on biota range from depletion of energy reserves and altered metabolism to immunological, neurotoxic effects and behavioral effects. This paper presents a critical review of current scientific knowledge in terms of reasons to study the effects of small plastics present in the environment, what has been assessed so far; most common methodologies. Research and technical developments requirements are also presented. Overall, it is clear the need for standardization of procedures and communication of results.



Magnetotactic bacteria are a heterogeneous group of Gram-negative prokaryotes, which all produce special magnetic organelles called magnetosomes. The magnetosome consists of a magnetic nanoparticle, either magnetite (Fe3O4) or greigite (Fe3S4), embedded in a membrane, which renders the systems colloidaly stable, a desirable property for biotechnological applications. Although these bacteria are able to regulate the formation of magnetosomes through a biologically-controlled mechanism, the environment in general and the physico–chemical conditions surrounding the cells in particular also influence biomineralization. This work thus aims at understanding how such external conditions, in particular the extracellular oxidation reduction potential, influence magnetite formation in the strain Magnetospirillum magneticum AMB-1. Controlled cultivation of the microorganisms was performed at different redox potential in a bioreactor and the formation of magnetosomes was assessed by microscopic and spectroscopic techniques. Our results show that the formation of magnetosomes is inhibited at the highest potential tested (0 mV), whereas biomineralization is facilitated under reduced conditions (- 500 mV). This result improves the understanding of the biomineralization process in MTB and provides useful information in sight of a large scale production of magnetosomes for different applications.

Omodeo-Salé, S., Ondrak, R., Arribas, J., Mas, R., Guimerà, J., Martínez, L., 2019. Petroleum systems modelling in a fold-and-thrust belt setting: The inverted Cameros Basin, north-central Spain. Journal of Petroleum Geology 42, 145-171.


The Mesozoic Cameros Basin, northern Spain, was inverted during the Cenozoic Alpine orogeny when the Tithonian – Upper Cretaceous sedimentary fill was uplifted and partially eroded. Tar sandstones outcropping in the southern part of the basin and pyrobitumen particles trapped in potential source rocks suggest that hydrocarbons have been generated in the basin and subsequently migrated. However, no economic accumulations of oil or gas have yet been found. This study reconstructs the evolution of possible petroleum systems in the basin from initial extension through to the inversion phase, and is based on structural, stratigraphic and sedimentological data integrated with petrographic and geochemical observations. Petroleum systems modelling was used to investigate the timing of source rock maturation and hydrocarbon generation, and to reconstruct possible hydrocarbon migration pathways and accumulations.

In the northern part of the basin, modelling results indicate that the generation of hydrocarbons began in the Early Berriasian and reached a peak in the Late Barremian – Early Albian. The absence of traps during peak generation prevented the formation of significant hydrocarbon accumulations. Some accumulations formed after the deposition of post‐extensional units (Late Cretaceous in age) which acted as seals. However, during subsequent inversion, these reservoir units were uplifted and eroded.

In the southern sector of the basin, hydrocarbon generation did not begin until the Late Cretaceous due to the lower rates of subsidence and burial, and migration and accumulation may have taken place until the initial phases of inversion. Sandstones impregnated with bitumen (tar sandstones) observed at the present day in the crests of surface anticlines in the south of the basin are interpreted to represent the relics of these palaeo‐accumulations.

Despite a number of uncertainties which are inherent to modelling the petroleum systems evolution of an inverted and overmature basin, this study demonstrates the importance of integrating multidisciplinary and multi‐scale data to the resource assessment of a complex fold‐and‐thrust belt.

Osli, L.N., Shalaby, M.R., Islam, M.A., 2019. Hydrocarbon generation modeling and source rock characterization of the Cretaceous–Paleocene Taratu Formation, Great South Basin, New Zealand. Journal of Petroleum Exploration and Production Technology 9, 125-139.

https://doi.org/10.1007/s13202-018-0511-y

Hydrocarbon generation modeling and source rock characterization have been carried out on rock samples of the Taratu Formation in the Great South Basin, New Zealand. The Paleocene and Late Cretaceous Taratu Formation samples from Tara-1 well are utilized for geochemical studies. Rock-Eval pyrolysis results show that Taratu formation accommodates organic matter of excellent quantity and quality, with proliferous kerogen type II-III (oil and gas prone) and minor kerogen type III (gas prone). Hydrogen index (HI) of this formation ranges from 165.0 to 327.5 mg HC/g TOC and only Late Cretaceous source rock samples are thermally mature, with maximum pyrolysis temperature (Tmax) up to 459 °C and vitrinite reflectance (% Ro) from 0.40 to 1.15% Ro. One-dimensional basin modeling shows a best fit in a calibration of measured and modeled temperatures and vitrinite reflectance. The top of oil window was encountered 51 Ma ago at 3100 m and gas generation took place at 4132 m in 8 Ma ago.

Ostrander, C.M., Nielsen, S.G., Owens, J.D., Kendall, B., Gordon, G.W., Romaniello, S.J., Anbar, A.D., 2019. Fully oxygenated water columns over continental shelves before the Great Oxidation Event. Nature Geoscience 12, 186-191.

https://doi.org/10.1038/s41561-019-0309-7

Late Archaean sedimentary rocks contain compelling geochemical evidence for episodic accumulation of dissolved oxygen in the oceans along continental margins before the Great Oxidation Event. However, the extent of this oxygenation remains poorly constrained. Here we present thallium and molybdenum isotope compositions for anoxic organic-rich shales of the 2.5-billion-year-old Mount McRae Shale from Western Australia, which previously yielded geochemical evidence of a transient oxygenation event. During this event, we observe an anticorrelation between thalium and molybdenum isotope data, including two shifts to higher molybdenum and lower thalium isotope compositions. Our data indicate pronounced burial of manganese oxides in sediments elsewhere in the ocean at these times, which requires that the water columns above portions of the ocean floor were fully oxygenated—all the way from the air–sea interface to well below the sediment–water interface. Well-oxygenated continental shelves were probably the most important sites of manganese oxide burial and mass-balance modelling results suggest that fully oxygenated water columns were at least a regional-scale feature of early Earth’s oceans 2.5 billion years ago.



Highly active gas venting and outcrops of gas hydrates were recently found at the Umitaka Spur, on the eastern margin of the Japan Sea, through seafloor observations using a remotely operated vehicle (ROV). This was followed by sampling by using conventional coring techniques. In this study, we deployed a long-term osmotic fluid sampling system (OsmoSampler) to record geochemical changes in the shallow sedimentary environment over time. The OsmoSampler collected interstitial water at 30 cm below seafloor (cmbsf), providing us with a continuous daily record of the concentrations of SO4

2−, Cl−, CH4, and C2H6 dissolved in interstitial waters over one year. General mean concentrations of SO4

2− and Cl− repeatedly showed synchronous increases and decreases over both long-term (i.e. dozens of days) and short-term (i.e. 3–5 days) periods. Such fluctuations relative to background seawater concentrations were likely caused by saline and fresh water generation due to gas hydrate formation and dissolution. The CH4 concentration was significantly higher (>1 mM) during large fluctuations in SO4

2− and Cl− over the first 3 months, which was attributable to gas-venting activity. This high venting activity of CH4 could have promoted the rapid, large-scale formation of gas hydrate. The CH4 concentration decreased gradually after the first 3 months, and was accompanied by a period of relatively low SO4

2− and Cl− concentrations due to the predominance of gas hydrate dissolution around the sampling site. In later months, the C2H6 concentration approached ∼1 μM and was accompanied by occasional, positive CH4 spikes, reflecting the release of trapped gases associated with the dissolution of hydrates. These processes are essentially controlled by the fluctuations in gas concentrations along the gas migration path, and are well-characterized by shallow interstitial water geochemistry.

Palmer, M., Venter, S.N., Coetzee, M.P.A., Steenkamp, E.T., 2019. Prokaryotic species are sui generis evolutionary units. Systematic and Applied Microbiology 42, 145-158.


Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources). HGT-based genetic conversions therefore causes homogenization, while genetic introductions drive divergence of populations upon fixation of genetic variants. The impact of HGT in different prokaryotic species may vary substantially and can range from very low levels to rampant HGT, producing chimeric groups of isolates. Combined with other evolutionary processes, these varying levels of HGT causes diversity space to be occupied by unique groups that are mostly incomparable in terms of genetic similarity, genomic cohesion and evolutionary age. As a result, the conventional, cut-off based metrics for species delineation are not adequate. Rather, a pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokaryotic species. Following this approach, all prokaryotic species may be regarded as unique and each of their own kind (sui generis). Taxonomic decisions thus require evolutionary information that integrates vertical inheritances with all possible sources of genetic heterogeneity to ultimately produce robust and biologically meaningful classifications.

Pang, S., Pu, W., Xie, J., Chu, Y., Wang, C., Shen, C., 2019. Investigation into the properties of water-in-heavy oil emulsion and its role in enhanced oil recovery during water flooding. Journal of Petroleum Science and Engineering 177, 798-807.


This paper described an investigation into the properties of water-in-heavy oil emulsion and its role in enhanced oil recovery (EOR). Effect of pH and salinity on emulsion stability, droplet size and distribution as well as rheological behavior were researched. Core flooding experiments were conducted to study the role of emulsion on EOR. Results indicated that stability of emulsions decreased as salinity increased. The presence of salt leads to a rise in droplet size and a drop in uniformity of distribution. Besides, emulsion formed at pH of 7 was characterized by the least stability, largest droplet size and unevenest droplet size distribution. An increase or decrease in pH both improved emulsion stability and reduced droplet size. Equally, rheological property of emulsion was greatly affected by salinity and pH. In relatively low shear rate region (<250 s−1), emulsion viscosity decreased as salinity increased; opposite trend was confirmed when shear rate exceeded 250 s−1. As a whole, shear thinning behavior was more pronounced in lower salinity and pH environment. Specifically, Newtonian behavior of emulsions were observed in high salinity and non-acidic condition in shear rate region of 60s−1-400s−1. The core flooding experiments showed that the formation of in-situ emulsion exhibited good mobility control ability, resulting in the improvement of sweep efficiency. In-situ emulsion prolonged the low-water-cut production period, giving rise to the enhancement of heavy oil recovery during waterflooding.

Park, S., Steen, C.J., Lyska, D., Fischer, A.L., Endelman, B., Iwai, M., Niyogi, K.K., Fleming, G.R., 2019. Chlorophyll–carotenoid excitation energy transfer and charge transfer in Nannochloropsis oceanica for the regulation of photosynthesis. Proceedings of the National Academy of Sciences 116, 3385-3390.


Significance: Manipulating the nonphotochemical quenching (NPQ) capabilities of photosynthetic organisms is known to result in increased crop productivity. However, optimization of yields also requires a detailed molecular understanding of the mechanism of NPQ in vivo with specific attention to the roles of the carotenoid zeaxanthin and various ∆pH-sensing proteins, such as photosystem II subunit S and stress-related antenna proteins (e.g., LHCX). Here, to investigate such in vivo NPQ mechanisms, we report transient absorption spectroscopy measurements on live cells of Nannochloropsis oceanica. We show that two fundamental processes proposed as NPQ mechanisms are active in N. oceanica and specifically require violaxanthin de-epoxidase as well as the LHCX1 protein. These findings have implications for optimizing the yields of algal biofuels.

Abstract: Nonphotochemical quenching (NPQ) is a proxy for photoprotective thermal dissipation processes that regulate photosynthetic light harvesting. The identification of NPQ mechanisms and their molecular or physiological triggering factors under in vivo conditions is a matter of controversy. Here, to investigate chlorophyll (Chl)–zeaxanthin (Zea) excitation energy transfer (EET) and charge transfer (CT) as possible NPQ mechanisms, we performed transient absorption (TA) spectroscopy on live cells of the microalga Nannochloropsis oceanica. We obtained evidence for the operation of both EET and CT quenching by observing spectral features associated with the Zea S1 and Zea●+ excited-state absorption (ESA) signals, respectively, after Chl excitation. Knockout mutants for genes encoding either violaxanthin de-epoxidase or LHCX1 proteins exhibited strongly inhibited NPQ capabilities and lacked detectable Zea S1 and Zea●+ ESA signals in vivo, which strongly suggests that the accumulation of Zea and active LHCX1 is essential for both EET and CT quenching in N. oceanica.

Parkes, R.J., Berlendis, S., Roussel, E.G., Bahruji, H., Webster, G., Oldroyd, A., Weightman, A.J., Bowker, M., Davies, P.R., Sass, H., 2019. Rock-crushing derived hydrogen directly supports a methanogenic community: significance for the deep biosphere. Environmental Microbiology Reports 11, 165-172.

https://doi.org/10.1111/1758-2229.12723

Microbial populations exist to great depths on Earth, but with apparently insufficient energy supply. Earthquake rock fracturing produces H2 from mechanochemical water splitting, however, microbial utilization of this widespread potential energy source has not been directly demonstrated. Here, we show experimentally that mechanochemically generated H2 from granite can be directly, long-term, utilized by a CH4 producing microbial community. This is consistent with CH4 formation in subsurface rock fracturing in the environment. Our results not only support water splitting H2 generation as a potential deep biosphere energy source, but as an oxidant must also be produced, they suggest that there is also a respiratory oxidant supply in the subsurface which is independent of photosynthesis. This may explain the widespread distribution of facultative aerobes in subsurface environments. A range of common rocks were shown to produce mechanochemical H2, and hence, this process should be widespread in the subsurface, with the potential for considerable mineral fuelled CH4 production.

Parviainen, A., Loukola-Ruskeeniemi, K., 2019. Environmental impact of mineralised black shales. Earth-Science Reviews 192, 65-90.


Black shales are sedimentary rocks containing >0.5% of organic carbon. They host polymetallic deposits which have been mined for Cu, Ni, Zn, Mn, P, Mo, V, U, Au and PGE (platinum group elements). Even sub-economic occurrences provide potential risk of acid rock drainage when exposed to oxic surface environment. The natural acid neutralisation potential varies depending on the adjacent rock units, especially on the presence of calcareous rocks. The chemical and mineralogical composition of black shale is reflected in the quality of the surface waters and groundwater. Cu, Ni, Pb, U and Zn are recognised as major pollutants though the environmental impact is characteristically polymetallic just like the black shale occurrences. Hence, the environmental impacts have to be evaluated in each occurrence.

The Proterozoic Ni–Zn–Cu–Co deposit at Talvivaara, Finland, is reviewed in more detail as an example of a large, low-grade deposit that is currently exploited with open pit mining and a bioleaching process, together with the Proterozoic Central African Copperbelt, the Cambrian U-Mo deposits in Sweden, the Cambrian Ni–Mo–PGE deposits in China and the Cambrian-Ordovician U deposits in South-Korea, the Devonian Ni–Zn–PGE occurrences in Yukon, Canada, and Kentucky, USA, and the Permian Cu-Ag deposits in Poland and Germany. The mineralised horizons may be merely few centimetres thick like in Yukon or hundreds of metres thick like at Talvivaara. Both natural and anthropogenic environmental impacts of black shales are reviewed world-wide, and based on the overview of the state-of-the-art an integrated research approach is suggested for the comprehensive assessment of the risk.

Black shales are natural sources of soil and water contamination. At Talvivaara, the geochemical background includes higher than average concentrations of Ni, Cu, Zn and Mn in glacial till, peat, surface waters and groundwater as well as in stream and lake sediments. Bioaccumulation by plants has been reported in China and Korea. Even endemic diseases have been proposed to be linked with the contamination derived from the weathering and leaching of harmful elements from black shale. Anthropogenic actions exposing the black shale bedrock and associated soils to oxic conditions further intensifies acid rock drainage.

Regional or nation-wide mapping of the black shales is recommended to detect potential risk areas. Finland has recently completed the country-wide mapping program of black shales with airborne geophysics integrated with geological, petrophysical and geochemical studies. The black shale database is actively used in regional planning and by environmental authorities, research institutes and consulting companies. In the case of the historical black shale mining areas like in the Kupferschiefer in Germany, restoration measures have been applied to prevent further acid mine drainage. In active and future mining projects, a comprehensive environmental impact assessment with effective monitoring programmes and closure plans play a crucial role in the prevention of acid mine drainage from the black shale -associated deposits.



Biochemical markers developed initially for food-web studies of terrestrial and shallow-water environments have only recently been applied to deep-sea ecosystems (i.e. in the early 2000s). For the first time since their implementation, this review took a close look at the existing literature in the field of deep-sea trophic ecology to synthesize current knowledge. Furthermore, it provided an opportunity for a preliminary analysis of global geographic (i.e. latitudinal, along a depth gradient) trends in the isotopic (δ15N, δ13C) and fatty acid composition of deep-sea taxa. Results revealed significant

relationships along the latitudinal and bathymetric gradients. Deep-sea animals sampled at temperate and polar latitudes displayed lower isotopic ratios and greater proportions of essential ω3 long-chain polyunsaturated fatty acids (LC-PUFA) than did tropical counterparts. Furthermore, δ15N and δ13C ratios as well as proportions of arachidonic acid increased with increasing depth. Since similar latitudinal trends in the isotopic and fatty acid composition were found in surface water phytoplankton and particulate organic matter, these results highlight the link across latitudes between surface primary production and deep-water communities. Because global climate change may affect quantity and quality (e.g. levels of essential ω3 PUFA) of surface primary productivity, and by extension those of its downward flux, the dietary intake of deep-sea organisms may likely be altered. In addition, because essential ω3 PUFA play a major role in the response to temperature variations, climate change may interfere with the ability of deep-sea species to cope with potential temperature shifts. Importantly, methodological disparities were highlighted that prevented in-depth analyses, indicating that further studies should be conducted using standardized methods in order to generate more reliable global predictions.

Paterson, J.R., Edgecombe, G.D., Lee, M.S.Y., 2019. Trilobite evolutionary rates constrain the duration of the Cambrian explosion. Proceedings of the National Academy of Sciences 116, 4394-4399.


Significance: The Cambrian explosion was arguably the most important biological event after the origin of life. Extensive research has been devoted to understanding when it began but far less on when this burst of evolution ended. We present a quantitative study that addresses these issues, using a large new dataset of Cambrian trilobites, the most abundant and diverse organisms during this time. Using probabilistic clock methods, we calculate rates of evolution in the earliest trilobites virtually identical to those throughout their Cambrian fossil history. We conclude that the Cambrian explosion was over by the time the typical Cambrian fossil record commences and reject an unfossilized Precambrian history for trilobites, solving a problem that had long troubled biologists since Darwin.

Abstract: Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.

Pavlov, V.E., Fluteau, F., Latyshev, A.V., Fetisova, A.M., Elkins-Tanton, L.T., Black, B.A., Burgess, S.D., Veselovskiy, R.V., 2019. Geomagnetic secular variations at the Permian-Triassic boundary and

pulsed magmatism during eruption of the Siberian Traps. Geochemistry, Geophysics, Geosystems 20, 773-791.

https://doi.org/10.1029/2018GC007950

The tempo of Large Igneous Province emplacement is crucial to determining the environmental consequences of magmatism on the Earth. Based on detailed flow-by-flow paleomagnetic data from the most representative Permian-Triassic Siberian Traps lava stratigraphy of the northern Siberian platform, we present new constraints on the rate and duration of the volcanic activity in the Norilsk and Maymecha-Kotuy regions. Our data indicate that volcanic activity there occurred during a limited number of short volcanic pulses, each consisting of multiple individual eruptions, and that the total duration of discrete eruption pulses did not exceed ~10,000 years (hiatuses are not included). Our study confirms the occurrence of a thick interval in the lower part of the Norilsk lava sections, which contains a record of geomagnetic reversal and excursion. Based on combined evidence from paleomagnetic secular variation and typical timescales for such reversals, we conclude that the ~1-km-thick lava stratigraphy, corresponding to ~20,000 km3 of basalt, of the Kharaelakh, Norilsk, and Imangda troughs was formed during a brief, but voluminous, eruptive period of several thousand years or less. Our data further suggest that the ore-bearing Norilsk-type intrusions are coeval or nearly coeval with the boundary between the Morongovsky and Mokulaevsky formations. We calculated a new Siberian Permian-Triassic paleomagnetic pole Norilsk-Maymecha-Kotuy (NMK): PLat = 52.9°, PLong = 147.1°, A95 = 4.3°, K = 23.2, and N = 49 lava flows. It is shown that geomagnetic field variations circa 252 Ma were similar to those observed in the latest Cenozoic.

Payler, S.J., Biddle, J.F., Sherwood Lollar, B., Fox-Powell, M.G., Edwards, T., Ngwenya, B.T., Paling, S.M., Cockell, C.S., 2019. An ionic limit to life in the deep subsurface. Frontiers in Microbiology 10, 426. doi: 410.3389/fmicb.2019.00426.


The physical and chemical factors that can limit or prevent microbial growth in the deep subsurface are not well defined. Brines from an evaporite sequence were sampled in the Boulby Mine, UK between 800 m and 1300 m depth. Ionic, hydrogen and oxygen isotopic composition were used to identify two brine sources, an aquifer situated in strata overlying the mine, and another ambiguous source distinct from the regional groundwater. The ability of the brines to support microbial replication was tested with culturing experiments using a diversity of inocula. The examined brines were found to be permissive for growth, except one. Testing this brine’s physicochemical properties showed it to have low water activity and to be chaotropic, which we attribute to the high concentration of magnesium and chloride ions. Metagenomic sequencing of the brines that supported growth showed their microbial communities to be similar to each other and comparable to those found in other hypersaline environments. These data show that solutions high in dissolved ions can shape the microbial diversity of the continental deep subsurface biosphere. Furthermore, under certain circumstances, complex brines can establish a hard limit to microbial replication in the deep biosphere, highlighting the potential for subsurface uninhabitable aqueous environments at depths far shallower than a geothermally-defined limit to life.

Payler, S.J., Mirmalek, Z., Hughes, S.S., Kobs Nawotniak, S.E., Brady, A.L., Stevens, A.H., Cockell, C.S., Lim, D.S.S., 2019. Developing intra-EVA science support team practices for a human mission to Mars. Astrobiology 19, 387-400.

https://doi.org/10.1089/ast.2018.1846

During the BASALT research program, real (nonsimulated) geological and biological science was accomplished through a series of extravehicular activities (EVAs) under simulated Mars mission conditions. These EVAs were supported by a Mission Support Center (MSC) that included an on-site, colocated Science Support Team (SST). The SST was composed of scientists from a variety of disciplines and operations researchers who provided scientific and technical expertise to the crew while each EVA was being conducted (intra-EVA). SST management and organization developed under operational conditions that included Mars-like communication latencies, bandwidth constraints, and EVA plans that were infused with Mars analog field science objectives. This paper focuses on the SST workspace considerations such as science team roles, physical layout, communication interactions, operational techniques, and work support technology. Over the course of BASALT field deployments to Idaho and Hawai‘i, the SST team made several changes of note to increase both productivity and efficiency. For example, new roles were added for more effective management of technical discussions, and the layout of the SST workspace evolved multiple times during the deployments. SST members' reflexive adjustments resulted in a layout that prioritized face-to-face discussions over face-to-data displays, highlighting the importance of interpersonal communication during SST decision-making. In tandem with these workspace adjustments, a range of operational techniques were developed to help the SST manage discussions and information flow under time pressure.

Peck, W.D., Ayash, S.C., Klapperich, R.J., Gorecki, C.D., 2019. The North Dakota integrated carbon storage complex feasibility study. International Journal of Greenhouse Gas Control 84, 47-53.


The Energy & Environmental Research Center is investigating the feasibility of safely, permanently, and economically storing 50 million tonnes of CO2 in central North Dakota, United States, over a 25-year operational period, should a business case for CO2 storage emerge. The study is part of the U.S. Department of Energy (DOE) National Energy Technology Laboratory CarbonSAFE initiative and addresses the technical and nontechnical challenges of commercially deploying a CO2 storage project. Evaluation of cores from two stratigraphic test wells demonstrate that the Broom Creek Formation (sandstone) is an excellent candidate for the geologic storage of CO2 and the overlying Opeche Formation a competent cap rock.

Pei, Y., Chen, Z.-Q., Fang, Y., Kershaw, S., Wu, S., Luo, M., 2019. Volcanism, redox conditions, and microbialite growth linked with the end-Permian mass extinction: Evidence from the Xiajiacao section (western Hubei Province), South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 194-208.


A new Permian–Triassic boundary microbialite (PTBM) is described from the Xiajiacao section of western Hubei Province, South China. The new microbialite, 3.16m thick, comprises a thin layer of stromatolite and a thick thrombolite unit. An irregular contact separates the uppermost Permian skeletal packstone from the post-extinction stromatolite, but it is not yet possible to discriminate whether it was formed by submarine solution in the wake of ocean acidification or subaerial exposure due to regional regression, or a combination of both. The stromatolite shows “cabbage-like” morphology, and the thrombolite is characterized by centimetric clotted texture. Abundant columns of the microproblematica structure Gakhumella, coccoid-like spheroids, bacterial clump-like spheroids, and hollow spheroids are recognized in both stromatolites and thrombolites and may have played an important role in accretion of the microbialites. Pyrite framboid analysis indicates that microbialites

may have been affected by lower dysoxic to upper dysoxic conditions in the immediate aftermath of the Permian–Triassic extinction. Stratigraphic abundance of both high-temperature grains (β-quartz and glassy balls) peaked ~20cm below the biotic extinction horizon, implying that either intensive volcanic eruption occurred only just prior to biotic extinction, or volcanism was still intensive during biotic extinction, but volcanic grains were not deposited in the Xiajiacao locality, likely due to the shallow, agitated environment caused by the regional regression. Overall, microbial bloom, indicated by the widespread PTBMs, seems to have been little affected by the contemporaneous volcanism.



Organic nanopores in shale gas reservoirs are the main storage space for free gas and adsorbed gas and directly affect the occurrence mode and movement of shale gas. In this study, field emission-scanning electron microscopy (FE-SEM), low-pressure gas (N2 and CO2) adsorption and mercury injection capillary pressure (MICP) analyses were performed and interpreted with statistical and fractal analyses to investigate the organic pore structure in the Upper Ordovician Wufeng shale (O3w) and the Lower Silurian lower member of Longmaxi shale (S1l). It was found that organic pores in 15 samples from 8 layers of the Wufeng-Longmaxi shale section are usually developed in discrete organic matter particles, organic matter associated with clay minerals and organic matter associated with pyrite framboids. The size, shape and quantity of organic pores vary greatly. The organic pores in Wufeng Formation (layer 1) are densely developed in organic matter particles with relatively small sizes and irregular shapes. The organic pores in the lower part of the lower member of Longmaxi Formation (layers 3, 4 and 5) are less developed and have relatively larger pore sizes with an elliptical shape. In contrast, the organic pores in the upper part of the lower member of Longmaxi Formation (layers 6, 7, 8 and 9) are the least developed, with elliptical shapes and pore sizes in between the two cases above. A higher value of fractal dimension refers a more complex form and this value of whole organic pores with full range of sizes (Dwop) is the largest and followed by organic macropores (Dop>50), organic pores with pore sizes between 4 nm and 50 nm (Dop4-50), and organic pores with pore sizes less than 4 nm (Dop<4). The fractal dimension of the upper part of the lower member of Longmaxi Formation (layers 6, 7, 8 and 9) is lower than that of both the Wufeng Formation (layer 1) and the lower part of the lower member of Longmaxi Formation (layers 3, 4 and 5). Possible causes leading to pore complexity and heterogeneity include the TOC content, pore size, mineral composition and tectonic effect. Wufeng shale is located at the bottom of Wufeng-Longmaxi shale weakness zone and had experienced more tectonic compression, nappe-slip and reconstruction, which may be the main reason that organic nanopores in Wufeng shale (layer 1) are more complex than other layers.

Peng, W., Liu, Q., Feng, Z., Fang, C., Gong, D., Li, P., Lyu, Y., Wang, P., 2019. First discovery and significance of liquid mercury in a thermal simulation experiment on humic kerogen. Energy & Fuels 33, 1817-1824.


We found for the first time enriched liquid mercury beads in a thermal simulation experiment on humic kerogen extracted from coal, which provided some kind of direct evidence that mercury can be released from coal measure during maturation. In the simulation experiment, mass distribution of liquid mercury beads is between 0.0083 and 0.2242 g; their content in simulated gas ranges from

372.5 to 2776.3 ng/m3; and their yield was from 0.3102 × 10–3 to 7.4312 × 10–3 g/g sample. Along with this thermal simulation experiment and previous studies, three genetic models of mercury in gas reservoirs are summarized: source-rock controlling type, fault-controlling type, and source-rock/fault joint controlling type. Mercury in source-rock-controlling gas reservoirs is mainly derived from source rocks, which are generally coal measures. Mercury in fault-controlling gas reservoirs is mainly derived from deep geologic fluids, with relatively small contribution from source rocks. The transitional source-rock/fault joint controlling type mainly develops in tectonic activity zones where source rocks can be either sapropelic or humic. Liquid mercury collected for the first time in a simulation experiment has important theoretical significance for the exploration and development of natural gas, as well as important practical significance for the prevention of mercury accidents in natural gas exploration and production.

Penko, L., Bajt, O., 2019. Aliphatic and polycyclic aromatic hydrocarbons in surface seawater of the Gulf of Trieste (northern Adriatic). Marine Pollution Bulletin 142, 103-111.


Concentrations, spatial distribution and sources of aliphatic hydrocarbons (AH) and polycyclic aromatic hydrocarbons (PAH) were determined in surface seawater of the Gulf of Trieste, northern Adriatic. This area is one of the most industrialized and urbanized areas in the northern Adriatic with intense maritime traffic. The surface seawater samples were collected at 31 sites and total hydrocarbon concentrations were determined. In general, concentrations (0.1 to 43.2 μg l−1, mean 4.8 μg l−1, Chrysene equivalents) were higher in summer. Concentrations of total aliphatic hydrocarbons were from 17.2 to 2326.5 μg l−1 (mean 543.3 μg l−1). The major component was the unresolved complex mixture (UCM), comprising from 78% to 97% of the total aliphatic hydrocarbons. Total PAH concentrations varied from 89 ng l−1 to 294 ng l−1 (mean 179 ng l−1). The most contaminated sites were the marina of San Giusto and the municipal harbor of Piran.

Different evaluation indeces were applied to determine the origin of hydrocarbons. The prevailing origin of aliphatic hydrocarbons is petrogenic, with the significant contribution of the biogenic at some sites. The results presented indicate the fresh inputs of hydrocarbons, which are subject to intense degradation processes. The PAH group profile showed the predominance of 2–3 ring PAHs. PAHs were of mixed origin with more pronounced petrogenic origin, presumably due to oil spills from ships and boats. The presence of a relatively high content of perylene in seawater is an indication of its terrestrial input.

According to the presented results and compared to results from different areas worldwide, the seawater in the Gulf of Trieste can still be considered slightly to moderately polluted with PAHs.

Penman, D.E., Keller, A., D'Haenens, S., Kirtland Turner, S., Hull, P.M., 2019. Atlantic deep-sea cherts associated with Eocene hyperthermal events. Paleoceanography and Paleoclimatology 34, 287-299.

https://doi.org/10.1029/2018PA003503

Chert, porcelainite, and other siliceous phases are exceptionally common in Atlantic sedimentary records of the early Eocene, but the origins of these facies remain enigmatic. The early Eocene was also the warmest interval of the entire Cenozoic Era, punctuated by numerous discrete warming events termed “hyperthermals,” the largest of which is termed the Paleocene‐Eocene Thermal Maximum (~56 Ma). Here we present new and published lithologic and carbon isotope records of silica‐bearing lower Eocene sediments and suggest a link between the ubiquitous Atlantic cherts of

that time period and hyperthermal events. Our data demonstrate that many of these Atlantic siliceous horizons coincide with negative carbon isotope excursions (a hallmark of hyperthermal events), including a previously unrecognized record of the Paleocene‐Eocene Thermal Maximum in the South Atlantic. Hyperthermal‐associated silica burial appears to be focused in the western middle to high latitudes of both the North and South Atlantic, with no association between siliceous facies and hyperthermal events found in the Pacific. We also present a new model of the coupled carbon and silica cycles (LOSiCAR) to demonstrate that enhanced silicate weathering during these events would require a rapid increase in total marine silica burial. Model experiments that include previously suggested transient reversals in the pattern of deep‐ocean circulation during hyperthermals demonstrate that such a mechanism can explain the apparent focusing of elevated silica burial into the Atlantic. This combination—a silicate weathering feedback in response to global warming along with a circulation‐driven focusing of silica burial—represents a new mechanism for the formation of deep‐sea cherts in lower Eocene Atlantic sedimentary records and may be relevant to understanding chert formation in other intervals of Earth history.

Penny, D., Hall, T., Evans, D., Polkinghorne, M., 2019. Geoarchaeological evidence from Angkor, Cambodia, reveals a gradual decline rather than a catastrophic 15th-century collapse. Proceedings of the National Academy of Sciences 116, 4871-4876.


Significance: Contrasting models exist to explain the movement of urban populations following the 15th-century demise of Angkor. Here we present geoarchaeological data from the urban core of Angkor that indicate a protracted decline in land use intensity during the 14th century rather than an abrupt demographic collapse. These results argue against traditional explanations for the demise of Angkor, which emphasize the role of interventionist foreign powers in forcing collapse, and imply a more complex and protracted transformation.

Abstract: Alternative models exist for the movement of large urban populations following the 15th-century CE abandonment of Angkor, Cambodia. One model emphasizes an urban diaspora following the implosion of state control in the capital related, in part, to hydroclimatic variability. An alternative model suggests a more complex picture and a gradual rather than catastrophic demographic movement. No decisive empirical data exist to distinguish between these two competing models. Here we show that the intensity of land use within the economic and administrative core of the city began to decline more than one century before the Ayutthayan invasion that conventionally marks the end of the Angkor Period. Using paleobotanical and stratigraphic data derived from radiometrically dated sediment cores extracted from the 12th-century walled city of Angkor Thom, we show that indicia for burning, forest disturbance, and soil erosion all decline as early as the first decades of the 14th century CE, and that the moat of Angkor Thom was no longer being maintained by the end of the 14th century. These data indicate a protracted decline in occupation within the economic and administrative core of the city, rather than an abrupt demographic collapse, suggesting the focus of power began to shift to urban centers outside of the capital during the 14th century.

Peoples, L.M., Grammatopoulou, E., Pombrol, M., Xu, X., Osuntokun, O., Blanton, J., Allen, E.E., Nunnally, C.C., Drazen, J.C., Mayor, D.J., Bartlett, D.H., 2019. Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology 10, 347. doi: 310.3389/fmicb.2019.00347.


Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments – the Mariana and Kermadec trenches – to evaluate the biogeography of microbes at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating the potential connectivity of microbes between geographically isolated sediments. Despite the diversity of microbes identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.

Peris-Díaz, M.D., Rodak, O., Sweeney, S.R., Krężel, A., Sentandreu, E., 2019. Chemometrics-assisted optimization of liquid chromatography-quadrupole-time-of-flight mass spectrometry analysis for targeted metabolomics. Talanta 199, 380-387.


Mass spectrometry-based metabolomics is characterized by a vast number of variables leading to a great degree of complexity. In this work, we aimed to simplify this process with a stepped chemometric optimization of the both funnel technology (funnel exit DC, FDC; funnel RF LP, FLC; funnel RF HP, FRP) and ion source parameters (Octopolo, Oct; and Fragmentor, Frag) of a quadrupole-time of flight (qTOF) for a human urinary metabolites. The workflow comprised a Box-Behnken experimental design with 47 experiments followed by the identification and quantification of a set of metabolites using high-resolution full-scan MS mode and feature extraction with an inclusion list. Metabolite peak areas were grouped according to abundance (high and low) and modeled by Random Forest regression (variance explained >85%). The full three-level factorial design consisting in 243 experiments was predicted and top 10 solutions for desirability function and those comprising the Pareto front were extracted and investigated. To guarantee the quality of results, we compared the Pareto front solutions with those achieved by standard instrumental parameters suggested by the manufacturer. A set of five solutions were identified that increased the mean peak area by 56 – 59% and 17%, for high- and low-abundance metabolites, respectively. The optimal parameters were determined to be: FLP, 100V; FDC, 40 and 30V; Frag, 275 and 400V; and Oct, 600 and 800V. The methodology applied throughout this work represents a flexible strategy to optimize instrumental parameters and exploit the performance of a qTOF MS detector.

Perrot, V., Landing, W.M., Grubbs, R.D., Salters, V.J.M., 2019. Mercury bioaccumulation in tilefish from the northeastern Gulf of Mexico 2 years after the Deepwater Horizon oil spill: Insights from Hg, C, N and S stable isotopes. Science of The Total Environment 666, 828-838.


Mercury (Hg) concentration in fish of the Gulf of the Mexico (GoM) is a major concern due to the importance of the GoM for U.S. fisheries. The Deepwater Horizon (DWH) oil spill in April 2010 in the northern GoM resulted in large amounts of oil and dispersant released to the water column, which potentially modified Hg bioaccumulation patterns in affected areas. We measured Hg species (methylmercury (MMHg) and inorganic Hg (IHg)) concentrations, and light (C, N and S) and Hg stable isotopes in muscle and liver tissues from tilefish (Lopholatilus chamaleonticeps) sampled in 2012 and 2013 along the shelf break of the northeastern GoM. Fish located close to the mouth of the Mississippi River (MR) and northwest of the DWH well-head (47 km) showed significantly lower Hg levels in muscle and liver than fish located further northeast of the DWH (>109 km), where 98% of tilefish had Hg levels in the muscle above US consumption advisory thresholds (50% for tilefish close to the DWH). Differences in light and Hg stable isotopes signatures were observed between these two areas, showing higher δ15N, and lower δ202Hg, Δ199Hg and δ34S in fish close to the DWH/MR. This suggests that suspended particles from the MR reduces Hg bioavailability at the base of the GoM food chains. This phenomenon can be locally enhanced by the DWH that resulted in increased particles in the water column as evidenced by the marine snow layer in the sediments. On the other hand, freshly deposited Hg associated with organic matter in more oligotrophic marine waters enhanced Hg bioaccumulation in local food webs. Comparing Hg isotopic composition in liver and muscle of fish indicates specific metabolic response in fish having accumulated high levels of MMHg.

Phukan, R., Gogoi, S.B., Tiwari, P., 2019. Enhanced oil recovery by alkaline-surfactant-alternated-gas/CO2 flooding. Journal of Petroleum Exploration and Production Technology 9, 247-260.

https://doi.org/10.1007/s13202-018-0465-0

The volumetric sweep efficiencies of CO2 flooding for enhanced oil recovery (EOR) are generally low due to problems of viscous fingering and gravity override. This paper attempts to study a relatively new and promising method to reduce the mobility of CO2 flooding and increase oil recovery under reservoir conditions. Referred to as alkaline-surfactant-alternated-gas/CO2 (ASAG) flooding, this method is essentially the synergic combination of chemical and immiscible CO2 flooding. In this work, chemical formulations were identified through foam stability tests based on their foaming ability coefficients. The selected formulations were further tested for their capabilities to reduce oil–water interfacial tensions (IFT) to ultra-low value. With the best performing formulations, the laboratory-scale core flooding experiments were conducted to evaluate their EOR potential. The core flooding experiments were performed with sandstone reservoir core samples from two different depths of a major depleted oil field of Upper Assam Basin, India. This study reports the successful application of a natural anionic surfactant (black liquor) as a co-surfactant and foaming agent during ASAG flooding. It was observed that higher oil recovery of 14.26% original oil in place (OOIP) was obtained by surfactant-alternated-gas (SAG) flooding compared to 12.03% OOIP by immiscible CO2 alternated with brine (WAG) flooding. The highest residual oil recovery of 20% OOIP was obtained for ASAG flooding with the alkali, surfactant and black liquor in the chemical slug. Oil recovery performances during SAG and ASAG flooding were found to be better for core samples with lower porosity–permeability due to stronger foam formation in lower permeability cores.



The atmosphere of the early Earth is hypothesized to have been rich in reducing gases such as hydrogen (H2). H2 has been proposed as the first electron donor leading to ATP synthesis due to its ubiquity throughout the biosphere as well as its ability to easily diffuse through microbial cells and its low activation energy requirement. Even today, hydrogenase enzymes enabling the production and oxidation of H2 are found in thousands of genomes spanning the three domains of life across aquatic, terrestrial, and even host-associated ecosystems. Even though H2 has already been proposed as a universal growth and maintenance energy source, its potential contribution as a driver of biogeochemical cycles has received little attention. Here, we bridge this knowledge gap by providing an overview of the classification, distribution, and physiological role of hydrogenases. Distribution of these enzymes in various microbial functional groups and recent experimental evidence are finally integrated to support the hypothesis that H2-oxidizing microbes are keystone species driving C cycling along O2 concentration gradients found in H2-rich soil ecosystems. In conclusion, we suggest focusing on the metabolic flexibility of H2-oxidizing microbes by combining community-level and individual-level approaches aiming to decipher the impact of H2 on C cycling and the C-cycling potential of H2-oxidizing microbes, via both culture-dependent and culture-independent methods, to give us more insight into the role of H2 as a driver of biogeochemical processes.

Pico, Y., Alfarhan, A., Barcelo, D., 2019. Nano- and microplastic analysis: Focus on their occurrence in freshwater ecosystems and remediation technologies. TrAC Trends in Analytical Chemistry 113, 409-425.


Plastic pollution is a global problem since 2016 when its production reached 322 million tonnes, excluding fibers. Daily discharges of microplastics (MPs, defined as <5 mm in size) are estimated in the range of 50,000 up to 15 million particles, whereas no information on nanoplastic (NP, <100 nm) release is available yet. Different processes further degraded these materials producing more MPs and NPs. This review attempts to fill the void of information on the state-of-art analysis of MPs and NPs (recently identified as emerging contaminants) and provides a critical overview on modern instrumentation, newly developed workflows, and promising techniques for their characterization (Raman and FT-IR spectroscopies and microscopies, pyrolysis and thermal desorption gas chromatography, imaging techniques, etc.). Available analytical methods, validation as well as applications with cells have been taken into account. MP and NP sampling, identification, and characterization are discussed. Finally, recent applications to establish their occurrence in freshwater ecosystems and the effectiveness of the proposed remediation technologies are considered.

Ping, H., Chen, H., George, S.C., Li, C., Hu, S., 2019. Relationship between the fluorescence colour of oil inclusions and thermal maturity in the Dongying Depression, Bohai Bay Basin, China: Part 2. fluorescence evolution of oil in the context of petroleum generation, expulsion and cracking under geological conditions. Marine and Petroleum Geology 103, 306-319.


Abundant measured data from source rocks, crude oils and oil inclusions in the Dongying Depression were used to identify the oil generation, expulsion and cracking stages under geological conditions, so as to build a fluorescence evolutionary model that considers all petroleum generation, expulsion and cracking processes. In the model, oil generation consists of three successive processes: bitumen generation, bitumen decomposition into oil, and oil cracking. These three stages are strongly controlled by thermal stress in the Dongying Depression. Kerogen decomposition into bitumen occurs at around 85 °C (0.42 %Ro), while NSO compounds in the bitumen begin to crack into oil at around

120 °C (0.67 %Ro). Competition between bitumen generation and NSO compound cracking leads to peak bitumen generation occurring at around 130 °C (0.75 %Ro). After that, the main phase of oil generation from intense bitumen decomposition occurs. A transition at approximately 160 °C between bitumen decomposition into oil and the inferred start of oil cracking corresponds to 4000 m (0.98–1.11 %Ro). During the bitumen generation and main oil generation stages, the fluorescence colours of the expelled oils are mainly yellow and orange, and a fluorescence blueshift of the oils only occurs during the main oil generation stage. In the late oil generation stage (∼160 °C), the fluorescence colours of the oils may be close to blue. With increasing burial, once the source rock and reservoir temperatures reach the threshold conditions for oil cracking (160 °C), an intense blueshift of the oil occurs in both source rocks and reservoirs, and even in oil inclusions. This blueshift is shown by a decreased dispersion in the fluorescence colour distribution of oil inclusions with increasing burial, from multiple colours at temperatures <160 °C, to only blue colours at temperatures >160 °C. Therefore, in oil-prone source rocks containing Type I and II kerogen, a blue fluorescence colour of oil appears to be strongly related to the secondary cracking process. Blue fluorescent oil inclusions generally have higher thermal maturities than oil inclusions with green or yellow fluorescence for oil-prone source rocks. This relationship is based on the assumption that the oil was not from a gas-prone source-rock, and that secondary alteration processes can be excluded, including migration fractionation, gas deasphalting, trapping fractionation, and phase separation. Furthermore, blue fluorescent oil inclusions may be a good indicator for oil-prone source rocks, which is significant for evaluation of source rock quality in deepwater and ultra deepwater areas in offshore basins.

Pino, M., Abarzúa, A.M., Astorga, G., Martel-Cea, A., Cossio-Montecinos, N., Navarro, R.X., Lira, M.P., Labarca, R., LeCompte, M.A., Adedeji, V., Moore, C.R., Bunch, T.E., Mooney, C., Wolbach, W.S., West, A., Kennett, J.P., 2019. Sedimentary record from Patagonia, southern Chile supports cosmic-impact triggering of biomass burning, climate change, and megafaunal extinctions at 12.8 ka. Scientific Reports 9, Article 4413.

https://doi.org/10.1038/s41598-018-38089-y

The Younger Dryas (YD) impact hypothesis posits that fragments of a large, disintegrating asteroid/comet struck North America, South America, Europe, and western Asia ~12,800 years ago. Multiple airbursts/impacts produced the YD boundary layer (YDB), depositing peak concentrations of platinum, high-temperature spherules, meltglass, and nanodiamonds, forming an isochronous datum at >50 sites across ~50 million km² of Earth’s surface. This proposed event triggered extensive biomass burning, brief impact winter, YD climate change, and contributed to extinctions of late Pleistocene megafauna. In the most extensive investigation south of the equator, we report on a ~12,800-year-old sequence at Pilauco, Chile (~40°S), that exhibits peak YD boundary concentrations of platinum, gold, high-temperature iron- and chromium-rich spherules, and native iron particles rarely found in nature. A major peak in charcoal abundance marks an intense biomass-burning episode, synchronous with dramatic changes in vegetation, including a high-disturbance regime, seasonality in precipitation, and warmer conditions. This is anti-phased with northern-hemispheric cooling at the YD onset, whose rapidity suggests atmospheric linkage. The sudden disappearance of megafaunal remains and dung fungi in the YDB layer at Pilauco correlates with megafaunal extinctions across the Americas. The Pilauco record appears consistent with YDB impact evidence found at sites on four continents.

Pires, L.O., Winter, A., Trevisan, O.V., 2019. Dolomite cores evaluated by NMR. Journal of Petroleum Science and Engineering 176, 1187-1197.


Nuclear Magnetic Resonance (NMR) is a very versatile technique that allows the characterization of several petrophysical properties such as porosity, pore size distribution and fluid saturation and, unlike other techniques, it is possible to be applied on field scale through well loggings and in laboratory scale on the analysis of samples. In this paper, NMR measurements were performed in several samples with different saturation conditions in order to obtain as main information that can be inferred from the application of this technique at the laboratory scale. Silurian dolomites were studied since they are common in many carbonate reservoirs. Several petrophysical properties of these rocks were evaluated from NMR T2 relaxation time distributions at different conditions and compared with common techniques used in laboratory. Three fluids pairs were used: air/brine; mineral oil/brine; and crude oil/brine. The use of different fluids was required depending on the property that was being studied. Nitrogen porosity, commonly used in the petrophysical characterization, was compared to a porosity obtained by the NMR, and an optimum correlation was obtained between the results of these two techniques. T2 relaxation time limits were defined in order to separate micro/mesopores and meso/macropores limits. Using these limit ranges, the pore size distribution was evaluated and it was compared to the pore size distribution obtained when the T2 distribution is scaled by the surface relaxivity value. It was observed that about 80% of the porous medium was composed of macropores, but the evaluation of only the T2 relaxation times provided higher fraction of macropores. The T2cutoff

values obtained were in accordance to the values referenced in the literature for vuggy carbonates. From the NMR measurements performed before and after waterflooding was possible to determine the residual oil saturations, which values were similar to the values obtained by mass balance. Finally, comparing the T2 distributions before and after the aging process, it was observed that there was an increase of fluid fraction in lower relaxation times after the aging process, indicating that NMR measurements could be used to evaluate the wettability alteration of the surface. The results obtained in the quantification of the wettability from the T2 relaxation times were very different in relation to the wettability quantification provided by Amott-Harvey Wettability Index.

Pomerantz, A.E., Bostrom, N.W., Kleinberg, R.L., Crace, E., Weng, T.-C., Sokaras, D., Nordlund, D., 2019. Electronic structure of naturally occurring aromatic carbon. Energy & Fuels 33, 2099-2105.


Aromatic carbon in fused-ring systems can be classified into two forms of electronic structure: aromatic sextets, which have large highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gaps and resemble benzene; and isolated double bonds, which have small HOMO–LUMO gaps and resemble olefins. The relative abundance of aromatic sextets versus isolated double bonds in mixtures can be probed by carbon X-ray Raman spectroscopy. Here, we report the carbon X-ray Raman spectra of a wide variety of forms of naturally occurring aromatic carbon: kerogen (insoluble organic carbon in sedimentary rocks, which is the most abundant form of naturally occurring organic carbon in the Earth’s crust) over a range of types and thermal maturities, fresh materials of a variety of forms, and coal and petroleum asphaltenes (toluene soluble and heptane insoluble materials, which represent organic carbon resulting from extensive thermal processing). It is observed that all these materials are dominated by aromatic sextets over isolated double bonds. On the basis of the diversity of materials analyzed, it is concluded that naturally occurring organic carbon is generally dominated by aromatic sextets over isolated double bonds. This conclusion is rationalized in terms of statistical and thermodynamic effects.

Potgieter, H., de Coning, P., Bekker, R., Rohwer, E., Amirav, A., 2019. The pre-separation of oxygen containing compounds in oxidised heavy paraffinic fractions and their identification by GC-MS with supersonic molecular beams. Journal of Mass Spectrometry 54, 328-341.

https://doi.org/10.1002/jms.4340

Abstract The heavy petroleum fractions produced during refining processes need to be upgraded to useable products to increase their value. Hydrogenated heavy paraffinic fractions can be oxidised to produce high value products that contain a variety of oxygenates. These heavy oxygenated paraffinic fractions need to be characterised to enable the control of oxidation processes and to understand product properties. The accurate identification of the oxygenates present in these fractions by electron ionisation (EI) mass spectrometry is challenging due to the complexity of these heavy fractions. Adding to this challenge is the limited applicability of EI mass spectral libraries due to the absence of molecular ions from the EI mass spectra of many oxygenates. The separation of oxygenates from the complex hydrocarbon matrix prior to high temperature GC-MS (HT-GC-MS) analysis reduces the complexity of these fractions and assists in the accurate identification of these oxygenates. Solid phase extraction (SPE) and supercritical fluid chromatography (SFC) were employed as prefractionation techniques. GC-MS with supersonic molecular beams (SMBs) (also named GC-MS with cold-EI) utilises a SMB interface with which EI is done with vibrationally cold sample compounds in a fly-through ion source (cold-EI) resulting in a substantial increase in the molecular ion signal intensity in the mass spectrum. This greatly enhances the accurate identification of the oxygenates in these fractions. This study investigated the ionisation behaviour of oxygenated compounds using cold-EI. The prefractionation by SPE and SFC and the subsequent analysis with GC-MS with cold-EI were applied to an oxygenated heavy paraffinic fraction.

Potts, L.D., Perez Calderon, L.J., Gubry-Rangin, C., Witte, U., Anderson, J.A., 2019. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. Marine Pollution Bulletin 142, 169-177.


Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.

Pratt, B.R., Kimmig, J., 2019. Extensive bioturbation in a middle Cambrian Burgess Shale–type fossil Lagerstätte in northwestern Canada. Geology 47, 231-234.


Mudstones hosting Burgess Shale–type preservation of soft-bodied fossils are commonly held to be characterized by little to no bioturbation. This has been taken as evidence for bottom-water dysoxia or anoxia, along with anaerobic conditions in the sediment, which favored preservation of soft tissues by hindering decay. Although invisible on fresh and weathered surfaces, laminated claystone comprising the middle Cambrian (Drumian) Ravens Throat River Lagerstätte in the Rockslide Formation of the Mackenzie Mountains, northwestern Canada, is revealed by preparation of surfaces sawn parallel to

bedding to exhibit extensive burrowing. Four types of burrows are distinguished: (1) rare large forms averaging 15 mm in diameter; (2) backfilled vertical burrows 3–6 mm wide; (3) oblique to horizontal burrows 2–4 mm wide and typically with meniscate backfilling; and (4) tiny, short, mostly vertical burrows 0.5–1 mm in diameter. The third group is the most common, locally completely bioturbating laminae and penetrating worm carcasses; it conforms to Planolites. A variety of ethologies is indicated, with the large type seemingly serving as a dwelling burrow and the smaller ones from deposit-feeding. Although dysoxic bottom conditions probably developed occasionally, the widespread burrowing argues for predominantly oxic conditions, and it indicates that restriction of bioturbation was probably not the most important factor leading to soft-tissue preservation. Bioturbation might be more common in other Cambrian Lagerstätten than is currently believed, and it is possible that low-oxygen conditions at the seafloor were not fundamentally necessary for Burgess Shale–type preservation.

Prince, J.K.G., Rainbird, R.H., Wing, B.A., 2019. Evaporite deposition in the mid-Neoproterozoic as a driver for changes in seawater chemistry and the biogeochemical cycle of sulfur. Geology 47, 375-379.

https://doi.org/10.1130/G45464.1

We utilized a novel approach to modeling the oceanic sulfur cycle by combining δ34S and Δ33S curves from sulfate evaporite minerals in order to investigate redox conditions during the mid-Neoproterozoic. This technique allowed us to estimate the oxidized and reduced proportions of the total oceanic sulfur sink. Isotopic data from the mid-Neoproterozoic Minto Inlet Formation (Victoria Island, Northwest Territories, Canada; ca. 850 Ma) show a limited range (16.8‰ ± 1.4‰) in δ34S of seawater sulfate and a sulfur cycle that is strongly shifted toward the sulfate sink (pyrite burial fraction, ƒp, = 0.2), suggesting oxidizing conditions in the ocean and atmosphere at the time of deposition. These evaporites and others, which were deposited contemporaneously within a huge intracontinental basin, acted as a chemical pump, removing sulfate from the oceans and oxygen from the atmosphere to be buried as sulfate evaporites.

Psillakis, E., 2019. Vortex-assisted liquid-liquid microextraction revisited. TrAC Trends in Analytical Chemistry 113, 332-339.


In 2010, we proposed vortex-assisted liquid-liquid microextraction (VALLME) that used vortex agitation to disperse microliters of a water-immiscible solvent into an aqueous sample. After extraction, the two phases were separated by centrifugation and the extracting solvent was collected and used for analysis.

The seemingly easy steps of VALLME involve complex and poorly understood processes that require consideration of solvent drop breakup and coalescence plus the problem of interphase analyte mass transfer. The overall aim of this review is to transfer knowledge from other disciplines and improve current understanding of VALLME. Initially, the fundamental hydrodynamic and interfacial science concepts of emulsion formation and phase separation applying to VALLME are presented. Building on this knowledge, the effects of several experimental parameters on VALLME are discussed. Advancing the current (and limited) knowledge on the fundamentals behind VALLME is critical to allow cognitive control and full exploitation of the method.

Puri, A.W., Liu, D., Schaefer, A.L., Yu, Z., Pesesky, M.W., Greenberg, E.P., Lidstrom, M.E., 2019. Interspecies chemical signaling in a methane-oxidizing bacterial community. Applied and Environmental Microbiology 85, Article e02702-02718.


Abstract: Multiple species of bacteria oxidize methane in the environment after it is produced by anaerobic ecosystems. These organisms provide reduced carbon substrates for species that cannot oxidize methane themselves, thereby serving a key role in these niches while also sequestering this potent greenhouse gas before it enters the atmosphere. Deciphering the molecular details of how methane-oxidizing bacteria interact in the environment enables us to understand an important aspect that shapes the structures and functions of these communities. Here we show that many members of the Methylomonas genus possess a LuxR-type acyl-homoserine lactone (acyl-HSL) receptor/transcription factor that is highly homologous to MbaR from the quorum-sensing (QS) system of Methylobacter tundripaludum, another methane oxidizer that has been isolated from the same environment. We reconstitute this detection system in Escherichia coli and use mutant and transcriptomic analysis to show that the receptor/transcription factor from Methylomonas sp. strain LW13 is active and alters LW13 gene expression in response to the acyl-HSL produced by M. tundripaludum. These findings provide a molecular mechanism for how two species of bacteria that may compete for resources in the environment can interact in a specific manner through a chemical signal.

Importance: ethanotrophs are bacteria that sequester methane, a significant greenhouse gas, and thereby perform an important ecosystem function. Understanding the mechanisms by which these organisms interact in the environment may ultimately allow us to manipulate and to optimize this activity. Here we show that members of a genus of methane-oxidizing bacteria can be influenced by a chemical signal produced by a possibly competing species. This provides insight into how gene expression can be controlled in these bacterial communities via an exogenous chemical signal.

Qian, K., Ning, J., Liu, X., Zhang, Y., 2019. A rock physics driven Bayesian inversion for TOC in the Fuling shale gas reservoir. Marine and Petroleum Geology 102, 886-898.


Total organic content (TOC) is an important indicator in the evaluation of the organic abundance and production potential of shale reservoirs. The conventional approach to TOC estimation is to correlate TOC with inverted elastic parameters in a linearized empirical equation. However, this approach ignores complex rock physics properties (such as complex mineralogy and pore space) in the shale while generating smooth, low resolution results. This paper proposes a rock physics-based method to forward model the seismic and elastic response of the shale reservoir and then invert using a Bayesian approach to derive key parameters, such as the TOC, total porosity and the fractional volume of brittle minerals, and to delineate the sweet-spots in an unconventional shale reservoir.

Qiu, X., Yao, Y., Wang, H., Shen, A., Zhang, J., 2019. Halophilic archaea mediate the formation of proto-dolomite in solutions with various sulfate concentrations and salinities. Frontiers in Microbiology 10, 480. doi: 410.3389/fmicb.2019.00480.


In the past several decades, sulfate concentration and salinity have been considered to be the two essential hydrochemical factors in the formation of dolomite, yet arguments against this hypothesis

have existed simultaneously. To clarify the effects of sulfate concentration and salinity in the mineralization of dolomite, we conducted experiments on dolomite precipitation mediated by a halophilic archaeon, Natrinema sp. J7-1with various sulfate concentrations and salinities. This strain was cultured in a series of Modified Growth Media (MGM) with salinities of ¬¬¬140‰, 200‰ and 280‰. Cells in the post-log phase were harvested and used to mediate the formation of dolomite in solutions with various sulfate concentrations of 0 mM, 3 mM, 29.8 mM and 100 mM and salinities of 140‰, 200‰ and 280‰. X-ray Diffraction (XRD) spectra showed that proto-dolomite, monohydrocalcite and aragonite formed in samples with cells, yet only aragonite was detected in samples without cells. Proto-dolomite was found in all biotic samples, regardless of the variation in salinity and sulfate concentration. Moreover, the relative abundances of proto-dolomite in the precipitates were positively correlated with the salinities of the media but were uncorrelated with the sulfate concentrations of the solutions. Scanning Electronic Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS) results showed that all the proto-dolomites were sphere or sphere aggregates with a mole ratio of Mg/Ca close to 1.0. No obvious variations in morphology and Mg/Ca were found among samples with various sulfate concentrations or salinities. This work reveals that a variation of sulfate concentration in solution (from 0 mM to 100 mM) does not affect the formation of dolomite mediated by halophilic archaea, but an increase of salinity (from 140‰ to 280‰) enhances this process. Our results indicate that under natural conditions, an increase in salinity may be more significant than the decrease of sulfates in microbe-mediated dolomite formation.



Geochemical models typically represent organic matter (OM) as consisting of multiple, independent pools of compounds, each accessed by microorganisms at different rates. However, recent findings indicate that organic compounds can interact within microbial metabolisms. The relevance of interactive effects within marine systems is debated and a mechanistic understanding of its complexities, including microbe-substrate relationships, is lacking. As a first step toward uncovering mediating processes, the interactive effects of distinct pools of OM on the growth and respiration of marine bacteria, individual strains and a simple, constructed community of Roseobacter lineage members were tested. Isolates were provided with natural organic matter (NOM) and different concentrations (1, 4, 40, 400 μM-C) and forms of labile organic matter (acetate, casamino acids, tryptone, coumarate). The microbial response to the mixed substrate regimes was assessed using viable counts and respiration in two separate experiments. Two marine bacteria and a six-member constructed community were assayed with these experiments. Both synergistic and antagonistic growth responses were evident for all strains, but all were transient. The specific substrate conditions promoting a response, and the direction of that response, varied amongst species. These findings indicate that the substrate conditions that result in OM interactive effects are both transient and species-specific and thus influenced by both the composition and metabolic potential of a microbial community.

Rabinovitch, J., Katz, I., 2019. Surface deposition of molecular contaminants in the Mars 2020 rover wake. Planetary and Space Science 168, 1-14.


The Mars 2020 rover has very strict contamination control requirements as it will cache samples on the surface of Mars for possible future return. It is known that the rover will outgas a minor amount of molecular contaminant on the surface of Mars, and numerical simulations using STAR-CCM+ are performed in order to predict the magnitude of the contaminant deposition to the Martian surface in the vicinity of the rover. Outgassing from the Rover Warm Electronics Bay (WEB) is predicted to be the dominant source of contamination for this scenario, and is therefore considered in this work. A flat terrain (i.e., no local topography) and a nominal rover orientation (i.e., no rocks under rover wheels, etc.) is also assumed. This analysis is performed in order to determine whether or not the M2020 rover WEB could self-contaminate a potential sampling site if the rover were to remain in the same location for an extended period of time. Simulations are performed under a variety of surface wind conditions, and it is determined that the predicted level of molecular contaminant deposition to the surface near the rover due to WEB outgassing and the model considered could be a maximum of 9 ng of organic contaminant in one specific location near the rover if the rover were to remain stationary for 100 sols.

Raidla, V., Pärn, J., Schloemer, S., Aeschbach, W., Czuppon, G., Ivask, J., Marandi, A., Sepp, H., Vaikmäe, R., Kirsimäe, K., 2019. Origin and formation of methane in groundwater of glacial origin from the Cambrian-Vendian aquifer system in Estonia. Geochimica et Cosmochimica Acta 251, 247-264.


Groundwater in the Cambrian-Vendian aquifer system in Estonia is characterised by the most depleted isotopic composition known in Europe (δ18O down to −23‰). The water most likely originates from glacial meltwater recharge from the Fennoscandian Ice Sheet in the Pleistocene. The aquifer system is characterised by relative high methane concentrations (up to 50% of dissolved gases, estimated absolute concentration up to 1600 μmol L−1), the origin of which has so far remained unclear. In this paper, we focus on the origin of methane, the factors controlling its spatial distribution and its isotope geochemistry in the aquifer system. The data reveal a large spatial variability in methane concentration, δ13CCH4 and δ2HCH4 values (from −6 to −105‰ and from −220 to −420‰, respectively). We show that local oxidation processes rather than different pathways of methane formation, have affected the initial isotopic composition of methane. Using the least modified δ13CCH4 values (from −85 to −105‰), we conclude that methane most likely originates from the organic material overridden by the Fennoscandian Ice Shield during the Late Weichselian glaciation, that was carried into the aquifer system with infiltrating glacial meltwater. The estimated δ18O values of the water, where the methane was formed, are −17 ± 1.5‰ supporting the inference that the methane was formed during the Middle Weichselian interstadial. The study shows that groundwater of glacial origin in the Cambrian-Vendian aquifer system can serve as an alternative palaeoenvironmental archive to be used for studying the variations in climatic and environmental conditions in Northern Europe during glacial–interglacial cycles of the Pleistocene.

Raj, G., Larkin, E., Lesimple, A., Commins, P., Whelan, J., Naumov, P., 2019. In situ monitoring of the inhibition of asphaltene adsorption by a surfactant on carbon steel surface. Energy & Fuels 33, 2030-2036.


Simple surfactants have proven to be some of the most effective agents to mitigate the deposition of asphaltenes on pipeline walls; however, the best practices for their application are often empirical, and the actual mechanisms of their action remain elusive. Here, inhibition of asphaltene adsorption as

viscoelastic films on carbon steel by a surfactant, dodecylbenzenesulfonic acid (DBSA), was directly monitored using quartz crystal microbalance with dissipation. Different protocols for application of the inhibitor were assessed, including treatment of the clean surface before adhesion and application by premixing and postprecipitation. Asphaltenes were found to form a tightly bound viscoelastic layer on the carbon steel surface, and administering DBSA on preadsorbed asphaltenes removes most (86.5%) of this adsorbate. Premixing of DBSA and asphaltenes to simulate the commonly used application method results in a very short contact time (∼35 s) before most of asphaltenes (86.0%) are desorbed from the surface. Pretreatment of the metal surface with DBSA was found to be particularly effective, and it results in nearly complete (98.5%) removal. The efficacy of DBSA in organic scale removal, mainly asphaltenes, over prolonged time by repeated treatment was also investigated. The results indicate that alternating application of toluene and DBSA is the most effective protocol that prevents the loosely bound toluene-soluble fraction of asphaltenes to act as a nucleation layer that triggers the onset of growth of the asphaltene layers.

Rao, A., Roncal-Herrero, T., Schmid, E., Drechsler, M., Scheffner, M., Gebauer, D., Kröger, R., Cölfen, H., 2019. On biomineralization: Enzymes switch on mesocrystal assembly. ACS Central Science 5, 357-364.


Cellular machineries guide the bottom-up pathways toward crystal superstructures based on the transport of inorganic precursors and their precise integration with organic frameworks. The biosynthesis of mesocrystalline spines entails concerted interactions between biomolecules and inorganic precursors; however, the bioinorganic interactions and interfaces that regulate material form and growth as well as the selective emergence of structural complexity in the form of nanostructured crystals are not clear. By investigating mineral nucleation under the regulation of recombinant proteins, we show that SpSM50, a matrix protein of the sea urchin spine, stabilizes mineral precursors via vesicle-confinement, a function conferred by a low-complexity, disordered region. Site-specific proteolysis of this domain by a collagenase initiates phase transformation of the confined mineral phase. The residual C-type lectin domain molds the fluidic mineral precursor into hierarchical mesocrystals identical to structural crystal modules constituting the biogenic mineral. Thus, the regulatory functions of proteolytic enzymes can guide biomacromolecular domain constitutions and interfaces, in turn determining inorganic phase transformations toward hybrid materials as well as integrating organic and inorganic components across hierarchical length scales. Bearing striking resemblance to biogenic mineralization, these hybrid materials recruit bioinorganic interactions which elegantly intertwine nucleation and crystallization phenomena with biomolecular structural dynamics, hence elucidating a long-sought key of how nature can orchestrate complex biomineralization processes.



Fuels produced from microalgae are a promising alternative for fuels from fossil resources. Algae biomass may be transformed by hydrothermal liquefaction (HTL) into biocrudes, which need upgrading by hydrotreatment to meet transportation fuel requirements. In this study, analyses of HTL biocrude catalytically hydrogenated in a batch reactor at temperatures between 360 and 400 °C and residence times between 2.5 and 10.2 h are presented. Selected samples were investigated by

comprehensive gas chromatography mass spectrometry (GC×GC) using flame ionization (FID) or mass spectrometry (MS). The main components of the samples before and after the hydrogenation are hydrocarbons of different unsaturation including alkanes, alkenes, monocyclic and bicyclic hydrocarbons and monocyclic aromatic hydrocarbons. Also, small amounts of polyaromatic hydrocarbons are formed. The most frequent class of heteroatomic compounds are nitrogen and oxygen containing compounds. Oxygen containing compounds are primarily of phenolic nature, whilst nitrogen containing compounds show aromatic amine (alkylated aniline and isomers) and pyrrolic structures (alkylated indoles and carbazoles and isomers). Upon proceeding hydrogenation, an increasing content of lower molecular weight hydrocarbons is observed. The analyses allow to track the decrease of heteroatomic compounds and reveal the structure of refractory compounds. Ultimately, the results allow to identify optimum parameters for the hydrogenation of HTL biocrudes from algae, which correspond to a maximum yield of hydrocarbons and acceptable levels of heteroatomic compounds.

Raymond, A., Lambert, L.L., Costanza, S.H., 2019. Are coal balls rare? A cyclostratigraphic analysis of coal-ball occurrence in North America. International Journal of Coal Geology 206, 65-79.


From the perspective of Phanerozoic time, coal balls are rare, apparently limited to a 24 m.y. interval (323–299 Ma) in the Pennsylvanian and earliest Permian. Yet within this interval, coal balls occur in many coals. Approximately 82 transgressive-regressive sedimentary cycles have been described for the Midcontinent, Illinois and Appalachian basins of North America during the mid-to-late Pennsylvanian. One third (27/82) have coal balls, including 57% of major cycles, 36% of intermediate cycles and 16% of minor cycles. Coal-ball occurrence in the Donets Basin is similar: over an interval of about 4 m.y. (~315–311 Ma, latest Bashkirian to mid-Moscovian), 39% (11/28) of transgressive-regressive cycles have coal balls. As North American paleoclimate became drier, tree ferns replaced lycopsids as the dominant plant in peat swamps at the Desmoinesian/Missourian boundary, and coal-ball occurrence declined. Overall, 47% of cycles (19/40) with lycopsid or cordaitean dominance have coal balls, whereas 19% (8/42) of cycles with tree fern dominance have coal balls (p < .004). While 32% (6/19) of minor cycles with lycopsid or cordaitean dominance have coal balls, no minor cycle with tree fern dominance has coal balls.

This pattern may reflect the relative abundance of coal in the Late Pennsylvanian, with drier paleotropical climates in the Missourian-Virgilian leading to less paleotropical coal, fewer mines and a lower probability of discovering Missourian and Virgilian coal balls. However, average cycle duration decreased from 150 kyr in the Desmoinesian to ~100 kyr in the Missourian and Virgilian, and faster rates of relative sea-level rise could have affected coal-ball abundance, particularly if coal balls formed in marine swamps, with more rapid transgression leading to thinner coals, or to freshwater coals directly overlain by marine sediments. Rygel et al. (2008) suggested that Missourian-Virgilian cycles recorded more erosional relief than Desmoinesian cycles, consistent with increased amplitude and rates of sea-level rise during each glacial-eustatic cycle. Changes in Missourian-Virgilian cycles may have been augmented by stratigraphic attenuation as sediment filled the antecedent topography.


https://doi.org/10.1007/s11242-018-1207-y

The possibility of broaching, or the release of fluids at the seafloor due to a damaged or faulty well, is a hazard that must be assessed in the well permitting process. This paper describes a numerical simulation study of a real-life scenario where a complex, permeable sandy formation, connected to the seafloor via known chimneys/seeps, is intersected by a damaged production well that drains another deeper, gas-bearing formation. The objective of the study is to determine the transport and fate of hydrocarbon reservoir fluids (gas and brines) escaping into the sandy formation through the casing shoe of the failed well, and to determine the time it takes for these contaminants to reach the ocean floor. We conducted a detailed simulation study to represent the conditions, properties, and behavior of the system under such failure conditions, and we investigated the migration of gas and brine for a range of reservoir and chimney properties. A key conclusion is that, for such complex systems, modeling the three-dimensional geometry of the system in detail is the key to describing transport and assessing the time and magnitude of potential releases. For the system studied here, transport times range from under 2 years (highest permeabilities) to many decades, ensuring significant time to respond to potential broaching hazards. Under the conditions investigated in this study, we also determine that gas-dominated releases associated with low rates of water flow into the sandy formation are likely to cause hydrate formation that can reduce permeabilities in the colder, upper regions of the chimneys and possibly mitigate releases.

Ren, B., Duncan, I., 2019. Modeling oil saturation evolution in residual oil zones: Implications for CO2 EOR and sequestration. Journal of Petroleum Science and Engineering 177, 528-539.


Residual oil zones (ROZs) are extensively developed in carbonate formations in the Permian Basin, West Texas. These ROZs have the potential both for economically-viable CO2 enhanced oil recovery (CO2-EOR) and for significant volumes of associated CO2 sequestration. The accepted model for ROZ formation is based on the hydrodynamic effects of tectonically-controlled increased water flow in aquifers at the base of oil fields. The nature of this process is modelled using a commercial reservoir simulator in this work. These simulations explore the effects of strength of aquifer flow, flow direction, and capillary pressure on the nature and distribution of oil saturations in ROZs. A special emphasis was on understanding the impact of heterogeneity of capillary pressures in ROZ reservoirs. These factors determine the thickness of ROZs, the magnitude of oil saturation, and the slope of water-oil contacts. Understanding the magnitude of oil saturation and how it varies within ROZs is important in determining reserves, and evaluating both EOR and sequestration potential. The geometry of ROZs are established slowly, especially for small regional water fluxes, however oil saturations achieve almost steady states in relatively short time scales. The simulated oil saturation profiles found in this study are in reasonable agreement with the measured profile published for the San Andres Seminole Unit's ROZ. The results support the plausibility of the hydrodynamic model, but do not rule out other models for the origin of ROZs.

Ren, G., Yan, Y., Nie, Y., Lu, A., Wu, X., Li, Y., Wang, C., Ding, H., 2019. Natural extracellular electron transfer between semiconducting minerals and electroactive bacterial communities occurred on the rock varnish. Frontiers in Microbiology 10, 10:293. doi: 210.3389/fmicb.2019.00293.


Rock varnish is a thin coating enriched with manganese (Mn) and iron (Fe) oxides. The mineral composition and formation of rock varnish elicit considerable attention from geologists and

microbiologists. However, limited research has been devoted to the semiconducting properties of these Fe/Mn oxides in varnish and relatively little attention is paid to the mineral–microbe interaction under sunlight. In this study, the mineral composition and bacterial communities on varnish from the Gobi Desert in Xinjiang, China were analyzed. Results of principal components analysis and t–test indicated that more electroactive genera such as Acinetobacter, Staphylococcus, Dietzia and Pseudomonas gathered on varnish bacterial communities than on substrate rock and surrounding soils. We then explored the culture of varnish, substrate and soil samples in media and the extracellular electron transfer (EET) between bacterial communities and mineral electrodes under light/dark condition for the first time. Orthogonal electrochemical experiments demonstrated that the most remarkable photocurrent density of 6.1 ± 0.4 μA/cm2 was observed between varnish electrode and varnish microflora. Finally, based on Raman and 16S rRNA gene sequencing results, coculture system of birnessite and Pseudomonas (the major Mn oxide and one common electroactive bacterium in varnish) was established for mechanism study. A steadily growing photocurrent (205 μA at 100 h) under light was observed with a stable birnessite after 110 h. However, only 47 μA was generated in the dark control and birnessite was reduced to Mn2+ in 13 h, suggesting that birnessite helped deliver electrons instead of serving as an electron acceptor under light. Our study demonstrated that electroactive bacterial communities were positively correlated with Fe/Mn semiconducting minerals in varnish, and diversified EET process occurred on varnish under sunlight. These phenomena may influence bacterial community structure in natural environments over time.

Reynolds, D.J., Hall, I.R., Slater, S.M., 2019. An integrated carbon and oxygen isotope approach to reconstructing past environmental variability in the northeast Atlantic Ocean. Palaeogeography, Palaeoclimatology, Palaeoecology 523, 48-61.


The combined influence of temperature and the isotopic composition of the seawater (δ18Ow) often precludes the use of oxygen isotope (δ18O) records, derived from marine carbonates, to reconstruct absolute seawater temperatures, without the application of an independent δ18Ow proxy. Here we investigate the application of carbon isotope records (δ13Cshell), derived from the long-lived marine bivalve Glycymeris glycymeris, as a proxy for δ18Ow variability. Our analyses indicate G. glycymeris δ13Cshell data derived from growth increments >20 years of age contain strong ontogenetic trends (−0.013‰ yr−1, R = 0.98, P < 0.001, N = 51). These analyses demonstrate that, coupled with the ontogenetic trends, 54% of the variability in G. glycymeris δ13Cshell records can be explained by a combination of the marine Suess effect and physical (salinity and riverine input) and biological processes (primary production). The application of these δ13Cshell data in conjunction with co-registered δ18Oshell and growth increment width series, each of which have been shown to be sensitive to seawater temperature and primary productivity respectively, can therefore provide new insights into past environmental variability and help constrain uncertainties on reconstructions of past seawater temperature variability.

Rezaei, F., Izadi, H., Memarian, H., Baniassadi, M., 2019. The effectiveness of different thresholding techniques in segmenting micro CT images of porous carbonates to estimate porosity. Journal of Petroleum Science and Engineering 177, 518-527.


The effectiveness of various thresholding techniques in segmenting micro X-ray computed tomography (XCT) images of porous carbonates has been investigated using experimental analysis. A comparison between directly measured and image-derived porosities clearly exhibited that the

application of different segmentation methods produced vastly different results. The obtained results demonstrated the importance of the segmentation step for quantitative pore space analysis. In this research, three global thresholding methods and three locally adaptive thresholding methods were examined and only a few of the tested methods yielded acceptable results. Generally, locally adaptive methods generated better results; however, as the performance of global methods were reduced because of presence of anhydrite concentrations in the studied samples, a pre-segmentation for determining the anhydrite phase increased the performance of GT methods dramatically. As a result, two-threshold Otsu method yielded the best outcome. The novelty of this work is to compare the performance of different methods in segmentation of XCT images and to focus on the carbonates of one of the southern oilfields of Iran.



Concerning the potential positive role of water in oil emulsification in enhancing oil recovery, the current research builds on finding reasons responsible for the considerable water in oil emulsification observed in the produced fluid during carbonate sand pack floodings in the previous works. Allowing a systematic comparison, the results on floodings of three Fe3O4-based nanocomposites were selected from previous studies. The XRD and FESEM of nanocomposites, zeta potentials, stability of synthetic emulsions, IFT, bulk and interfacial oil/water viscosities, and asphaltene adsorption in the presence of nanocomposites were analyzed. The XRD and FESEM results showed a successful synthesis for all nanocomposites. Zeta potential measurements showed values far above −40 mV, which confirm a good stability for all nanocomposites in the base fluid. In terms of emulsion stability, microscopic images showed that all synthesized nanocomposites had better performance in stabilizing synthetic emulsion droplets as compared to Fe3O4 NPs. IFT measurements indicated an 18–21 mN/m decrease with the addition of nanocomposites to the seawater. The bulk viscosity measurements indicated that Fe3O4/Chitosan nanocomposites present in the aqueous phase increase the water/oil (30/70 vol%) emulsion viscosity up to 334 cp. The interfacial viscosity measurements also showed a reduced oil/water interfacial viscosity by the addition of nanocomposites to the aqueous phase, which is probably due to the increased presence of asphaltene molecules at the interface. In the end, the absorbed asphaltene particles by nanocomposites were measured using batch adsorption experiments and fitted to the BET adsorption isotherm. The results showed that by deploying at the interface, Fe3O4-based nanocomposites are highly capable of asphaltene adsorption, which can stabilize the water in oil emulsions.

Rickard, D., 2019. How long does it take a pyrite framboid to form? Earth and Planetary Science Letters 513, 64-68.


Framboids are defined as microscopic, sub-spheroidal clusters of equant and equidimensional microcrystals. The microcrystals are usually constituted of pyrite and framboidal pyrite is one of the most abundant mineral textures in the natural environment. They are of particular interest to geochemists, sedimentologists, paleobiologists and materials scientists because of their potential paleoenvironmental significance, their widespread involvement in fossilization and their potential for the manufacture of self-organizing materials. Here I use a simple diffusion-nucleation model to compute framboid formation times. The results show that pyrite framboids take between 3 h and 3 yr

to form depending on framboid size. The time taken for the average sedimentary framboid to form is about 5 days and the average syngenetic framboid forms within 3 days. The shorter formation times for syngenetic compared with diagenetic framboids helps explain the smaller size relative size distributions of syngenetic framboids. This has led to the use of framboid size-frequency measurements as proxies for ancient euxinia. The relatively rapid formation of pyrite framboids explains how pyrite infills and preserves soft tissues before cell lysis and before deformation through burial has been initiated. One unexpected consequence of the model is that it further explains how commonly observed groups of framboids can form contemporaneously.

Rickard, D., 2019. Sedimentary pyrite framboid size-frequency distributions: A meta-analysis. Palaeogeography, Palaeoclimatology, Palaeoecology 522, 62-75.


Framboids, microscopic sub-spheroidal aggregates of pyrite microcrystals, are found in sediments of all ages and framboid size-frequency distributions are widely used to determine the oxygenation states of paleo-waters. Sedimentary framboid populations display unimodal log-normal size distributions as a consequence of the multiplicative central limit theorem in probability theory. The application of additive statistics to framboid populations and their consequent characterization in terms of arithmetic means and standard deviations is wrong because it predicts a subset of framboids with negative diameters.

A meta–analysis of 377 sets of measurements of the diameters of 48,063 pyrite framboids from 104 sediment and sedimentary rock locations shows that the geometric mean diameter of sedimentary framboids is 6.2 μm and the geometric standard deviation is 1.5. Ninety-five percent of all sedimentary framboids have geometric mean diameters between 2.9 and 13.9 μm. The geometric mean diameter of modern syngenetic framboids formed within euxinic water columns is 4.7 μm and that of diagenetic framboids formed within sediments is 6.7 μm. The estimated measurement error is ±10%.

Framboid mean diameters can be used to help discriminate the oxygenation state of paleo-waters. A minimum number of 30 measurements is required and ideally ≥100 measurements are recommended. The conflicting evidence reported in the literature for the application of framboid size-frequency measurements results mainly from the intrinsic nature of statistical analyses: there is always a finite chance that a particular framboid size-frequency distribution is a result of either syngenetic or diagenetic processes. Including the systematic stereological error in framboid size measurements, the geometric mean size range for syngenetic framboids is 2.9–10.9 μm and that for diagenetic framboids 3.1–20.9 μm. This suggests a significant overlap in geometric mean diameters of framboids from euxinic and non-euxinic environments between ~3 and ~11 μm. Geometric mean framboid diameters within this size range are not robust proxies for paleo-water oxygenation conditions. The origin of the smaller sizes of syngenetic compared with diagenetic framboids appears to be related to the limited time available for framboid crystal growth within the water column. The statistical uncertainty in assigning particular framboid size-frequency distributions to defined oxygenation conditions results mainly from (a) some diagenetic framboids forming over a limited time, thereby also producing smaller framboids and (b) mixtures of syngenetic and diagenetic framboid populations through unavoidable time-averaging of samples. The absence of any significant differences in the sizes of modern and ancient framboids indicates that framboids do not continue to grow over extended time periods: once formed they remain the same over geologic time periods and only change through infilling, overgrowth and recrystallization. The result is that ancient framboids may sample the contemporary paleoenvironment in the sedimentary system in which they are found.

Rincón-Molina, C.I., Hernández-García, J.A., Rincón-Rosales, R., Gutiérrez-Miceli, F.A., Ramírez-Villanueva, D.A., González-Terreros, E., Peña-Ocaña, B.A., Palomeque-Domínguez, H., Dendooven, L., Ruíz-Valdiviezo, V.M., 2019. Structure and diversity of the bacterial communities in the acid and thermophilic crater-lake of the volcano “El Chichón”, Mexico. Geomicrobiology Journal 36, 97-109.

https://doi.org/10.1080/01490451.2018.1509158

El Chichón is an active volcano located in the Chiapas Volcanic Arc characterized by high temperatures, low pH, and large heavy metal concentrations. High temperatures are known to affect microorganisms, so the bacterial community structure was investigated in crater-lake sediment at a ‘low’ 50 °C and a ‘high’ 92 °C by sequencing the 16S rRNA bacterial gene. Most metal concentrations, and bacterial richness, and diversity indexes were higher at 50 °C than at 92 °C. Fifteen phyla were found in the sediment at 50 °C dominated by Actinobacteria (33.1%), Proteobacteria (29.1%) and Acidobacteria (20.1%). Nine phyla dominated by Firmicutes (52.7%, mostly Alicyclobacillus and Sulfobacillus) and Proteobacteria (44.8%, mostly Bradyrhizobium, Methylobacterium, Sediminibacterium) were detected in the sediment at 92 °C. The predictive functional profiling indicated metabolic pathways related to amino acid metabolism, membrane transport, replication, and repair as the most important. It was found that although a large number of bacterial groups were well adapted to 92 °C, the higher temperature reduced strongly, the bacterial diversity and species richness in the El Chichón volcano crater-lake system, and altered the bacterial community structure and their functionality.

Rios Mendoza, L.M., Balcer, M., 2019. Microplastics in freshwater environments: A review of quantification assessment. TrAC Trends in Analytical Chemistry 113, 402-408.


Microplastic (MP) studies in freshwater environments are gaining attention due to the huge quantities of plastic particles reported from lakes and rivers and the potential for negative impacts in these environments. Different units have been used to report MP densities, which makes it difficult to compare data and can result in reports of extremely high concentrations that do not reflect the original sample size. We recommended that the density of MPs from bulk samples be reported as number L−1, while density from net samples should be reported as number m−3. If the density of MPs from net samples is expressed on an areal basis, values should be reported as number/1000 m2, and not as number km−2. Spectroscopy (ATR-μFT-IR and μRAMAN) and Pyrolysis-Gas Chromatography coupled to Mass Spectrometry are techniques that could be used for quantitative identification of the various types of polymers in MP particles.

Rishworth, G.M., Edwards, M.J.K., Cónsole-Gonella, C., Perissinotto, R., 2019. Modern active microbialite-metazoan relationships in peritidal systems on the Eastern Cape coast of South Africa: Ecological significance and implication for the palaeontological record. Journal of African Earth Sciences 153, 1-8.


Modern microbialites are useful partial analogues of their ancient counterparts and especially can provide clues on the conditions to which they were once exposed to. One of the conundrums which has been slow to solve is the role that grazing and burrowing metazoans had towards disrupting the Phanerozoic microbial mats that formed microbialites, especially those of the laminar variety,

stromatolites. Here we use a modern occurrence where rare active microbialites along the southern African coastline are forming in direct association with a metazoan community. We show that these associations demonstrate clear evidence of burrows and trace marks from the metazoans, reflecting direct occupation of the microbialite matrix by some taxa. Importantly, these permanent burrows appear to form (mostly) without disruption to the microbialite consolidation, but rather are constructed along the same axis of that of the microbialite. Furthermore, stromatolitic layering is also observed in direct association with active metazoans. This provides further evidence for the refugia hypothesis which suggests that under certain conditions metazoans are not necessarily restrictive of microbialite integrity. This is explained by the selective forces acting against the destructive influence of metazoans because of the refugia benefits (oxygen, predation, exposure) that they accrue from this habitat. This calls for a reinterpretation of some palaeontological observations.

Robert, J., McGuire, C.C., Nagel, S., Lawrence, B.P., Andino, F.D.J., 2019. Developmental exposure to chemicals associated with unconventional oil and gas extraction alters immune homeostasis and viral immunity of the amphibian Xenopus. Science of The Total Environment 671, 644-654.


Although aquatic vertebrates and humans are increasingly exposed to water pollutants associated with unconventional oil and gas extraction (UOG), the long-term effects of these pollutants on immunity remains unclear. We have established the amphibian Xenopus laevis and the ranavirus Frog Virus 3 (FV3) as a reliable and sensitive model for evaluating the effects of waterborne pollutants. X. laevis tadpoles were exposed to a mixture of equimass amount of UOG chemicals with endocrine disrupting activity (0.1 and 1.0 μg/L) for 3 weeks, and then long-term effects on immune function at steady state and following viral (FV3) infection was assessed after metamorphosis. Notably, developmental exposure to the mixture of UOG chemicals at the tadpole stage affected metamorphic development and fitness by significantly decreasing body mass after metamorphosis completion. Furthermore, developmental exposure to UOGs resulted in perturbation of immune homeostasis in adult frogs, as indicated by significantly decreased number of splenic innate leukocytes, B and T lymphocytes; and a weakened antiviral immune response leading to increased viral load during infection by the ranavirus FV3. These findings suggest that mixture of UOG-associated waterborne endocrine disruptors at low but environmentally–relevant levels have the potential to induce long-lasting alterations of immune function and antiviral immunity in aquatic vertebrates and ultimately human populations.

Roberts, J.J., Leplastrier, A., Feitz, A.J., Shipton, Z.K., Bell, A.F., Karolytė, R., 2019. Structural controls on the location and distribution of CO2 emission at a natural CO2 spring in Daylesford, Australia. International Journal of Greenhouse Gas Control 84, 36-46.


Secure storage of CO2 is imperative for carbon capture and storage technology, and relies on a thorough understanding of the mechanisms of CO2 retention and leakage. Observations at CO2 seeps around the world find that geological structures at a local and regional scale control the location, distribution and style of CO2 emission. Bedrock-hosted natural CO2 seepage is found in the Daylesford region in Victoria, Australia, where many natural springs contain high concentrations of dissolved CO2. Within a few meters of the natural Tipperary Mineral Spring, small CO2 bubble streams are emitted from bedrock into an ephemeral creek. We examine the relationship between structures in the exposed adjacent outcropping rocks and characteristics of CO2 gas leakage in the stream, including CO2 flux and the distribution of gas emissions. We find that degassing is clustered within ˜1 m of a shale-sandstone geological contact. CO2 emission points are localised along bedding

and fracture planes, and concentrated where these features intersect. The bubble streams were intermittent, which posed difficulties in quantifying total emitted CO2. Counterintuitively, the number of bubble streams and CO2 flux was greatest from shale dominated rather than the sandstone dominated features, which forms the regional aquifer. Shallow processes must be increasing the shale permeability, thus influencing the CO2 flow pathway and emission locations. CO2 seepage is not limited to the pool; leakage was detected in subaerial rock exposures, at the intersection of bedding and orthogonal fractures. These insights show the range of spatial scales of the geological features that control CO2 flow. Microscale features and near surface processes can have significant effect on the style and location and rates of CO2 leakage. The intermittency of the bubble streams highlights challenges around characterising and monitoring CO2 stores where seepage is spatially and temporally variable. CCS monitoring programmes must therefore be informed by understanding of shallow crustal processes and not simply the processes and pathways governing CO2 fluid flow at depth. Understanding how the CO2 fluids leaked by deep pathways might be affected by shallow processes will inform the design of appropriate monitoring tools and monitoring locations.

Robertson, A.D., Paustian, K., Ogle, S., Wallenstein, M.D., Lugato, E., Cotrufo, M.F., 2019. Unifying soil organic matter formation and persistence frameworks: the MEMS model. Biogeosciences 16, 1225-1248.


Soil organic matter (SOM) dynamics in ecosystem-scale biogeochemical models have traditionally been simulated as immeasurable fluxes between conceptually defined pools. This greatly limits how empirical data can be used to improve model performance and reduce the uncertainty associated with their predictions of carbon (C) cycling. Recent advances in our understanding of the biogeochemical processes that govern SOM formation and persistence demand a new mathematical model with a structure built around key mechanisms and biogeochemically relevant pools. Here, we present one approach that aims to address this need. Our new model (MEMS v1.0) is developed from the Microbial Efficiency-Matrix Stabilization framework, which emphasizes the importance of linking the chemistry of organic matter inputs with efficiency of microbial processing and ultimately with the soil mineral matrix, when studying SOM formation and stabilization. Building on this framework, MEMS v1.0 is also capable of simulating the concept of C saturation and represents decomposition processes and mechanisms of physico-chemical stabilization to define SOM formation into four primary fractions. After describing the model in detail, we optimize four key parameters identified through a variance-based sensitivity analysis. Optimization employed soil fractionation data from 154 sites with diverse environmental conditions, directly equating mineral-associated organic matter and particulate organic matter fractions with corresponding model pools. Finally, model performance was evaluated using total topsoil (0–20 cm) C data from 8192 forest and grassland sites across Europe. Despite the relative simplicity of the model, it was able to accurately capture general trends in soil C stocks across extensive gradients of temperature, precipitation, annual C inputs and soil texture. The novel approach that MEMS v1.0 takes to simulate SOM dynamics has the potential to improve our forecasts of how soils respond to management and environmental perturbation. Ensuring these forecasts are accurate is key to effectively informing policy that can address the sustainability of ecosystem services and help mitigate climate change.

Rochman, C.M., Brookson, C., Bikker, J., Djuric, N., Earn, A., Bucci, K., Athey, S., Huntington, A., McIlwraith, H., Munno, K., De Frond, H., Kolomijeca, A., Erdle, L., Grbic, J., Bayoumi, M., Borrelle, S.B., Wu, T., Santoro, S., Werbowski, L.M., Zhu, X., Giles, R.K., Hamilton, B.M., Thaysen, C., Kaura, A., Klasios, N., Ead, L., Kim, J., Sherlock, C., Ho, A., Hung, C., 2019. Rethinking microplastics as a diverse contaminant suite. Environmental Toxicology and Chemistry 38, 703-711.

https://doi.org/10.1002/etc.4371

Microplastics are not microplastics are not microplastics, just like pesticides are not pesticides are not pesticides. “Microplastics,” like other classes of chemical contaminants, is a catch‐all term for a variety of unique chemical compounds. Yet, many scientific publications, policy reports, and media articles present microplastics as if they are simply a single compound or type of material.

Such simple communications have consequences, leading to simplified studies and protocols that may be inadequate to inform us of the sources and fate of microplastics, as well as their biological and ecological implications. For example, studying the fate and effects of one plastic type with a specific shape and size does not tell us the fate and effects of microplastics in general. Moreover, not recognizing the diversity of materials in a microplastics sample may overlook the complexity necessary to inform robust quality analysis and quality control (QA/QC) needed in sampling and analytical measurement techniques. For instance, some methods are better at recovering specific sizes, shapes, or types of microplastics.

Simplifying microplastics as a single compound has also led to confusion around the need for new policies and strategies to reduce future emissions of microplastics. For example, some policymakers and scientists are under the impression that banning microbeads from rinse‐off personal care products has eliminated future releases of microplastics in general to the environment. In reality, such bans eliminate only one source of the diverse and complex emerging global contaminant suite that is “microplastics.” This can be compared to banning one specific use of a pesticide (e.g., in the home), leaving the market full of other applications of diverse pesticides that need to continue to be assessed for environmental persistence, bioavailability, and toxicity.

In our Focus article, we make the case that it is necessary to rethink microplastics (plastic particles <5 mm in size) and consider them a suite or class of contaminants, in the same way we do for pesticides, trace metals, or flame retardants. Microplastics are diverse; they come from many different product types; incorporate a broad range of sizes, colors, and morphologies; are composed of various polymers; and include a broad array of chemical additives (Figure 1 and Textboxes 1 and 2). This diversity is important to consider, and thinking of them like we do other classes of contaminants may help us advance methods for sampling and analysis and help us better understand the sources from which they enter the environment; their fate in water, sediment, and organisms; their toxicity; and relevant policies for mitigation.



A single domestic dog (Canis familiaris) tooth was recovered from the Mesolithic site of Blick Mead in the Stonehenge landscape. As no human remains were recovered from the site, the dog tooth provides a potential proxy for reconstructing human diet. Previous studies have shown that domestic dogs often have similar δ13C and δ15N values to their human companions. Incremental dentine carbon and nitrogen isotope analysis and bulk enamel carbon, oxygen and strontium isotope analysis were obtained from the tooth to produce a life-history profile of the dog's diet and mobility. The δ13C and δ15N values indicate that there was little variation in the dog's diet between c.2 and 6 months of age. δ15N values range between +7.9 to +8.7‰, (mean +8.5‰), whereas δ13C values range between −21.3 and −20.5‰, (mean −20.9‰). These data suggest that the dog was consuming predominantly terrestrial herbivorous protein, with the possible inclusion of freshwater fish. The enamel 87Sr/86Sr

ratio of 0.70796 can only be obtained from a chalk landscape, such as is found at Blick Mead and elsewhere in southern and southeastern Britain, or basalt terrains which are rare in southern Britain. The enamel δ18O(SMOW) value of 25.7‰ is not consistent with the dog residing at Blick Mead but appropriate contemporaneous data from dogs is currently lacking. The results are thus consistent with the dog originating in a chalk or possibly basaltic terrain elsewhere in Britain and Ireland or that the dog resided locally at a time when the climate was colder than present.

Rogers, K.L., Bosman, S.H., Lardie-Gaylord, M., McNichol, A., Rosenheim, B.E., Montoya, J.P., Chanton, J.P., 2019. Petrocarbon evolution: Ramped pyrolysis/oxidation and isotopic studies of contaminated oil sediments from the Deepwater Horizon oil spill in the Gulf of Mexico. PLOS ONE 14, Article e0212433.

https://doi.org/10.1371/journal.pone.0212433

Hydrocarbons released during the Deepwater Horizon (DWH) oil spill weathered due to exposure to oxygen, light, and microbes. During weathering, the hydrocarbons’ reactivity and lability was altered, but it remained identifiable as “petrocarbon” due to its retention of the distinctive isotope signatures (14C and 13C) of petroleum. Relative to the initial estimates of the quantity of oil-residue deposited in Gulf sediments based on 2010–2011 data, the overall coverage and quantity of the fossil carbon on the seafloor has been attenuated. To analyze recovery of oil contaminated deep-sea sediments in the northern Gulf of Mexico we tracked the carbon isotopic composition (13C and 14C, radiocarbon) of bulk sedimentary organic carbon through time at 4 sites. Using ramped pyrolysis/oxidation, we determined the thermochemical stability of sediment organic matter at 5 sites, two of these in time series. There were clear differences between crude oil (which decomposed at a lower temperature during ramped oxidation), natural hydrocarbon seep sediment (decomposing at a higher temperature; Δ14C = -912‰) and our control site (decomposing at a moderate temperature; Δ14C = -189‰), in both the stability (ability to withstand ramped temperatures in oxic conditions) and carbon isotope signatures. We observed recovery toward our control site bulk Δ14C composition at sites further from the wellhead in ~4 years, whereas sites in closer proximity had longer recovery times. The thermographs also indicated temporal changes in the composition of contaminated sediment, with shifts towards higher temperature CO2 evolution over time at a site near the wellhead, and loss of higher temperature CO2 peaks at a more distant site.

Rojas-Jimenez, K., Rieck, A., Wurzbacher, C., Jürgens, K., Labrenz, M., Grossart, H.-P., 2019. A salinity threshold separating fungal communities in the Baltic Sea. Frontiers in Microbiology 10, 680. doi: 610.3389/fmicb.2019.00680.


Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world’s largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of

Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.

Román, S., Ortiz-Álvarez, R., Romano, C., Casamayor, E.O., Martin, D., 2019. Microbial community structure and functionality in the deep sea floor: Evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain). Frontiers in Marine Science 6, 108. doi: 110.3389/fmars.2019.00108.

https://www.frontiersin.org/article/10.3389/fmars.2019.00108

Understanding community assembly and processes driving diversity in deep-sea environments is a major challenge in marine microbial ecology. The deep sea represents the largest ecosystem on Earth, but its remoteness makes the microbial community composition and functionality largely unknown. Moreover, microbial-focused studies comparing different deep-sea habitats like dynamic submarine canyons and slope ecosystems altogether are rare. The present work aims to study the deep-sea seafloor microbial communities (Bacteria and Archaea) of the Blanes Canyon and its adjacent western open slope (NW Mediterranean) at ca. 1500 m deep, in autumn and spring, and along the vertical sediment profile. Microbial assemblages were studied in terms of abundance, diversity (α and β), community structure and functional potential through 16S rRNA tag-sequencing to assess their adaptations to the canyon’s idiosyncrasy. Furthermore, the relationships of microbes with environmental variables and a potential predator (nematodes) were also assessed. We observed overall marked differences between canyon and open slope microbial assemblages, although their phyla composition was similar. Both the dominant and richest phyla showed significant differences in proportion between canyon and slope. Bacterial diversity was higher in the canyon than in the open slope, together with nematode abundances. Microbial assemblages were more heterogeneous and showed a higher temporal variability in the canyon than in the open slope. Microbial abundances along the vertical sediment profile showed high heterogeneity in the canyon while on the slope consistently decreased with depth. Nematode and microbial abundances were correlated in the more stable slope environments, while in the canyon phytodetritics inputs (Chl a and Chl a: phaeo) and organic carbon seem to play a role in controlling microbial diversity and abundance. Grain size was correlated with microbial abundances and explained part of the variability in the community structure. Predicted functional profiles differed per habitat and sediment layer, and specific metabolisms appear to be distinctively enhanced, such as aerobic pathways in the most superficial sediment layers in the canyon. Overall, we observed specific patterns of nutrient inputs, microbial composition, and predicted functionality, which may affect higher trophic levels (i.e, Meiofaunal nematodes). This study highlights the importance of canyon heterogeneity in shaping microbial communities.



Greenhouse gas (GHG) emissions of carbon dioxide (CO2) and methane (CH4) from streambeds are currently understudied. There is a paucity of research exploring organic matter (OM) controls on GHG production by microbial metabolic activity in streambeds, which is a major knowledge gap given the increased inputs of allochthonous carbon to streams, especially in agricultural catchments. This study aims to contribute to closing this knowledge gap by quantifying how contrasting OM contents in different sediments affect streambed GHG production and associated microbial metabolic

activity. We demonstrate, by means of an incubation experiment, that streambed sediments have the potential to produce substantial amounts of GHG, controlled by sediment OM quantity and quality. We observed streambed CO2 production rates that can account for 35% of total stream evasion estimated in previous studies, ranging between 1.4 and 86% under optimal conditions. Methane production varied stronger than CO2 between different geologic backgrounds, suggesting OM quality controls between streambed sediments. Moreover, our results indicate that streambed sediments may produce much more CO2 than quantified to date, depending on the quantity and quality of the organic matter, which has direct implications for global estimates of C fluxes in stream ecosystems.



In some previous studies, the ratio between a di-unsaturated highly branched isoprenoid (HBI) lipid termed IPSO25 and a structurally related tri-unsaturated counterpart (HBI III) (IPSO25/HBI III) has been used as a proxy measure of variable sea ice cover in the Antarctic owing to their production by certain sea ice algae and open water diatoms, respectively. To investigate this further, we quantified selected lipids and their photo- and autoxidation products in samples of suspended particulate matter (SPM) collected at different water depths in the polynya region west of the Dalton Iceberg Tongue (East Antarctica). The results obtained confirm the high efficiency of photo- and autoxidation processes in diatoms from the region. The systematic increase of the ratio IPSO25/HBI III with water depth in the current samples appeared to be dependent on the sampling site and was due to both (i) a relatively higher contribution of ice algae to the deeper samples resulting from their increased aggregation and therefore higher sinking rate, or (ii) a stronger abiotic degradation of HBI III during settling through the water column. Analyses of samples taken from the water-sediment interface and some underlying near-surface sediments revealed a further increase of the ratio IPSO25/HBI III, indicative of further differential oxidation of the more unsaturated HBI. Unfortunately, specific oxidation products of HBI III could not be detected in the strongly oxidized SPM and sediment samples, likely due to their lability towards further oxidation. In contrast, oxidation products of HBI III were detected in weakly oxidized samples of phytoplanktonic cells collected from Commonwealth Bay (also East Antarctica), thus providing more direct evidence for the involvement of photo- and/or autoxidation of HBI III in the region. This oxidative alteration of the ratio IPSO25/HBI III between their source and sedimentary environments might need to be considered more carefully when using this parameter for palaeo sea ice reconstruction purposes in the Antarctic.


https://doi.org/10.1130/G45812.1

The snowball Earth hypothesis proposes that if polar ice sheets were to advance equatorward of a mid-latitude threshold, runaway ice-albedo effects would lead to a stable, globally ice-covered climate state that would require extremely high atmospheric pCO2 levels (supplied by volcanic degassing over millions of years) for deglaciation. Geologic evidence, including globally distributed and low-latitude glacial deposits, suggests that two such global glaciations occurred during the Neoproterozoic. We model the coupled carbon and silica cycles through a snowball Earth event, including the extremely high pCO2 and dramatically accelerated chemical weathering of its aftermath. The enhanced delivery of dissolved weathering products to the ocean induces elevated sedimentary

burial of CaCO3 (deposited as “cap carbonates”) and SiO2. Uncertainty in the relative importance of carbonate versus silicate weathering allows a wide range of possible CaCO3 burial magnitude, potentially dwarfing that of SiO2. However, total SiO2 burial is insensitive to weathering strengths, and is set by the amount of CO2 required for deglaciation (∼1019 mol). Chert associated with Marinoan post-glacial cap carbonates in Africa and Mongolia corroborate modeled predictions of elevated SiO2 burial.

Roopnarine, P.D., Angielczyk, K.D., Weik, A., Dineen, A., 2019. Ecological persistence, incumbency and reorganization in the Karoo Basin during the Permian-Triassic transition. Earth-Science Reviews 189, 244-263.


The geological persistence of biotic assemblages and their reorganization or destruction by mass extinctions are key features of long-term macroevolutionary and macroecological patterns in the fossil record. These events affected biotic history disproportionately and left permanent imprints on global biodiversity. Here we hypothesize that the geological persistence and incumbency of paleocommunities and taxa are maintained by patterns of biotic interactions that favour the ecological persistence and stable coexistence of interacting species. Equally complex communities produced by alternative macroevolutionary histories, and hence of different functional structure, may support less stable species coexistence, and are therefore less persistent. However, alternative communities with the same functional structure as a persistent paleocommunity, but variable clade richnesses, tend to be as or more stable than observed palecommunities, thus demonstrating that geological persistence is not the result of constrained patterns, or ecological locking. Numerically modeled food webs for seven tetrapod-dominated paleocommunities spanning the traditionally-recognized Permian-Triassic boundary in the Karoo Basin of South Africa, show that incumbency before the Permian-Triassic mass extinction was maintained by a dynamically stable, community-level system of biotic interactions, thereby supporting the hypothesis. The system's structure was lost through successive extinction pulses, and replaced initially by a rich but geologically ephemeral Early Triassic fauna, which itself was replaced by a novel Middle Triassic community with renewed incumbency. The loss of persistence and incumbency, therefore, did not result simply from the extinction of species; instead the largest declines were accompanied by the addition of new species to the system in the earliest aftermath of the event. We therefore further hypothesize that ecological reorganization and evolutionary innovation in the wake of mass extinctions play key roles in the destruction of highly stable, preexisting systems of biotic interaction. In the case of the Karoo Basin paleocommunities, we estimate that a return to stable interactions, and thus incumbency, was achieved in approximately 4–17 Ma.

Roose, A., Toubin, C., Dusanter, S., Riffault, V., Duflot, D., 2019. Classical molecular dynamics study of small-chain carboxylic acid aerosol particles. ACS Earth and Space Chemistry 3, 380-389.


The growth of small valeric (pentanoic) and glutaric (pentanedioic) acid aerosol particles from 20 to 500 molecules has been investigated at room temperature using classical molecular dynamics simulations. As a result of a higher propensity to form hydrogen bonds, glutaric acid aggregates are shown to be denser than their valeric counterpart. The addition of water molecules with water/acid ratios of 1:1 and 2:1 has then been studied in the case of the diacid. At a low water content, water primarily forms small islands on the surface. When the amount of water increases, it penetrates deeper into the aggregate but a significant fraction remains at the surface. A Connolly surface

analysis reveals that the surface is mostly covered by hydrogen atoms from CH2 groups, with acidic hydrogens being saturated and not available at the surface, for both dry and wet particles. These atomic distributions could impact the reactivity of such particles with gas-phase oxidants and the uptake of trace gases.



Marine short-lived halogenated compounds, emitted from algae, phytoplankton, and other marine biota, significantly affect both the troposphere and the stratosphere. Here, we show that such compounds might also be photochemically produced through photosensitized reactions in surface water. Gas-phase products were detected and identified by high-resolution mass spectrometry, more particularly by means of an atmospheric pressure chemical ionization source coupled to an Orbitrap mass spectrometer. Under simulated solar irradiation, halogenated organic compounds were produced and detected in the gas phase when a proxy of dissolved organic matter, i.e., 4-benzoylbenzoic acid, was excited into its triplet state. We present a mechanism explaining the formation of a variety of such halogenated compounds. These photochemical reactions take place at the air/sea interface and are, therefore, a potential source of short-lived halogenated compounds in the atmosphere, participating in the tropospheric halogen cycle.

Roy, P.S., Ryu, C., Dong, S.K., Park, C.S., 2019. Development of a natural gas methane number prediction model. Fuel 246, 204-211.


The methane number (MN) of natural gas is predicted using mathematical modeling and machine learning techniques which can be incorporated into a sensor. Natural gas quality is known to vary seasonally and regionally depending on the geological region. MN is defined by the gas composition and also related to the knocking resistance in a natural gas engine. This article presents the results of two different methods to predict MN, which are Multiple Regression (MR) and Support Vector Regression (SVR) that can be further specified by three kernel types: linear, polynomial, and Gaussian distributions. The analysis of the 4 methods - MR, linear SVR, polynomial SVR, and Gaussian SVR - shows that each predicts MN with a root mean square error of ±1.06, ±1.08, ±0.54, and ±0.20 respectively. About 37% of the predictions made by MR are under the ±0.5 error range. 40% of linear SVR, 52% of polynomial SVR, and 98% of Gaussian SVR predictions are within the ±0.5 error range. The SVR using Gaussian kernel outperforms the other three methods in accuracy. The results can enable the technology needed to develop an intelligent sensor that can estimate the MN of natural gas online and in real-time, economically and reliably, overall increasing fuel efficiency and emission performance.

Russell, S.L., 2019. Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis. FEMS Microbiology Letters 366, Article fnz013.

https://dx.doi.org/10.1093/femsle/fnz013

Symbiotic associations between bacteria and eukaryotes exhibit a range of transmission strategies. The rates and distributions of transmission modes have not been thoroughly investigated across associations, despite their consequences on symbiont and host evolution. To address this empirically, I compiled data from the literature on bacteria-multicellular eukaryote associations for which transmission mode data was available. Of the total 528 analyzed symbioses, 21.2% were strictly horizontally transmitted, 36.0% exhibited some form of mixed mode transmission and 42.8% were strictly vertically transmitted. Controlling for phylogenetically independent symbiosis events revealed modes were approximately equally distributed among the 113 independent associations, at 32.1%+/−0.57% horizontal, 37.8%+/−1.4% mixed mode and 31.1%+/−1.3% vertical transmission. Binning symbioses by environment revealed an abundance of vertical transmission on land and a lack of it in aquatic environments. The naturally occurring uneven distribution of taxa among environments prevented controlling for host/symbiont phylogeny. However, the results were robust over a large number of independently evolved associations, suggesting that many vertically transmitted bacteria are capable of mixed mode transmission and barriers exist that reduce the rate of horizontal transmission events. Thus, both the environment type and host/symbiont taxa influence symbiont transmission mode evolution.

Sakran, S., Shehata, A.A., Osman, O., El-Sherbiny, M., 2019. Superposed tectonic regimes in west Beni Suef basin, Nile Valley, Egypt: Implications to source rock maturation and hydrocarbon entrapment. Journal of African Earth Sciences 154, 1-19.


The present study contributes to the knowledge of the structural architecture and kinematic evolution of the West Beni Suef basin, by means of detailed seismic interpretation. This basin is one of several in a NW–SE oriented Early Cretaceous basin system occurring at the northeast corner of the African plate. We used the patterns of growth sedimentation above the limbs of growth folds, and in the downthrows of normal faults as kinematic indictors. Two phases of strike slip tectonics during the Santonian and Campanian–Maastrichtian superposing an Early Cretaceous rifting are verified in this basin. The Santonian and Campanian–Maastrichtian strike slip tectonics are represented by an E–W strike slip fault zone associated with NE growth folds and NW growth normal faults as well as ENE, WNW and E–W strike slip fault segments. The Early Cretaceous rifting facilitates the maturation of the deeper source rocks such as Lower Cretaceous shales of the Kharita Formation. Moreover, the strike slip tectonic events played a major role in the maturation of the shallow depth Cenomanian–Turonian Abu Roash “F” Member through entrapment in a releasing bend at the central part of the study area. The structures associated with the two tectonic regimes include, horsts, normal fault propagation folds and strike slip related anticlines, which formulated the main structural traps in the study area.

Salacup, J.M., Farmer, J.R., Herbert, T.D., Prell, W.L., 2019. Alkenone paleothermometry in coastal settings: Evaluating the potential for highly resolved time series of sea surface temperature. Paleoceanography and Paleoclimatology 34, 164-181.

https://doi.org/10.1029/2018PA003416

Abstract The unsaturation ratios of alkenones have been applied widely to reconstruct pelagic sea surface temperatures (SSTs). However, applications to costal settings have been hampered by the effects of salinity and nutrient dynamics. Here we present a 4.5-year-long record of alkenones in water column particulate organic matter from sites in Narragansett Bay (RI, USA) spanning wide ranges in salinity and nutrients, and a 300-year alkenone record from two Narragansett Bay sediment

cores. Particulate organic matter results suggest that there are two distinct alkenone producing populations. One is a widespread population that blooms in summer (July?September) and displays alkenones typical of Group III producers?the basis for the widely applied marine Uk’37 temperature index. The other population is confined to brackish waters in the Providence River during spring salinity minima and displays alkenone profiles consistent with Group I production—the first detection of Group I in a brackish nonlacustrine environment. The sedimentary alkenone profiles consist of only Group III alkenone distributions, allowing for the reconstruction of a 300-year-long record of Narragansett Bay SST. Comparison of the most recent 100 years of this reconstruction with local and regional instrumental SST records shows excellent agreement, confirming a regional pattern of SST rise in the coastal northeastern United States that exceeds global or hemispheric rates. Group III alkenone production in coastal settings may be common and may open the way to high resolution local and regional SST reconstruction.

Salese, F., Pondrelli, M., Neeseman, A., Schmidt, G., Ori, G.G., 2019. Geological evidence of planet-wide groundwater system on Mars. Journal of Geophysical Research: Planets 124, 374-395.

https://doi.org/10.1029/2018JE005802

Abstract: The scale of groundwater upwelling on Mars, as well as its relation to sedimentary systems, remains an ongoing debate. Several deep craters (basins) in the northern equatorial regions show compelling signs that large amounts of water once existed on Mars at a planet‐wide scale. The presence of water‐formed features, including fluvial Gilbert and sapping deltas fed by sapping valleys, constitute strong evidence of groundwater upwelling resulting in long term standing bodies of water inside the basins. Terrestrial field evidence shows that sapping valleys can occur in basalt bedrock and not only in unconsolidated sediments. A hypothesis that considers the elevation differences between the observed morphologies and the assumed basal groundwater level is presented and described as the “dike‐confined water” model, already present on Earth and introduced for the first time in the Martian geological literature. Only the deepest basins considered in this study, those with bases deeper than −4000 m in elevation below the Mars datum, intercepted the water‐saturated zone and exhibit evidence of groundwater fluctuations. The discovery of these groundwater discharge sites on a planet‐wide scale strongly suggests a link between the putative Martian ocean and various configurations of sedimentary deposits that were formed as a result of groundwater fluctuations during the Hesperian period. This newly recognized evidence of water‐formed features significantly increases the chance that biosignatures could be buried in the sediment. These deep basins (groundwater‐fed lakes) will be of interest to future exploration missions as they might provide evidence of geological conditions suitable for life.

Plain Language Summary: Most previous studies on Mars relevant groundwater have proposed models, but few have looked at the geological evidence of groundwater upwelling in deep closed basins in the northern hemisphere equatorial region. Geological evidence of groundwater upwelling in these deep basins is a key point that will help to validate present‐day models and to better constraint them in the future. Observations in the northern hemisphere show evidence of a planet‐wide groundwater system on Mars. The elevations of these water‐related morphologies in all studied basins lie within the same narrow range of depths below Mars datum and notably coincide with the elevation of some ocean shorelines proposed by previous authors.

Sambamoorthy, G., Sinha, H., Raman, K., 2019. Evolutionary design principles in metabolism. Proceedings of the Royal Society B: Biological Sciences 286, Artcile 20190098.


Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein–protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.


https://doi.org/10.1080/01490451.2018.1497732

The use of biological means for ground improvement have become popular, which generally works through the process called microbially-induced calcium carbonate precipitation (MICP). Many studies indicate successful application of MICP based improvement with multiple bacteria and on several soils. Given the proven performance of MICP, this study aims to examine the MICP process by comparing the calcium carbonate precipitation ability of widely studied bacteria, i.e., Sporosarcina pasteurii and relatively under-recognized bacteria, i.e., Bacillus licheniformis to outline the formation success. For this purpose, two different sands were tested for observing precipitation behavior using a series of syringe tests. Furthermore, the effect of concentration and inclusion of calcium chloride for nutrition of bacteria, saturation with water, and hybrid use of two bacteria were investigated in some tests for diversification. X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive x-ray spectroscopy (EDS) were used for the interpretation of results. Results indicated that Sporosarcina pasteurii had performed superior over Bacillus licheniformis when achieving calcium carbonate precipitation in tests for both sands. In addition, many intriguing SEM images contributed to the literature of MICP monitoring, highlighting the effects of the variables investigated.

Sarma, V.V.S.S., Yadav, K., Behera, S., 2019. Role of eddies on organic matter production and f-ratios in the Bay of Bengal. Marine Chemistry 210, 13-23.


In order to examine the sources of nutrients and f-ratios in the cyclonic (CE) and anticyclonic eddy (ACE), the content and isotopic composition of carbon and nitrogen in suspended particulate organic matter (POM) were analyzed in one CE and two ACEs in the western Bay of Bengal (BoB). Relatively higher concentrations of Chlorophyll-a (Chl-a) and nutrients were observed in the CE and no-eddy (NE) regions than ACE region. Higher concentrations of particulate organic carbon (POC) and nitrogen (PN) were observed in the CE and NE than ACE in the BoB. Isotope mixing model (SIAR) suggested that POM pool mainly consists of marine plankton biomass (~80%) and contribution of terrestrial organic matter is insignificant (<20%). The depth of nitracline was

shallower in the CE due to divergence while it was deeper in the ACEs due to convergence of upper ocean. The isotopic composition of nitrogen in the POM varied between 2.4% and 8.5‰ and relatively lower values were associated with deeper nitracline depth in the ACE and vice versa in the CE. This suggests that upward mixing of subsurface nitrate supported primary production in the CE and regenerated nitrogen in the ACE region. The estimated f-ratios using δ15NPOM and depth of nitracline were almost double in the CE (0.31 ± 0.04) and NE (0.28 ± 0.05) than ACEs (0.19 ± 0.09) in the BoB. Though upward mixing of subsurface low DO water intensified oxygen minimum zone (OMZ) below 75 m in the CE region, enhanced phytoplankton biomass and its export may further intensify. In contrast, convergence of DO rich surface water and low f-ratios in the ACE resulted in weaker OMZ. This study suggests that eddies significantly influence primary and export productions that may lead to modifications in intensity of OMZ in the BoB. >50 eddies form every year in the BoB and its impact on primary and export production leading to intensification/weakening of OMZ should be evaluated using both observations and models.

Schablitsky, J.M., Witt, K.E., Madrigal, J.R., Ellegaard, M.R., Malhi, R.S., Schroeder, H., 2019. Ancient DNA analysis of a nineteenth century tobacco pipe from a Maryland slave quarter. Journal of Archaeological Science 105, 11-18.


Archaeologists often struggle with the challenge of linking historic-period artifact assemblages with specific communities. In particular, small home sites discovered on historic plantations are often difficult to identify as an African American or white tenant house since the material culture appears similar. The discipline also struggles with how to identify the expression of specific West African cultures in their archaeological assemblages. Here, we discuss how DNA was successfully extracted and analyzed from a clay tobacco pipe stem collected from an African American slave quarter in Maryland, USA, and what this information can and cannot reveal about the people present at the site. We successfully identified DNA from a woman, and genome-wide analyses revealed she was closely related to Mende living in present-day Sierra Leone, West Africa. The ability to recover genetic data from personal artifacts now provides archaeologists a viable tool to address questions about communities and ancestral origins. Furthermore, these findings hold the potential to connect living descendants with their ancestors’ homes.

Schieber, J., Miclăuș, C., Seserman, A., Liu, B., Teng, J., 2019. When a mudstone was actually a “sand”: Results of a sedimentological investigation of the bituminous marl formation (Oligocene), Eastern Carpathians of Romania. Sedimentary Geology 384, 12-28.


The bituminous marl formation (BMF) is an important source rock in Romania. At the study location, in the Eastern Carpathians, the BMF composition is dominated by calcite (coccolith debris, cement) and diagenetic silica, with the remainder consisting largely of detrital clays, quartz and minor feldspar. Abundant intervals with soft sediment deformation, likely slump deposits, alternate with thinly layered marls that may locally contain layers and lenses of rippled and cross-laminated sandstone. The latter suggest intermittent action of traction currents. Although the fine grained nature and abundant nanoplankton content of the marls suggest that they originated via pelagic settling through the water column, upon close inspection, they consist of flattened sand-size yet fine-grained aggregates (soft clasts). Experimental studies suggest that these were likely eroded from the seabed and transported in bedload by bottom currents. Inclined fabric elements within marls suggest that soft clasts formed ripples, and that marl layers are the depositional consequence of ripple migration.

Whereas typical marl layers probably reflect migration of small ripples of a few cm’s height, there are also cross-bedded marly beforms with ca. 20 cm pre-compaction relief that by size are muddy megaripples. Unlike in sand, where bedform hierarchy reflects increasing flow velocity, muddy megaripples more likely are a reflection of bottom current systems of substantial duration.

With marl layers as well as interbedded sands recording bottom current activity, the BMF represents a combination of slope processes and bottom current activity. The likely environment of deposition is a lower slope to basin setting with contour currents reworking pelagic sedimentation and intermittent sediment supply by slumping.



Soil denitrification is the most important terrestrial process returning reactive nitrogen to the atmosphere, but remains poorly understood. In upland soils, denitrification occurs in hotspots of enhanced microbial activity, even under well-aerated conditions, and causes harmful emissions of nitric (NO) and nitrous oxide (N2O). Timing and magnitude of such emissions are difficult to predict due to the delicate balance of oxygen (O2) consumption and diffusion in soil. To study how spatial distribution of hotspots affects O2 exchange and denitrification, we embedded porous glass beads inoculated with either Agrobacterium tumefaciens (a denitrifier lacking N2O reductase) or Paracoccus denitrificans (a complete denitrifier) in different architectures (random vs. layered) in sterile sand adjusted to different water saturations (30 %, 60 %, 90 %) and measured gas kinetics (O2, CO2, NO, N2O and N2) at high temporal resolution. Air connectivity, air distance and air tortuosity were determined by X-ray tomography after the experiment. The hotspot architecture exerted strong control on microbial growth and timing of denitrification at low and intermediate saturations, because the separation distance between the microbial hotspots governed local oxygen supply. Electron flow diverted to denitrification in anoxic hotspot centers was low (2–7 %) but increased markedly (17–27 %) at high water saturation. X-ray analysis revealed that the air phase around most of the hotspots remained connected to the headspace even at 90 % saturation, suggesting that the threshold response of denitrification to soil moisture could be ascribed solely to increasing tortuosity of air-filled pores. Our findings suggest that denitrification and its gaseous product stoichiometry do not only depend on the amount of microbial hotspots in aerated soil, but also on their spatial distribution. We demonstrate that combining measurements of microbial activity with quantitative analysis of diffusion lengths using X-ray tomography provides unprecedented insights into physical constraints regulating soil microbial respiration in general and denitrification in particular. This opens new avenues to use observable soil structural attributes to predict denitrification and to parameterize models. Further experiments with natural soil structure, carbon substrates and microbial communities are required to demonstrate this under realistic conditions.

Schneider, A.C., Mutterlose, J., Blumenberg, M., Heimhofer, U., Luppold, F.W., 2019. Palynofacies, micropalaeontology, and source rock evaluation of non-marine Jurassic–Cretaceous boundary deposits from northern Germany - Implications for palaeoenvironment and hydrocarbon potential. Marine and Petroleum Geology 103, 526-548.


The Jurassic–Cretaceous boundary interval of northern Germany is characterised by non-marine deposits attributed to the Purbeck and Wealden facies. These organic-rich sediments were deposited under restricted, brackish-lacustrine conditions in a palaeogeographically isolated basin (Lower Saxony Basin). Rock-Eval and δ13Corg measurements were performed to characterise the composition and distribution of the organic matter, to determine the kerogen type chemically, and to define the quantity and maturity of the organic matter. A strong correlation between the optical characteristics, documented by the palynofacies analysis, and the chemical kerogen analyses have led to a better understanding of the palaeoenvironment and the processes which caused the organic matter enrichment.

The samples studied from the basin center show a high petroleum generation potential, their estimated maturity is close to the onset of oil generation. Total organic carbon (TOC) concentrations of up to 18% have been measured, hydrogen index values reach up to 1185 mg HC/g TOC. The kerogen assemblages in two basinal successions are dominated by granular amorphous organic material (AOM), dinoflagellate cysts, and Botryococcus algae. In a more marginal succession continent-derived debris (phytoclasts, pollen and spores) is dominant. The AOM is interpreted to have originated either from phytoplankton (probably dinoflagellate cysts and Botryococcus), or its bacterial/archaeal degradation products formed under anoxic conditions. TOC-rich samples which are dominated by these amorphous kerogens show the highest petroleum potential, the AOM therefore plays a key role for the petroleum generation.

The long-term climatic and hydrological evolution of the Lower Saxony Basin, which is based on palynomorphs, ostracods, and benthic foraminifera, is here interpreted by a five-stage model. Fluctuations in the salinity of the water bodies are directly reflected by the ratio between different freshwater and brackish-marine organisms as well dinoflagellate cyst diversity; five different cyst morphogroups are used for palaeoenvironmental interpretations. The deposition of TOC-rich beds in the German Wealden can be best explained by both high primary productivity and the establishment of prolonged phases of bottom water anoxia in a brackish-lacustrine depositional environment. Ecological conditions supporting enhanced productivity and preservation of the algal/bacterial-derived organic matter were most favourable during the mid–late Berriasian (Wealden 1–4).

Schocke, L., Bräsen, C., Siebers, B., 2019. Thermoacidophilic Sulfolobus species as source for extremozymes and as novel archaeal platform organisms. Current Opinion in Biotechnology 59, 71-77.


Archaea dominate extreme habitats and possess unique cellular and metabolic properties with novel or modified metabolic pathways and unusual enzymes. Thermoacidophilic Sulfolobus species and their thermo(acido)philic enzymes gained special attention due to their adaptation toward two extremes, high temperature (75–80°C) and low pH (pH 2–5), that matches harsh process conditions in industrial applications. For different Sulfolobus species versatile genetic systems have been established and significant metabolic and physiological information from classical biochemistry and genetic as well as poly-omics and systems biology approaches is available. Their ease of growth under aerobic or microaerophilic conditions and established fermentation technologies gaining high cell yields promote Sulfolobus as source for extremozymes and as valuable novel platform organism for industrial biotechnology.

Schoelmerich, M.C., Müller, V., 2019. Energy conservation by a hydrogenase-dependent chemiosmotic mechanism in an ancient metabolic pathway. Proceedings of the National Academy of Sciences 116, 6329.

http://www.pnas.org/content/116/13/6329.abstract

Significance: Acetogenic bacteria are the most primordial living organisms. They can live solely on inorganic compounds by using carbon monoxide or molecular hydrogen as energy sources to fix carbon dioxide to acetate and rely on a chemiosmotic mechanism for energy conservation. Most microorganisms possess a complex respiratory chain that is composed of many different components to establish the chemiosmotic gradient. Here, we dissect the bioenergetics in a chemolithoautotrophic thermophilic acetogenic bacterium. This living fossil uses a simple respiration comprising only a hydrogenase and an ATP synthase for energy conservation. This two-module respiration system is sufficient to sustain primordial microbial life.

Abstract: The ancient reductive acetyl-CoA pathway is employed by acetogenic bacteria to form acetate from inorganic energy sources. Since the central pathway does not gain net ATP by substrate-level phosphorylation, chemolithoautotrophic growth relies on the additional formation of ATP via a chemiosmotic mechanism. Genome analyses indicated that some acetogens only have an energy-converting, ion-translocating hydrogenase (Ech) as a potential respiratory enzyme. Although the Ech-encoding genes are widely distributed in nature, the proposed function of Ech as an ion-translocating chemiosmotic coupling site has neither been demonstrated in bacteria nor has it been demonstrated that it can be the only energetic coupling sites in microorganisms that depend on a chemiosmotic mechanism for energy conservation. Here, we show that the Ech complex of the thermophilic acetogenic bacterium Thermoanaerobacter kivui is indeed a respiratory enzyme. Experiments with resting cells prepared from T. kivui cultures grown on carbon monoxide (CO) revealed CO oxidation coupled to H2 formation and the generation of a transmembrane electrochemical ion gradient (Δ~µion). Inverted membrane vesicles (IMVs) prepared from CO-grown cells also produced H2 and ATP from CO (via a loosely attached CO dehydrogenase) or a chemical reductant. Finally, we show that Ech activity led to the translocation of both H+ and Na+ across the membrane of the IMVs. The H+ gradient was then used by the ATP synthase for energy conservation. These data demonstrate that the energy-converting hydrogenase in concert with an ATP synthase may be the simplest form of respiration; it combines carbon dioxide fixation with the synthesis of ATP in an ancient pathway.

Schreuder, L.T., Hopmans, E.C., Castañeda, I.S., Schefuß, E., Mulitza, S., Sinninghe Damsté, J.S., Schouten, S., 2019. Late Quaternary biomass burning in Northwest Africa and interactions with climate, vegetation, and humans. Paleoceanography and Paleoclimatology 34, 153-163.

https://doi.org/10.1029/2018PA003467

Biomass burning on the African continent is widespread, and interactions with climate, vegetation dynamics, and biogeochemical cycling are complex. To obtain a better understanding of these complex relationships, African fire history has been widely studied, although mostly on relatively short timescales (i.e., years to kiloyears) and less commonly on long-term scales. Here we present a 192-kyr, continuous biomass-burning record from sub-Saharan Northwest Africa based on the fire biomarker levoglucosan in a marine sediment core offshore Guinea. Notable features of our record include an increase in levoglucosan accumulation at 80 ka and two peaks at 50?60 ka. The event at 80 ka is likely related to an overall increase in sedimentation rates rather than an increase in biomass burning in the Northwest African savanna region. Our record indicates that glacial/interglacial changes in regional climate and vegetation composition (C3 vs. C4 plants) were not a major influence on biomass burning over the last 192 kyr. However, we suggest that the burning events at 50-60 ka

might be caused by increased occurrence of C3 vegetation and human settlement in this region. At this time, the savanna region became wetter and fuel loads likely increased. Therefore, the region was more hospitable for humans, who likely used fire for hunting activities. Collectively, we hypothesize that on longer (glacial/interglacial) timescales, biomass burning, regional climate, and African vegetation are not necessarily coupled, while around 50-60 ka, higher fuel loads and human fire use may have influenced fire occurrence in sub-Saharan Northwest Africa.

Schuster, J.K., Harner, T., Su, K., Eng, A., Wnorowski, A., Charland, J.-P., 2019. Temporal and spatial trends of polycyclic aromatic compounds in air across the Athabasca oil sands region reflect inputs from open pit mining and forest fires. Environmental Science & Technology Letters 6, 178-183.


Results of a passive air monitoring study for polycyclic aromatic compounds (PACs) in the Athabasca oil sands region (AOSR) in Alberta, Canada, are reported. Polyurethane foam disk passive air samplers were deployed for consecutive 2-month periods from November 2010 to January 2016 at 15 sites. Samples were analyzed for polycyclic aromatic hydrocarbons (PAHs), alkylated PAHs (alkPAHs), and dibenzothiophene and its alkylated derivatives (DBTs). Concentrations in air were in the ranges of 0.3–43, 0.15–460, and 0.04–130 ng/m3 for ∑PAHs, ∑alkPAHs, and ∑DBTs, respectively. The increase in the levels of PACs in air at most sites was small but statistically insignificant over this 5-year period, which is consistent with expectations as in situ bitumen extraction techniques have become predominant over open pit mining in the area. Significant increases in PAC levels were observed at a site that is within a few kilometers of open pit mining that expanded over the study period. The 5-year regional trend for PACs in air provides a baseline against which planned future open pit mining projects (e.g., Teck Frontier) can be assessed for impact. Seasonal trends in concentrations in air were observed for more volatile PACs; concentrations in air were higher in winter than in summer. These trends were not observed for less volatile compounds. Two major forest fire episodes from April to July 2011 and during June and July 2015 resulted in greatly elevated levels for PAH and a small subset of alkylated PAHs but not for the majority of alkPAHs and DBTs. Increases in regional PAH concentrations associated with forest fire periods were consistent with estimates based on published emission factors for PAHs for wood combustion. Although forest fires are likely to be an important source of PAH concentrations in air across the AOSR, alkPAHs and DBTs appear to be primarily associated with emissions from oil sands mining operations. Air quality guidelines for alkPAHs and DBTs are still lacking.

Schüth, F., 2019. Making more from methane. Science 363, 1282-1283.


Methane, the major component in natural gas, is one of the most difficult molecules to activate in a controlled manner, because almost any initial oxidation product is easier to oxidize than methane itself and most of the product is carbon dioxide. Instead, methane is currently converted to syngas, a mixture of carbon monoxide and hydrogen, from which many useful products, such as methanol or Fischer-Tropsch hydrocarbons, can be synthesized in subsequent steps. However, syngas production is characterized by severe economies of scale. Economical plants must be very large, such as the so-called “MegaMethanol” plants or the Fischer-Tropsch Pearl complex in Qatar, where the total annual hydrocarbon production exceeds 10 million metric tons (MT). Thus, direct approaches for converting methane to valuable products that are also economical on a smaller scale are of extreme interest. Such processes could rescue so-called stranded natural gas that is produced in too small an amount and is too remote to transport economically. In the worst case, stranded natural gas extracted with other

fossil fuels is burned (“flared”; see the photo). On page 1326 of this issue, Díaz-Urrutia and Ott (1) at the Grillo company report a direct process that converts methane directly to methanesulfonic acid, a chemical with many industrial uses.


https://doi.org/10.1038/s41396-018-0324-5

Petroleum hydrocarbons reach the deep-sea following natural and anthropogenic factors. The process by which they enter deep-sea microbial food webs and impact the biogeochemical cycling of carbon and other elements is unclear. Hydrostatic pressure (HP) is a distinctive parameter of the deep sea, although rarely investigated. Whether HP alone affects the assembly and activity of oil-degrading communities remains to be resolved. Here we have demonstrated that hydrocarbon degradation in deep-sea microbial communities is lower at native HP (10 MPa, about 1000 m below sea surface level) than at ambient pressure. In long-term enrichments, increased HP selectively inhibited obligate hydrocarbon-degraders and downregulated the expression of beta-oxidation-related proteins (i.e., the main hydrocarbon-degradation pathway) resulting in low cell growth and CO2 production. Short-term experiments with HP-adapted synthetic communities confirmed this data, revealing a HP-dependent accumulation of citrate and dihydroxyacetone. Citrate accumulation suggests rates of aerobic oxidation of fatty acids in the TCA cycle were reduced. Dihydroxyacetone is connected to citrate through glycerol metabolism and glycolysis, both upregulated with increased HP. High degradation rates by obligate hydrocarbon-degraders may thus be unfavourable at increased HP, explaining their selective suppression. Through lab-scale cultivation, the present study is the first to highlight a link between impaired cell metabolism and microbial community assembly in hydrocarbon degradation at high HP. Overall, this data indicate that hydrocarbons fate differs substantially in surface waters as compared to deep-sea environments, with in situ low temperature and limited nutrients availability expected to further prolong hydrocarbons persistence at deep sea.

Scorrer, S., Azmy, K., Stouge, S., 2018. Carbon-isotope stratigraphy of the Furongian Berry Head Formation (Port au Port Group) and Tremadocian Watts Bight Formation (St. George Group), western Newfoundland, and the correlative significance. Canadian Journal of Earth Sciences 56, 223-234.


Carbon-isotope stratigraphy of the Furongian (stage 10; Upper Cambrian) and Tremadocian (lowermost Ordovician) reveals distinct variations from the carbonates of the Berry Head and Watts Bight formations of the East Isthmus Bay section that accumulated in a shallow-marine setting on the eastern Laurentian platform in a passive margin setting in western Newfoundland, Canada. The East Isthmus Bay δ13C values show insignificant correlation with their Sr (R2 = 0.04), Mn (R2 = 0.001) and Fe (R2 = 0.02) counterparts, implying preservation of at least near-primary C-isotope compositions. The investigated section is largely fossil poor, but the δ13C profile shows a pattern with distinct variations that can be matched with those of the western Laurentian Lawson Cove Auxiliary Boundary Stratigraphic Section and Point (ASSP) section, Utah, USA. Therefore, it was possible to reconstruct a conodont biozonal scheme by matching the δ13C profile with its counterpart from the Lawson Cove ASSP section. At the base of the East Isthmus Bay section, the δ13C profile exhibits a

broad excursion (the top of the Herllnmaria – Red Tops Boundary), which can be matched with the base of the Eoconodontus Zone (mid-Furongian), followed by an enrichment trend through the Cordylodus intermedius Zone (top Furongian). A positive excursion (Hirsutodontus simplex spike) is recorded in the Cordylodus intermedius Zone (top Cambrian), and a prominent positive peak characteristic for the Cordylodus lindstromi Zone is recorded from the top of the investigated section. The δ13C values of the Newfoundland carbonates are generally ∼1‰ Vienna Pee Dee Belemnite lower than those of Lawson Cove, which is likely attributable to a relatively higher productivity and (or) organic burial in the Utah region.

Sehlke, A., Mirmalek, Z., Burtt, D., Haberle, C.W., Santiago-Materese, D., Kobs Nawotniak, S.E., Hughes, S.S., Garry, W.B., Bramall, N., Brown, A.J., Heldmann, J.L., Lim, D.S.S., 2019. Requirements for portable instrument suites during human scientific exploration of Mars. Astrobiology 19, 401-425.

https://doi.org/10.1089/ast.2018.1841

Human explorers on the surface of Mars will have access to a far wider array of scientific tools than previous crewed planetary exploration missions, but not every tool will be compatible with the restrictions of this exploration. Spectrometers on flyby, orbital, and landed missions are currently used to determine the composition and mineralogy of geological materials of various types and sizes, from small fragments to celestial bodies in the solar system. Handheld spectrometers that are capable of in situ analyses are already used for geological exploration on Earth; however, their usefulness for human exploration missions and how data from multiple handheld instruments could be combined to enhance scientific return must be further evaluated. As part of the Biologic Analog Science Associated with Lava Terrains (BASALT) research project, we incorporated two handheld instruments, a visible-near infrared spectrometer and an X-Ray Fluorescence spectrometer, into simulated Mars exploration missions conducted on basaltic terrains in Idaho and Hawai'i. To understand the data quality provided by these handheld spectrometers, we evaluated their performance under varying conditions of measurement time, distance, angle, atmosphere, and sample matrix, and we compared data quality between handheld instruments and laboratory techniques. Here, we summarize these findings, provide guidelines and requirements on how to effectively incorporate these instruments into human exploration missions to Mars, and posit that future iterations of these instruments will be beneficial for enhancing science returned from human exploration missions.

Sehnal, L., Procházková, T., Smutná, M., Kohoutek, J., Lepšová-Skácelová, O., Hilscherová, K., 2019. Widespread occurrence of retinoids in water bodies associated with cyanobacterial blooms dominated by diverse species. Water Research 156, 136-147.


Cyanobacterial blooms represent a worldwide problem in freshwater as well as marine ecosystems as producers of various toxic compounds. This study provides environmentally important information about the common presence of mixtures of retinoids in various water bodies associated with the occurrence of cyanobacterial blooms dominated by many different species. The study documents, for the first time, that retinoids are produced by environmental cyanobacterial blooms dominated by species belonging to different genera such as Microcystis, Dolichospermum, Planktothrix, Woronichinia, Pseudanabaena and others. Samples of biomass of cyanobacterial blooms and their surrounding water were collected from seventeen independent freshwater bodies across the Czech Republic during summer 2015. Retinoid-like activity was detected by an in vitro reporter gene bioassay in water samples from 8 out of 17 localities with a maximal activity of 263 ng all-trans

retinoic acid equivalent (REQ)/L. In comparison, in vitro assessment of biomass extracts documented retinoid-like activity at 11 out of 17 localities with a maximal retinoid-like activity of 867 ng REQ/g dry mass (dm). Individual retinoids were detected by chemical analyses in all water samples and in 16 out of 17 biomass samples with 4keto-retinal and all-trans 5,6epoxy retinoic acid being detected in aquatic ecosystems for the first time. Further, all-trans 4keto retinoic acid and retinal were the most commonly detected compounds in both types of samples. With respect to retinoid-like activity, a large proportion was explained in some samples by contributions of individual detected retinoids calculated from their concentrations and relative potencies. However, results also indicate that other unknown compounds with a retinoic acid receptor-mediated mode of action were present. The revealed widespread production of retinoids by cyanobacterial blooms dominated by diverse species across various aquatic ecosystems and their common presence in both biomass and surrounding water raises concern namely because some retinoids belong to the most potent teratogens. These compounds need to be taken into consideration in the assessment of risks associated with massive cyanobacterial blooms.

Seibert, M.A., Lim, D.S.S., Miller, M.J., Santiago-Materese, D., Downs, M.T., 2019. Developing future deep-space telecommunication architectures: A historical look at the benefits of analog research on the development of solar system internetworking for future human spaceflight. Astrobiology 19, 462-477.

https://doi.org/10.1089/ast.2018.1915

Exploration analog field tests, missions, and deployments enable the integration and validation of new and experimental concepts and/or technologies through strategic experimental design. The results of these operations often create new capabilities for exploration and increase confidence in, and credibility of, emerging technologies, usually at very low cost and risk to the test subjects involved. While these experiments resemble missions 10–30 years into the future, insights obtained are often of immediate value. Knowledge gained in the field translates into strategic planning data to assist long-range exploration planners, and planners influence the experimental design of field deployments, creating a synergistic relationship. The Biologic Analog Science Associated with Lava Terrains (BASALT) communication architecture is a high-fidelity analog program that emulates conditions impacting future explorers on the martian surface. This article provides (1) a brief historical review of past analog operations that deliberately used elements of a flight-like telecommunication infrastructure to add fidelity to the test, (2) samples of the accomplishments made through analog operations, and (3) potentially significant deep-space telecommunication insights gained from the BASALT program in support of future extravehicular activity exploration of Mars. This article is paired with and complements Miller et al. in this issue which focuses on the telecommunication infrastructure utilized by the BASALT team during the field deployment.

Seo, S., Mastiani, M., Hafez, M., Kunkel, G., Ghattas Asfour, C., Garcia-Ocampo, K.I., Linares, N., Saldana, C., Yang, K., Kim, M., 2019. Injection of in-situ generated CO2 microbubbles into deep saline aquifers for enhanced carbon sequestration. International Journal of Greenhouse Gas Control 83, 256-264.


Carbon sequestration into deep saline aquifers has been considered a promising technology for mitigating heavy atmospheric carbon dioxide (CO2 ) concentration. When gaseous CO2 is continuously injected into these aquifers, resident brine near a wellbore area is rapidly evaporated while precipitating significant amounts of salt at pores, thereby damaging the aquifer media

unfavorable for subsequent CO2 injection. In addition, the continuous injection of CO2 at a large volume significantly hinders dissolution of CO2 into brine. In this study, we propose a new method of sequential water injection with gaseous CO2 for in-situ generation of micro-sized CO2 bubbles that minimizes the brine drying-out and simultaneously accelerates CO2 dissolution. We observed that, with this method, a partial volume of CO2 dissolves effectively into the co-injected water during pumping, thereby decreasing the rate of brine drying-out at pores. Another benefit of sequential injection is the significantly increased rate of CO2 hydration induced by the large surface-to-volume ratio of tiny bubbles at micro to nanoscale. To further accelerate CO2 hydration, we investigated reactive dynamics of bubble-driven CO2 hydration at different frequencies of sequential injection and pH levels of the solution. Operation at a higher frequency with higher basicity proved to be the most effective in decreasing the bubble size and therefore accelerating CO2 hydration into brine, which is a more feasible CO2 storage plan.



Production from offshore reservoirs has contributed significantly to supply required hydrocarbons in the past several decades. The world's ever-growing energy demand has made the industry extend exploration and production activities to much deeper waters and harsher offshore environments. However, development of offshore reservoirs is a challenging task, and the role of efficient and reliable reservoir characterization tools in successful offshore developments cannot be overstated. Reservoir analysis in terms of determination of the properties of rock and fluids and their interactions constitutes a major part of reservoir characterization. Traditionally, laboratory tests and measurements are considered the most reliable characterization approach. However, in many cases, reservoir rock and fluid samples might be unavailable or insufficient for all the required tests and measurements. Empirical correlations and theoretical relationships can be employed in the absence of or to augment experimental data. However, characteristic predictions obtained from this deterministic strategy can be highly uncertain due to sensitivity to the property ranges, oversimplifying assumptions, and local variations of properties in heterogeneous reservoirs. Various forms of connectionist techniques have recently been used as an alternative method for property predictions with higher accuracy and reliability. Yet, their applications have been mostly limited to research studies rather than industrial projects. Recently, Molecular Dynamics (MD) simulations have gained considerable attention in studying reservoir rock and fluid properties, interactions, and associated phenomena at the atomic level. In MD, the properties of interest are extracted from the analysis of time evolution of atomic positions and velocities by numerical solution of Newtonian equations for the motion of all the atoms in the system. This technique facilitates performing “computer experiments” that may otherwise be impossible, extremely costly, or very dangerous to conduct. In this paper, the MD simulation technique and its applications to investigate rock and fluid properties are reviewed. The MD theoretical concepts and procedures are addressed, particularly in reservoir analysis. The main advantages and disadvantages of MD are listed. This review manuscript will provide useful guidelines to characterize the reservoir rock and fluid and their behaviours in various petroleum reserves, which considerably help to conduct better design and optimal operation of production plants.

Shan, X., Du, S., Guo, X., 2019. Characteristics and evaluation of the high-quality source rocks of Cretaceous continental shale oil in Tonghua Basin, China. Acta Geologica Sinica - English Edition 93, 146-154.

https://doi.org/10.1111/1755-6724.13771

The presence of shale oil in the Cretaceous Hengtongshan Formation in the Tonghua Basin, drilled by the well TD-01, has been discussed in this geological investigation for the first time. To evaluate the high-quality source rocks of Cretaceous continental shale oil, the distribution characteristics and the evolution of the ancient environment, samples of shale were systematically analyzed in terms of sedimentary facies, organic geochemistry, and organic carbon isotopic composition. The results demonstrate that a TOC value of 1.5% represents the lower-limit TOC value of the high-quality source rocks. Source rocks have an aggregate thickness of 211 m and contain abundant organic matter, with TOC values of 2.69% on average and a maximum value over 5.44%. The original hydrocarbon-generative potential value (S1+S2) is between 0.18 mg/g and 6.13 mg/g, and the Ro is between 0.97% and 1.40%. The thermal maturation of the source rocks is relatively mature to highly mature. The δ13C value range is between –34.75‰ and –26.53‰. The ratio of saturated hydrocarbons to aromatic hydrocarbons is 1.55 to 5.24, with an average of 2.85, which is greater than 1.6. The organic types are mainly type II1, followed by type I. The organic carbon source was C3 plants and hydrophytes. The paleoclimate of the Hengtongshan Formation can be characterized as hot and dry to humid, and these conditions were conducive to the development of high-quality source rocks. A favorable paleoenvironment and abundant organic carbon sources provide a solid hydrocarbon generation base for the formation and accumulation of oil and gas in the shale of the Tonghua Basin.

Shang, N., Ding, M., Dai, M., Si, H., Li, S., Zhao, G., 2019. Biodegradation of malachite green by an endophytic bacterium Klebsiella aerogenes S27 involving a novel oxidoreductase. Applied Microbiology and Biotechnology 103, 2141-2153.

https://doi.org/10.1007/s00253-018-09583-0

Endophytic microorganisms can metabolize organic contaminants and assist in plant growth, thus facilitating the phytoremediation of polluted environments. An endophytic bacterium capable of decoloring malachite green (MG) was isolated from the leaves of the wetland plant Suaeda salsa and was identified as Klebsiella aerogenes S27. Complete decolorization of MG (100 mg/l) was achieved in 8 h at 30 °C and pH 7.0. Ultraviolet-visible spectroscopy and Fourier-transform infrared spectroscopy analyses indicated the degradation of MG by the isolate. The enzymic assays of the strain showed the triphenylmethane reductase (TMR) activity. A gene encoding putative TMR-like protein (named as KaTMR) was cloned and heterologously expressed in Escherichia coli. KaTMR showed only 42.6–43.3% identities in amino acids compared with well-studied TMRs, and it phylogenetically formed a new branch in the family of TMRs. The degraded metabolites by recombinant KaTMR were detected by liquid chromatography-mass spectrometry, showing differences from the products of reported TMRs. The biotransformation pathway of MG was proposed. Phytotoxicity studies revealed the less-toxic nature of the degraded metabolites compared to the dye. This study presented the first report of an endophyte on the degradation and detoxification of triphenylmethane dye via a novel oxidoreductase, thus facilitating the study of the plant-endophyte symbiosis in the bioremediation processes.


https://doi.org/10.1080/01490451.2018.1526987

Culture-dependent and independent approaches were used to understand the microbiota thriving in tertiary coalbed, located in Jammu and Kashmir, India. We observed changes in physicochemical properties of the surface sediment (CM1) and coalbed (CM2) which detailed the influence of environmental factors on the structure and capabilities of bacterial communities. A total of 316 bacterial isolates representing 35 genera were isolated. We noted comparable difference in uncultivable bacterial communities which revealed the predominance of Proteobacteria in both the study sites. Moreover, we observed differential abundance of phyla Actinobacteria (49.6%), Firmicutes (4.2%), and Bacteroidetes (0.8%) in CM1, whereas Actinobacteria (11%), Firmicutes (37.8%), and Bacteroidetes (2.3%) in CM2. Additionally, functional imputations using PICRUSt depicted ∼30% higher assemblage of major gene families in CM1 in comparison to CM2. Bacterial communities residing at CM1 were predominantly involved in methane oxidation, whereas CM2 communities found to play a vital process of conversion of coal to biogenic-methane enabling microbes to survive under constraints of high sulfur content, salt precipitation, and low nutrients and also provide clues to understand the potential of methanogenesis.

Sharma, M., Shukla, B., 2019. Akinetes from Late Paleoproterozoic Salkhan Limestone (>1600 Ma) of India: A proxy for understanding life in extreme conditions. Frontiers in Microbiology 10, 397. doi: 310.3389/fmicb.2019.0039.


Isolated elongate spore-like cells present in the >1600 Ma old Salkhan Limestone of the Semri Group, Vindhayan Supergroup, India are considered akinetes of the heterocystous cyanobacteria. Small to large size, and young (single walled) to mature (double walled) akinetes namely, Archaeoellipsoides bactroformis, A. conjuctivus, A. dolichos, A. elongatus, A. grandis, A. major and A. minor found in the stromatolitic and bedded cherts have been reported in the present paper. Their role in understanding extreme environmental conditions is a subject matter of this paper. Additionally, the occurrences of doubly-terminated quartz crystals and fan-fabrics in the Salkhan Limestone indicate adverse conditions for the survival of life forms. The depositional environment of the Salkhan Limestone, Vindhyan Supergroup is suggested to be shallow marine intertidal with pulses of the intermittent hypersaline regime during which akinetes, closely resembling those of extant Nostocaceans, were formed by the cyanobacteria for survival in the extreme conditions.

Shashkov, M.V., Sidelnikov, V.N., 2019. Orthogonality and quality of GC × GC separations for complex samples with ionic liquid stationary phases in first dimension. Chromatographia 82, 615-624.

https://doi.org/10.1007/s10337-018-3672-4

In this paper, the advantages of using a pyridinium and imidazolium ionic liquids in the first column for GC × GC separation of complex mixtures—coal pyrolysis product, bio-oil, and essential oil from Pituranthos scoparius—in comparison with polyethylenglycol phase has been demonstrated. The nearest neighbor distance (NND) approach to evaluate the separation quality and orthogonality has been used for the comparison of GC × GC separations for different ionic liquid columns in the first dimension. It was found that they give essentially different results for both the separation quality and orthogonality, evaluated using parameters derived from NND approach. For a mixture of coal pyrolysis products containing only two classes of compounds—phenols and aromatic compounds—the most polar ionic liquid bis4MPyC6 shows nearly the highest orthogonality and separation quality. In the case of separation bio-oil and essential oil, the best orthogonality was demonstrated for the least polar of the tested ionic liquids—bis3.5MPyC9. At the same time, the efficiency of columns exerts a significant effect on the separation quality parameter. As a result, this parameter has the

highest value for all mixtures tested using the polyethylene glycol (ZB-WAX) reference phase, which is the less polar from all series, but the most efficient.

Shekarifard, A., Daryabandeh, M., Rashidi, M., Hajian, M., Röth, J., 2019. Petroleum geochemical properties of the oil shales from the Early Cretaceous Garau Formation, Qalikuh locality, Zagros Mountains, Iran. International Journal of Coal Geology 206, 1-18.


A suite of petroleum geochemical techniques including Rock-Eval VI pyrolysis, carbon analyzer, kerogen petrography and palynofacies, vitrinite reflectance (VRr), elemental analysis of kerogen (CHONSFe), gas chromatography (GC), gas chromatography–mass spectrometry (GC–MS), pyrolysis ((PY)-GC) and carbon isotope (δ13C) analyses were performed on 123 outcrop samples from 10 locations to characterize the properties of organic matter and the petroleum potential of the oil shales from the Early Cretaceous Garau Formation at Qalikuh locality in the High Zagros (Iran). To characterize the mineralogy and chemistry of the oil shales X-ray diffraction (XRD) and X-ray fluorescence (XRF) were performed.

Together with our previous work (Rasouli et al., 2015), this is the first study in which organic geochemical and petrographical investigations on the Qalikuh oil shales were performed. Total organic carbon (TOC) content of the oil shales varies from 3.83 to 26.4 wt%, with a mean value of 16.5 wt%, suggesting excellent TOC content. The mean value of hydrogen index (HI = 557 mg HC/g TOC) and petroleum potential (S2 = 89 mg HC/g rock) for the oil shales is high, indicating the presence of highly oil-prone organic matter. Elemental analysis of kerogen shows the oil shales are predominantly enriched in Type II-S kerogen. The results of kerogen microscopy observations reveal that homogenous bitumen (as widespread cement by impregnation) and amorphous organic matter are the main organic components. The oil shales of the Garau Formation are mainly consisting of calcite minerals and therefore they are classified as organic-rich/highly bituminous limestone. Additional data from molecular geochemistry and biomarker parameters of GC and GC–MS (e.g. CPI, Pr/Ph, Pr/nC17, Ph/nC18, DBT/Phen and C29/C27 20R sterane) as well as carbon isotope data of extracted bitumen confirm the presence of marine Type II kerogen. These data also show the oil shales were deposited within a marine carbonate environment under anoxic/euxinic conditions.

Based on equivalent VRr, elemental analysis, microscopy evidence and biomarker maturity parameters the investigated oil shales from the Garau Formation are early mature and located in the oil generation window. The revised oil-yield calculation from Fischer Assay results confirms the occurrence of moderate to good commercial oil shales with oil yield of 83 l/ton rock on average. Moreover, preliminary analyses of PY-GC data indicate that the Qalikuh oil shales have also very good shale gas potential at over-mature state (i.e. VRr >1.3%).

Shi, J., Zhang, B., Qiu, R., Lai, C., Jiang, Y., He, C., Guo, J., 2019. Microbial chromate reduction coupled to anaerobic oxidation of elemental sulfur or zerovalent iron. Environmental Science & Technology 53, 3198-3207.


Chromate (Cr(VI)), as one of ubiquitous contaminants in groundwater, has posed a major threat to public health and ecological environment. Although various electron donors (e.g., organic carbon, hydrogen, and methane) have been proposed to drive chromate removal from contaminated water, little is known for microbial chromate reduction coupled to elemental sulfur (S(0)) or zerovalent iron

(Fe(0)) oxidation. This study demonstrated chromate could be biologically reduced by using S(0) or Fe(0) as inorganic electron donor. After 60-day cultivation, the sludge achieved a high Cr(VI) removal efficiency of 92.9 ± 1.1% and 98.1 ± 1.2% in two independent systems with S(0) or Fe(0) as the sole electron donor, respectively. The deposited Cr(III) was identified as the main reduction product based on X-ray photoelectron spectroscopy. High-throughput 16S rRNA gene sequencing indicated that Cr(VI) reduction coupled to S(0) or Fe(0) oxidation was mediated synergically by a microbial consortia. In such the consortia, S(0)- or Fe(0)-oxidizing bacteria (e.g., Thiobacillus or Ferrovibrio) could generate volatile fatty acids as metabolites, which were further utilized by chromate-reducing bacteria (e.g., Geobacter or Desulfovibrio) to reduce chromate. Our findings advance our understanding on microbial chromate reduction supported by solid electron donors and also offer a promising process for groundwater remediation.



The use of stable isotope techniques can assist in understanding interactions of plants with various abiotic and biotic processes. In the research, we focused on carbon (C) and nitrogen (N) isotopes because they are the most important resources influencing plant function and the biogeochemical cycles. The 13C/12C and 15N/14N ratios in plants and in soils and the relationships between these ratios and biological and environmental factors of widely distributed native C3 plants (couch grass, plantain and yarrow) collected from two sites in St. Petersburg, Russia were studied. The soil characteristics of the sites were rather different. This had a significant effect on the isotope ratios in plants and in soils resulting in a big difference between 13C/12C and between 15N/14N ratios in the soils, roots and leaves of the plants collected from the two sites. The variability of the C and N isotope ratios was also rather high among different plant species. Two main factors affected this variability: biological (plant species) and ecological (biogeochemical characteristics of soils). The 13C/12C and 15N/14N ratios of roots and especially leaves were typical for a particular plant species and could differ between different plant species growing simultaneously at the same site. The soil parameters (soil texture, pH, and concentrations of total C and N in the soil) were among main factors influencing the stable isotope ratios in the soil and in different parts of a plant. A strong positive relationship between 13C/12C and also between 15N/14N ratios in roots and leaves of the plants was observed. On the other hand, the correlation between ratios of 13C/12C and 15N/14N calculated only for leaves or only for roots was statistically significant and negative.

Sie, C.-Y., Nguyen, B., Castellanos Diaz, O., Verlaan, M., Nguyen, Q.P., 2019. Viscous oil recovery and in-situ deasphalting in fractured reservoirs – Part 2: Effect of solvent type and temperature. Fuel 247, 294-301.


This paper advances the understanding of the solvent-based EOR methods from our previous work by investigating the effect of solvent type and temperature on the recovery of viscous oil by liquid extraction using sandstone cores with an artificial fracture. The production mechanisms were identified through the analysis of oil production rate, ultimate recovery, and in-situ deasphalting in different sections of the core. The use of dichloromethane (DCM) was introduced as the reference to study the production without in-situ deasphalting whereas n-pentane injection was compared to that of n-butane injection to study the effect of paraffin length on production with in-situ deasphalting. Sustained high production rates, which deviate from the behavior of typical gravity drainage

processes, were observed in the cases with in-situ deasphalting. This discrepancy was attributed to the enhanced convection in the matrix due to the alteration of fracture aperture by asphaltene precipitation and deposition. Temperature has a significant impact on oil production through its effect on mass diffusivity as well as asphaltene rheology. The result of this work indicates that solvent selection is a key factor in the optimizing solvent EOR process and potential asphaltene deposition should be taken into consideration.

Sime, L.C., Hopcroft, P.O., Rhodes, R.H., 2019. Impact of abrupt sea ice loss on Greenland water isotopes during the last glacial period. Proceedings of the National Academy of Sciences 116, 4099-4104.

http://www.pnas.org/content/116/10/4099.abstract

Significance: The Dansgaard–Oeschger events contained in Greenland ice cores constitute the archetypal record of abrupt climate change. An accurate understanding of these events hinges on interpretation of Greenland records of oxygen and nitrogen isotopes. We present here the important results from a suite of modeled Dansgaard–Oeschger events. These simulations show that the change in oxygen isotope per degree of warming becomes smaller during larger events. Abrupt reductions in sea ice also emerge as a strong control on ice core oxygen isotopes because of the influence on both the moisture source and the regional temperature increase. This work confirms the significance of sea ice for past abrupt warming events.

Abstract: The Dansgaard–Oeschger events contained in Greenland ice cores constitute the archetypal record of abrupt climate change. An accurate understanding of these events hinges on interpretation of Greenland records of oxygen and nitrogen isotopes. We present here the important results from a suite of modeled Dansgaard–Oeschger events. These simulations show that the change in oxygen isotope per degree of warming becomes smaller during larger events. Abrupt reductions in sea ice also emerge as a strong control on ice core oxygen isotopes because of the influence on both the moisture source and the regional temperature increase. This work confirms the significance of sea ice for past abrupt warming events.Greenland ice cores provide excellent evidence of past abrupt climate changes. However, there is no universally accepted theory of how and why these Dansgaard–Oeschger (DO) events occur. Several mechanisms have been proposed to explain DO events, including sea ice, ice shelf buildup, ice sheets, atmospheric circulation, and meltwater changes. DO event temperature reconstructions depend on the stable water isotope (δ18O) and nitrogen isotope measurements from Greenland ice cores: interpretation of these measurements holds the key to understanding the nature of DO events. Here, we demonstrate the primary importance of sea ice as a control on Greenland ice core δ18O : 95% of the variability in δ18O in southern Greenland is explained by DO event sea ice changes. Our suite of DO events, simulated using a general circulation model, accurately captures the amplitude of δ18O enrichment during the abrupt DO event onsets. Simulated geographical variability is broadly consistent with available ice core evidence. We find an hitherto unknown sensitivity of the δ18O paleothermometer to the magnitude of DO event temperature increase: the change in δ18O per Kelvin temperature increase reduces with DO event amplitude. We show that this effect is controlled by precipitation seasonality.


https://doi.org/10.1029/2018GC007640

Microbial thiosulfate utilization and S-disproportionation could be important mechanisms of sulfate-formations on Earth and Mars. Sulfates on Mars date back to late-Noachian to Hesperian period. In contrast, the large sulfur/sulfate formations on Earth evolved under different chronological sequences. The S-cycle was provoked intermittently, permitting multiple appearances of the S-oxidizers on an evolutionary timescale. Hydrothermally altered deep-oceanic red clay sediments of the Central Indian Basin were examined as potential analogue for sulfur (S) oxidation on Mars. The basin sediments supported an active microbial S-metabolism that exhibited S-disproportionation coupled to microbial carbon-fixation through intermediate processes like thiosulfate utilization. Sulfur-oxidizers/thiotrophic denitrifiers were isolated in large numbers at circum-neutral pH, from these cold and dark abyssal Fe-oxide dominated organic-C starved clay. Experimental simulations under psychrophilic and thermo-tolerant conditions revealed the coexistence of an anaerobic, thermal component under the predominantly oxic, circum-neutral seafloor conditions. Multiple causative factors like hydrothermal seafloor circulation, in situ volcanism, and fracture zone reactivation could drive the widespread S-cycle activity in the Central Indian Basin, albeit at a low scale. It is postulated that these conditions are analogous to Great Oxidation Event situations on Earth, when S-oxidizers evolved and flourished. Experimental studies on microbial thiosulfate flux are few in spite of intense scientific interest in microbial S-disproportionation. To the best of our knowledge, this is a new report on regression model development for microbial thiosulfate flux. These clay-systems and their component microbes could serve as analogue to the ancient well-hydrated Noachian Mars and throw light on planetary hydration and desiccation mechanisms.

Sluijs, A., Peterse, F., Middelburg, J.J., Cramwinckel, M.J., Bijl, P.K., van der Ploeg, R., Schouten, S., Bohaty, S.M., Röhl, U., 2019. Harmful algae and export production collapse in the equatorial Atlantic during the zenith of Middle Eocene Climatic Optimum warmth. Geology 47, 247-250.


New palynological, sedimentological, and geochemical records spanning the Middle Eocene Climatic Optimum (MECO; ca. 40 Ma) in the equatorial Atlantic Ocean indicate that peak warming was associated with upper-ocean stratification, decreased export production, and possibly harmful algal blooms, followed by slight oxygen minimum zone expansion. Combining these findings with published MECO records suggests that export production collapse and benthos starvation during the zenith of MECO warmth were widespread in the Atlantic. Furthermore, comparison to records across the Paleocene-Eocene thermal maximum (ca. 56 Ma) at the same site suggests a similar system response to warming, but with different impact on benthic communities.

Smirnov, K.S., Forcisi, S., Moritz, F., Lucio, M., Schmitt-Kopplin, P., 2019. Mass difference maps and their application for the recalibration of mass spectrometric data in nontargeted metabolomics. Analytical Chemistry 91, 3350–3358.


Modern high-resolution mass spectrometry provides the great potential to analyze exact masses of thousands of molecules in one run. In addition, the high instrumental mass accuracy allows for high-precision formula assignments narrowing down tremendously the chemical space of unknown compounds. The adequate values for a mass accuracy are normally achieved by a proper calibration procedure that usually implies using known internal or external standards. This approach might not always be sufficient in cases when systematic error is highly prevalent. Therefore, additional

recalibration steps are required. In this work, the concept of mass difference maps (MDiMs) is introduced with a focus on the visualization and investigation of all the pairwise differences between considered masses. Given an adequate reference list of sufficient size, MDiMs can facilitate the detection of a systematic error component. Such a property can be potentially applied for spectral recalibration. Consequently, a novel approach to describe the process of the correction of experimentally derived masses is presented. The method is based on the estimation of the density of data points on MDiMs using Gaussian kernels followed by a curve fitting with an adapted version of the particle swarm optimization algorithm. The described recalibration procedure is examined on simulated as well as real mass spectrometric data. For the latter case, blood plasma samples were analyzed by Fourier transform ion cyclotron resonance mass spectrometry. Nevertheless, due to its inherent flexibility, the method can be easily extended to other low- and high-resolution platforms and/or sample types.

Smolarek-Lach, J., Marynowski, L., Trela, W., Wignall, P.B., 2019. Mercury spikes indicate a volcanic trigger for the Late Ordovician mass extinction event: An example from a deep shelf of the Peri-Baltic region. Scientific Reports 9, Article 3139.

https://doi.org/10.1038/s41598-019-39333-9

The Late Ordovician mass extinction (LOME) was the second largest Phanerozoic crisis, but its cause remains elusive. Several triggering mechanisms have been proposed over the years, including bioevolutionary events, oceanographic changes, and geotectonic processes. Here, we report the presence of Hg spikes in the Zbrza PIG-1 borehole from the Upper Ordovician deep shelf sections of the peri-Baltic region. A strong positive anomaly in the lower late Katian (Hg/TOC = 2537.3 ppb/wt%) was noted. No correlation between Hg and TOC (R2 = 0.07) was distinguished in the Hirnantian, although several positive anomalies were found. Because the Hg/Mo ratio showed trends very similar to those of Hg/TOC, it seems likely that TOC values reflect the redox conditions. In order to evaluate the role of anoxia in levels of Hg enrichment several redox indicators were measured. These showed that the elevated mercury values in the Hirnantian are not caused by anoxia/euxinia because euxinic biomarkers (maleimides and aryl isoprenoids) are present in very low abundance and pyrite framboids are absent. In total, positive Hg/TOC anomalies occur in the lower late Katian, at the Katian - Hirnantian boundary, and in the late Hirnantian. The lack of a strong Hg/TOC correlation, Ni enrichments, and the absence of ‘anoxic indicators’ (no biomarkers, no framboids, low Mo concentration) at these levels, supports the interpretation that Hg enrichment is due to enhanced environmental loading. We conclude that our Hg and Hg/TOC values were associated with volcanic pulses which triggered the massive environmental changes resulting in the Late Ordovician mass extinction.

Soliman, A., Slimani, H., 2019. The Cretaceous–Paleogene (K/Pg) boundary in the Dababiya Borehole, southern Egypt: An organic-walled dinoflagellate cyst approach. Cretaceous Research 98, 230-249.


For the first time, a dinoflagellate cyst analysis is provided for the Upper Cretaceous–lower Paleogene transition in the Dababiya borehole, near Luxor, southern Egypt. Rich and relatively well-preserved dinoflagellate cyst assemblages have been recovered; a total of 173 species and subspecies have been identified. Many of these were not previously known from Egyptian material. The biostratigraphical dinoflagellate cyst events recorded in the present study have allowed us to propose the first K/Pg boundary dinocyst zonation scheme for Egypt and to compare this with existing dinoflagellate cyst zonations worldwide. In ascending order, the observed latest Maastrichtian

dinoflagellate cyst events include successively the last occurrence (LO) of Cannosphaeropsis utinensis, the first occurrences (FOs) of Apteodinium fallax, Disphaerogena carposphaeropsis, Kenleyia leptocerata and the LOs of Alisogymnium euclaense, Dinogymnium spp. and Pterodinium cretaceum. The most significant early Danian dinoflagellate cyst events used in this study are the FOs of Danea californica, Carpatella cornuta, Cassidium fragile, Lanternosphaeridium reinhardtii, Senoniasphaera inornata and Membranilarnacia? tenella. The dinoflagellate cyst biostratigraphical results, calibrated with data from benthic and planktonic foraminifera and calcareous nannoplankton from the same set of samples, have enabled a more accurate identification of the Cretaceous–Paleogene (K/Pg) boundary than previously suggested for the succession studied.

Soltis, P.S., Folk, R.A., Soltis, D.E., 2019. Darwin review: angiosperm phylogeny and evolutionary radiations. Proceedings of the Royal Society B: Biological Sciences 286, Article 20190099.


Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.

Song, F., Wu, F., Feng, W., Liu, S., He, J., Li, T., Zhang, J., Wu, A., Amarasiriwardena, D., Xing, B., Bai, Y., 2019. Depth-dependent variations of dissolved organic matter composition and humification in a plateau lake using fluorescence spectroscopy. Chemosphere 225, 507-516.


In aquatic systems, dissolved organic matter (DOM) plays an important role in regulating the reactivity and transport of environmental pollutants. Fluorescence excitation-emission matrix (EEM) analysis combined with fluorescence regional integration (FRI) and parallel factorial analysis (PARAFAC) were applied to investigate the composition, humification degree and depth-dependent variation of DOM in Lake Baihua, China. The results showed that humic-like materials with more than 60% of percentage fluorescence response (Pi,n) were dominant in DOM. The molecular complexity and structural condensation of PARAFAC components showed the order of C1 (humic-like components) > C3 (protein-like components) > C4 (fulvic-like components) > C2 (fulvic-like components). The lower maximum fluorescence intensities (Fmax) of components in surface layers were attributed to photo-oxidation of DOM by radiation. With depths less than 16 m, the Fmax increases and decreases were attributed to accumulation of recalcitrant humic substances and microbial/abiotic degradation of particulate DOM, respectively. A combination of biological and humification indices could be used as indicators for distinguishing different degrees of humification and sources of DOM. DOM from Lake Baihua mainly originated from an aquatic bacterial source that consisted of an important/intermediate autochthonous component with a weak humic character. The fluorescence indices of PI,n/PII,n, PI+II+IV,n/PIII+V,n, C2, C1/C2 and C2/(C3+C4) were more suitable to determine the humification degree. Stronger humic characters and higher humification degree for DOM were present at depths of 10–13 m. The fluorescence spectroscopy combined with fluorescence

indices is convenient to investigate depth-dependent DOM characteristics and to assess water quality or pollution risk in lake systems.

Song, T., Tong, J., Tian, L., Chu, D., Huang, Y., 2019. Taxonomic and ecological variations of Permian-Triassic transitional bivalve communities from the littoral clastic facies in southwestern China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 108-123.


Immediately after the latest Permian mass extinction, bivalve faunas colonized the Permian-Triassic Transitional Beds (PTTB), especially in littoral clastic facies of South China. The Permian-Triassic (P-Tr) transitional bivalve fauna is composed of holdovers, long-term survivors and newly evolved taxa, and characterized by moderate diversity and high dominance. However, the taxonomy and ecology of this bivalve fauna of littoral clastic facies have not been well understood, especially in comparison with offshore marine records. This paper presents a study on a P-Tr transitional bivalve fauna from five sections of littoral clastic facies in southwestern China, and as such it contributes to a better knowledge of the ecological processes of benthic communities during the P-Tr transition. In total, 20 species in 13 genera of bivalves are identified from the PTTB in the lower part of the Kayitou Formation and the basal part of the Feixianguan Formation of the five sections. Cluster analysis suggests that the transitional bivalve fauna could be further divided into two successive communities (early and late communities), and each is composed of five assemblages. Promyalina–Neoschizodus community (early community) is characterized by presence of holdover taxa, high taxonomic diversity and evenness, and more abundant shallow infaunal suspension feeders. In Pteria community (late community), taxonomic diversity and evenness are much lower, and stationary epifaunal suspension feeders boost at the expense of shallow infaunal suspension feeders compared with the Promyalina–Neoschizodus community. Furthermore, the Promyalina–Neoschizodus community shows a clear spatial variation along environmental gradient from brackish lagoon to shallow marine settings, while the Pteria community is more uniform and homogeneous laterally. The Promyalina–Neoschizodus community in the studied region is of latest Permian age while the Pteria community should belong to the earliest Triassic. Consequently, a significant taxonomical and ecological turnover of bivalve communities occurred between the Promyalina–Neoschizodus community and the Pteria community during the extinction interval in southwestern China.

Song, Z., Chen, S., Zhao, F., Zhu, W., 2019. Whole metagenome of injected and produced fluids reveal the heterogenetic characteristics of the microbial community in a water-flooded oil reservoir. Journal of Petroleum Science and Engineering 176, 1198-1207.


In order to understand the subsurface microbial community and how it functions in a water-flooded reservoir, the whole metagenome of fluids from production and injection wells were sequenced using next-generation sequencing and then compared. Gene function was annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG), evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and hydrocarbon degradation databases. More biomass was detected in fluid from the injection well than in the production well. As a typical water-flooded reservoir, injection and production communities were dominated by Proteobacteria. In the production metagenome, more genes involved in denitrification and hydrocarbons utilization pathways, reflecting the strict anaerobic and oil-rich conditions in reservoirs. The higher abundance of genes responsible for methyl chemotaxis, aerotaxis and flagella indicate that the community in reservoirs is motivated to access limited nutrients and electron acceptors. Combined with knowledge of porous

flow, these metagenome results indicate that the microbial communities detected in produced fluids are actually derived from different habitats in the reservoir, which are established by the chromatographic effect of reservoir flooding. Furthermore, diverse flow patterns at pore scale could affect in situ proliferation and syntrophy between species, which could considerably shift the microbial composition in produced fluids.

Souza, V., Moreno-Letelier, A., Travisano, M., Alcaraz, L.D., Olmedo, G., Eguiarte, L.E., 2018. The lost world of Cuatro Ciénegas Basin, a relictual bacterial niche in a desert oasis. eLife 7, Article e38278.

https://elifesciences.org/articles/38278

Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is vital to the understanding of early evolutionary and ecological processes.

Spagnuolo, M., Yaguchi, A., Blenner, M., 2019. Oleaginous yeast for biofuel and oleochemical production. Current Opinion in Biotechnology 57, 73-81.


Current transportation fuels derived from petroleum can also be made from microbial systems. In particular, oleaginous yeast have naturally evolved high flux pathways for fatty acids in the form of neutral lipids, which can be converted into a variety of drop-in fuels. Here, we describe the recent advances in the use of the four most popular oleaginous yeasts for making lipids and other potential fuels – Yarrowia lipolytica, Lipomyces starkeyi, Rhodosporidium toruloides, and Cutaneotrichosporon oleaginosus. The paper is divided into three major sections focusing on (1) the important natural complex phenotypes of each yeast; (2) the development of metabolic engineering tools for each yeast; and (3) demonstrations of metabolic engineering in each yeast. At the end of each section, we provide our assessment, of which yeast is most promising in the near and long term for bioenergy production.

Spalding, C., Fischer, W.W., 2019. A shorter Archean day-length biases interpretations of the early Earth's climate. Earth and Planetary Science Letters 514, 28-36.


Earth's earliest sedimentary record contains evidence that surface temperatures were similar to, or perhaps even warmer than modern. In contrast, standard Solar models suggest the Sun was 25% less luminous at this ancient epoch, implying a cold, frozen planet—all else kept equal. This discrepancy, known as the Faint Young Sun Paradox, remains unresolved. Most proposed solutions invoke high concentrations of greenhouse gases in the early atmosphere to offset for the fainter Sun, though current geological constraints are insufficient to verify or falsify these scenarios. In this work, we

examined several simple mechanisms that involve the role played by Earth's spin rate, which was significantly faster during Archean time. This faster spin rate enhances the equator-to-pole temperature gradient, facilitating a warm equator, while maintaining cold poles. Results show that such an enhanced meridional gradient augments the meridional gradient in carbonate deposition, which biases the surviving geological record away from the global mean, toward warmer waters. Moreover, using simple atmospheric models, we found that the faster-spinning Earth was less sensitive to ice-albedo feedbacks, facilitating larger meridional temperature gradients before succumbing to global glaciation. We show that within the faster-spinning regime, the greenhouse warming required to generate an ice-free Earth can differ from that required to generate an Earth with permanent ice caps by the equivalent of 1–2 orders of magnitude of pCO2. Accordingly, the resolution of the Faint Young Sun problem depends significantly on whether the early Earth was ever, or even at times, ice-free.

Spivey, E.C., McMillen, J.C., Ryan, D.J., Spraggins, J.M., Caprioli, R.M., 2019. Combining MALDI-2 and transmission geometry laser optics to achieve high sensitivity for ultra-high spatial resolution surface analysis. Journal of Mass Spectrometry 54, 366-370.

https://doi.org/10.1002/jms.4335

Abstract A transmission geometry optical configuration allows for smaller laser spot size to facilitate high resolution MALDI mass spectrometry. This increase in spatial resolution (i.e. smaller laser spot size) is often associated with a decrease in analyte signal. MALDI-2 is a post-ionization technique which irradiates ions and neutrals generated in the initial MALDI plume with a second orthogonal laser pulse, and has been shown to improve sensitivity. Herein we have modified a commercial Orbitrap mass spectrometer to incorporate a transmission geometry MALDI source with MALDI-2 capabilities to improve sensitivity at higher spatial resolutions.

Stagno, V., 2019. Carbon, carbides, carbonates and carbonatitic melts in the Earth's interior. Journal of the Geological Society 176, 375-387.


Over recent decades, many experimental studies have focused on the effect of CO2 on phase equilibria and melting behaviour of synthetic eclogites and peridotites as a function of pressure and temperature. These studies have been of fundamental importance to understanding the origin of carbonated magmas varying in composition from carbonatitic to kimberlitic. The occurrence of diamonds in natural rocks is further evidence of the presence of (reduced) carbon in the Earth's interior. The oxygenation of the Earth's interior (i.e. its redox state) through time has strongly influenced the speciation of carbon from the mantle to mantle-derived magmas and, in turn, to the volcanic gases released to the atmosphere. This paper explains how the knowledge of the oxygen fugacity recorded by mantle rocks and determined through the use of appropriate oxy-thermobarometers allows modelling of the speciation of carbon in the mantle, its mobilization in the asthenospheric mantle by redox partial melting, and its sequestration and storage during subduction by redox freezing processes. The effect of a gradual increase of the mantle fO2 on the mobilization of C is here discussed along with the main variables affecting its transport by subduction into the mantle.

Stevens, A.H., Kobs Nawotniak, S.E., Garry, W.B., Payler, S.J., Brady, A.L., Miller, M.J., Beaton, K.H., Cockell, C.S., Lim, D.S.S., 2019. Tactical scientific decision-making during crewed astrobiology Mars missions. Astrobiology 19, 369-386.

https://doi.org/10.1089/ast.2018.1837

The limitations placed upon human explorers on the surface of Mars will necessitate a methodology for scientific exploration that is different from standard approaches to terrestrial fieldwork and prior crewed exploration of the Moon. In particular, the data transmission limitations and communication latency between Earth and Mars create a unique situation for surface crew in contact with a terrestrial science team. The BASALT research program simulated a series of extravehicular activities (EVAs) in Mars analog terrains under various Mars-relevant bandwidth and latency conditions to investigate how best to approach this problem. Here we discuss tactical decision-making under these conditions, that is, how the crew on Mars interacts with a team of scientists and support personnel on Earth to collect samples of maximum scientific interest. We describe the strategies, protocols, and tools tested in BASALT EVAs and give recommendations on how best to conduct human exploration of Mars with support from Earth-based scientists. We find that even with scientists supporting them, the crew performing the exploration must be trained in the appropriate scientific disciplines in order to provide the terrestrial scientists with enough information to make decisions, but that with appropriate planning and structure, and tools such as a “dynamic leaderboard,” terrestrial scientists can add scientific value to an EVA, even under Mars communication latency.

Stoeva, M.K., Coates, J.D., 2019. Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding. Microbiology 165, 254-269.

https://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000750

Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis – and potentially assimilatory sulfate pathways – relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.

Stratiev, D., Shishkova, I., Tankov, I., Pavlova, A., 2019. Challenges in characterization of residual oils. A review. Journal of Petroleum Science and Engineering 178, 227-250.


This paper passes over the literature for residual oil characterization. The methods for residual oil characterization are classified in: characterization based on physical and chemical bulk properties; characterization based on saturates, aromatics, resins, asphaltenes (SARA) analysis; and characterization based on the molecular modeling processes. The upper and lower limits of the values for physical and chemical bulk properties of the vacuum residual oils around the world are outlined. A variation of the physical and chemical bulk properties of SARA fractions originating from different vacuum residual oils is discussed. Correlations between refractive index and density, and between the vapor pressure osmometry (VPO) molecular weight of saturates and aromatics were found. A ratio between the lowest and the highest molecular weight of the vacuum residual oil saturate and aromatic fraction of 2.4 was found showing that the molecular weights of these SARA fractions are not fixed and can vary between 360 and 880 g/mole for the saturates, and 450 and 1080 g/mole for the aromatics. Assuming the same ratio in variation of molecular weights (MW) of the fractions resins and asphaltenes for the reviewed 41 vacuum residual oils suggests that the resins MW could vary in the range 800 ÷ 1800 g/mole and the asphaltenes MW may vary between 1000 and 3000 g/mole. The application of sophisticated analytical techniques showed a very big diversity in the species building the vacuum residual oils and different distribution of these species even for the same SARA fraction depending on the residual oil origin. The different approaches for “molecular reconstruction” of residual oils Monte Carlo (MC), Quadrature algorithm (QA), Entropy maximization (EM), quantitative structure-property relationship (QSPR), structure-oriented lumping (SOL), molecular type homologous series (MTHS) matrix, artificial neural network (ANN) and multiple linear regression (MLR) are reviewed. A conclusion is made that the advanced analytical and computational techniques are still an obligor to the chemical engineers working at the commercial residual oil conversion units who aim to optimize the conversion process performance.

Strbak, O., Dobrota, D., 2019. Archean iron-based metabolism analysis and the photoferrotrophy-driven hypothesis of microbial magnetotaxis origin. Geomicrobiology Journal 36, 278-290.

https://doi.org/10.1080/01490451.2018.1554013

Despite its biological and geological significance, the origin of microbial magnetosome biomineralization, as well as the evolution of magnetotaxis, is still not well understood. Recently, the origin of magnetotaxis has been proposed to already exist in the Archean Eon. However, the Archean environment was fully anoxic. Therefore, what was the reason for the evolution of magnetotaxis in the anoxic Archean ocean and what mechanism could lead to the formation of single domain-sized magnetite nanoparticles that are a necessary condition of magnetotaxis functionality? Since the genetically controlled magnetosomes formation is extremely energetically demanding, in this review, we analyze Archean anoxic iron-based metabolism and we delineate the alternative possibilities of non-genetically controlled magnetosomes precursor origin as a necessary condition of magnetotaxis emergence. We show that coupling of anoxygenic photosynthesis with ferrous iron as an electron donor, with anaerobic respiration with ferric iron as an electron acceptor, provided sufficient material for non-genetically controlled magnetite formation. The co-evolution of cyanobacteria is suggested as the possible environmental pressure responsible for the emergence of Archean magnetotaxis. In accordance with the hypothesis of the reactive oxygen species-protective function of the first magnetosomes, we show that the formation of single domain-sized magnetite nanoparticles did not have to be initially connected with magnetotaxis origin, neither had to be genetically controlled nor intracellular. Instead, it could result from the long-lasting ambient pressure of metabolically produced extracellular iron oxide minerals in photoferrotrophs together with the emergence of local oxygen oases. The presence of oxygen could favor cells with the ability to navigate into oxic-anoxic transition zones since the oxygen was entirely toxic to Archean life. This evolutionary advantageous

trait could finally result in a niche construction origin of genes responsible for intracellular magnetosome formation, which have remained preserved until today.

Su, L., Ajo-Franklin, C.M., 2019. Reaching full potential: bioelectrochemical systems for storing renewable energy in chemical bonds. Current Opinion in Biotechnology 57, 66-72.


The growing abundance of wind and solar power has driven interest in utilizing this renewable energy to make chemicals. One of the most efficient and sophisticated frameworks to solar-to-chemical conversion is bioelectrochemical systems that electrochemically couple inorganic catalysts and microorganisms. In particular, microbial electrosynthesis systems and biohybrid systems have used CO2 and electricity or light, respectively, to synthesize organic acids at energy efficiencies that exceed natural photosynthesis. In parallel, new methods have been recently developed to improve the poor mechanistic understanding of these and other bioelectrochemical systems. Deeper knowledge of these underlying molecular processes and creation of new architectures for bioelectrochemical systems are needed to make these promising technologies scale to a commercially relevant level.

Sugiura, K., Kobayashi, H., Inutsuka, S.-i., 2019. Collisional elongation: Possible origin of extremely elongated shape of 1I/‘Oumuamua. Icarus 328, 14-22.


Light curve observations of a recently discovered interstellar object 1I/‘Oumuamua suggest that this object has an extremely elongated shape with the axis ratio 0.3 or smaller. Planetesimal collisions can produce irregular shapes including elongated shapes. In this paper, we suggest that the extremely elongated shape of 1I/‘Oumuamua may be the result of such an impact. To find detailed impact conditions to form the extremely elongated objects, we conduct numerical simulations of planetesimal collisions using Smoothed Particle Hydrodynamics method for elastic dynamics with self-gravity and interparticle friction. Impacts into strengthless target planetesimals with radius 50 m are conducted with various ratios of impactor mass to target mass q, friction angles ϕd, impact velocities vimp, and impact angles θimp. We find that impacts with q ≥ 0.5, ϕd ≥ 40°, vimp ≤ 40 cm/s, and θimp ≤ 30° produce remnants with the ratio of intermediate to major axis length <0.3. This impact condition suggests that the parent protoplanetary disk in the planetesimal collision stage was weakly turbulent (α < 10−4 for the inner disk) and composed of planetesimals smaller than ∼7 km to ensure small impact velocity.

Suja, L.D., Chen, X., Summers, S., Paterson, D.M., Gutierrez, T., 2019. Chemical dispersant enhances microbial exopolymer (EPS) production and formation of marine oil/dispersant snow in surface waters of the subarctic northeast Atlantic. Frontiers in Microbiology 10, 553. doi: 510.3389/fmicb.2019.00553.


A notable feature of the Deepwater Horizon oil spill was the unprecedented formation of marine oil snow (MOS) that was observed in large quantities floating on the sea surface and that subsequently sedimented to the seafloor. Whilst the physical and chemical processes involved in MOS formation remain unclear, some studies have shown that extracellular polymeric substances (EPS) play a role in this process. Here, we report that during exposure of subarctic northeast Atlantic seawater to a chemical dispersant, whether in the presence/absence of crude oil, the dispersant stimulates the

production of significant quantities of EPS that we posit serves as a key building block in the formation of MOS. This response is likely conferred via de novo synthesis of EPS by natural communities of bacteria. We also describe the formation of marine dispersant snow (MDS) as a product of adding chemical dispersants to seawater. Differential staining confirmed that MDS, like MOS, is composed of glycoprotein, though MDS is more protein rich. Using barcoded-amplicon Illumina MiSeq sequencing, we analyzed, for the first time, the bacterial communities associated with MDS and report that their diversity is not significantly dissimilar to those associated with MOS aggregates. Our findings emphasize the need to conduct further work on the effects of dispersants when applied to oil spills at sea, particularly at different sites, and to determine how the product of this (i.e. MOS and MDS) affects the biodegradation of the oil.

Summons, R.E., Miller, K.E., Kotrc, B., Belmahadi, I., Buch, A., Eigenbrode, J.L., Freissinet, C., Glavin, D.P., Szopa, C., 2019. Reply to Comment by F. Kenig, L. Chou, and D. J. Wardrop on “Evaluation of the Tenax trap in the sample analysis at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater” by Miller et al., 2015. Journal of Geophysical Research: Planets 124, 648-650.

https://doi.org/10.1029/2018JE005641

Abstract: Kenig et al. comment on our 2015 reporting of laboratory analog experiments aimed at testing the stability of the hydrocarbon trap material used in the Sample Analysis on Mars (SAM) instrument on board the Curiosity Rover operating in Gale Crater on Mars. They propose chemical structures for some decomposition products of the Tenax TA polymer when it is exposed at high temperatures to the Cl2 and O2 gases formed by the thermal decomposition of perchlorate. Further, Kenig et al. propose that these decomposition products accumulate and then react further in cooler downstream sections of the SAM analytical pipeline to produce the chlorobenzene that was detected in the Cumberland mudstone of Gale Crater. However, numerous experiments conducted in the laboratory show that Tenax TA decomposition products only appear after repeated exposure to much higher levels of Cl2 and O2 than those seen by the flight instrument. Moreover, the sequence of chlorobenzene detections during gas chromatography-mass spectrometry experiments conducted on Mars cannot be explained by Tenax TA decomposition, nor can the detection of chlorobenzene in Evolved Gas Analysis experiments that involve pathways devoid of Tenax TA. Kenig et al. are incorrect in their assertion that Tenax TA decomposition products can account for the chlorobenzene detected on Mars by SAM.

Plain Language Summary: Calcium and magnesium salts of chlorate and perchlorate have been detected in surface sediments on Mars. The presence of these compounds, which emit corrosive gases when heated to high temperatures, can potentially compromise experiments aimed at detecting organic carbon compounds in Mars sediments. Perchlorate decomposition products also have the potential to damage components, namely the hydrocarbon trap, used in the construction of the Sample Analysis on Mars on instrument the Curiosity rover. In earlier work, we evaluated this possibility and provided evidence that the hydrocarbon trap was stable unless exposed to high concentrations of corrosive gases far beyond those that would be seen by the instrument operating on Mars. Experiments conducted by the SAM instrument have detected several organic compounds, including chlorobenzene, which cannot be explained by decomposition of organic materials carried on flight instrument. In particular, chlorobenzene was detected in the Cumberland mudstone in experiments that used pathways that did not include exposure to a hydrocarbon trap.

Original Article: Miller, K. E., Kotrc, B., Summons, R. E., Belmahdi, I., Buch, A., Eigenbrode, J. L., Freissinet, C., Glavin, D. P., & Szopa, C. ( 2015). Evaluation of the Tenax trap in the sample analysis

at Mars instrument suite on the Curiosity rover as a potential hydrocarbon source for chlorinated organics detected in Gale Crater. Journal of Geophysical Research: Planets, 120, 1446– 1459.

Comment: Summons, R.E., Miller, K.E., Kotrc, B., Belmahadi, I., Buch, A., Eigenbrode, J.L., Freissinet, C., Glavin, D.P., Szopa, C., 2019. Reply to Comment by F. Kenig, L. Chou, and D. J. Wardrop on “Evaluation of the Tenax Trap in the Sample Analysis at Mars Instrument Suite on the Curiosity Rover as a Potential Hydrocarbon Source for Chlorinated Organics Detected in Gale Crater” by Miller et al., 2015. Journal of Geophysical Research: Planets 124, 648-650.

Sun, M., Ren, G., Li, Y., Lu, A., Ding, H., 2019. Extracellular electron transfer between birnessite and electrochemically active bacteria community from red soil in Hainan, China. Geomicrobiology Journal 36, 169-178.

https://doi.org/10.1080/01490451.2018.1526986

The interplay between electrochemically active microorganisms (EAMs) and adjacent minerals universally occurs in natural environments, in which soil is an extremely typical and active one. We stimulated the extracellular electron transfer (EET) process between the bacterial community and birnessite in red soil (collected from Hainan, China) by constructing a microbial fuel cell equipped with synthetic birnessite cathode. Compared to graphite-cathode, the cell voltage of birnessite-cathode was increased by 22% when loading a 1000 Ω-resistance, indicating the EET between microbes and birnessite. Eleven genera of EAMs in red soil were confirmed through 16S rRNA analysis. Neither palpable novel mineral formation nor change of birnessite crystallinity was observed after reaction by Raman and SEM. As oxygen pumped into cathode chamber was the terminal electron acceptor, birnessite principally performed as an intermediate of holistic electron transfer process to favor the cathodic oxygen reduction.

Sun, R., Fan, Z., Yang, M., Pang, W., Li, Y., Song, Y., 2019. Experimental investigation into the dissociation of methane hydrate near ice-freezing point induced by depressurization and the concomitant metastable phases. Journal of Natural Gas Science and Engineering 65, 125-134.


Methane hydrate (MH) has been viewed as an important potential energy resource, drawing attention of its efficient exploitation. An intriguing phenomenon that gas hydrates dissociate in a slow rate and can preserve for long periods of time out of the stable region was considered as a performance of hydrates metastability. A mechanism that supercooled water can lead to the retarded dissociation of hydrates was proposed by researchers, which will affect the gas production efficiency and sediment safety during the exploitation of MH. In this work, experiments on MH dissociation and production of methane gas from porous MH sediment near ice-freezing point induced by depressurization were performed to obtain the evidence of the metastability of the gas hydrate system. A series of experiments at different production pressures, depressurization rates and initial water saturations were carried out to study the effects of supercooled water on gas production performance. The results show that the existence of supercooled water below the freezing point of water would retard the dissociation of MH, by which the gas production rate was slowed down. The duration of this metastable state of the system was dependent on the induction time of the ice formation during the MH dissociation process. The formation of ice would promote gas production from the sediment, while the formation was observed as a stochastic process at 2.0 MPa and 2.2 MPa. The method employed should be adjustable and amendable to investigate the metastability of the gas - liquid - gas

hydrate system and the related effects on gas production during depressurization-induced MH dissociation process below ice-freezing point in pilot scale.

Sun, S., Wang, Y., Zang, T., Wei, J., Wu, H., Wei, C., Qiu, G., Li, F., 2019. A biosurfactant-producing Pseudomonas aeruginosa S5 isolated from coking wastewater and its application for bioremediation of polycyclic aromatic hydrocarbons. Bioresource Technology 281, 421-428.


Although polycyclic aromatic hydrocarbons (PAHs) are considered as toxic and refractory pollutants, their biodegradation can be facilitated by biosurfactants. However, few studies have been performed to understand the potential isolation and application of biosurfactant-producing microorganism for promoting the in-situ removal of PAHs from wastewaters. In this work, a biosurfactant-producing strain S5 isolated from coking wastewater was identified as Pseudomonas aeruginosa. The biosurfactant produced by strain S5 was determined as glycolipid with a critical micelle concentration (CMC) of 96.5 mg/L, and reduced the surface tension from 72.2 to 29.6 mN/m. Addition indigenous P. aeruginosa S5 to coking wastewater effectively promoted the biodegradation of high weight molecular (HWM) PAHs (reduction from 9141.02 to 5117.16 µg/L in 15 days) in sludge phase. The results showed that the removal of PAHs in the sludge was enhanced by inoculating indigenous biosurfactant-producing microorganism in coking wastewater serving as an in-site remediation technology.

Sun, X., Wang, L., Luo, H., Song, Y., Li, Y., 2019. Numerical modeling for the mechanical behavior of marine gas hydrate-bearing sediments during hydrate production by depressurization. Journal of Petroleum Science and Engineering 177, 971-982.


Natural gas hydrate, which is called inflammable ice, has drawn global interest. Many countries have carried out the trial production of natural gas from marine gas hydrate formations. However, due to the failure of the bonded structure and the disappearance of the hydrate in the pores of formations, improper production might induce geological hazards such as submarine landslide, non-uniform subsidence and local large deformation of the formations. In this study, a constitutive model based on super-loading and sub-loading surface theory is proposed to investigate the mechanical behavior of gas hydrate-bearing sediments (GHBSs). The mechanical behavior of both GHBSs and the structured clay are modeled by introducing rotational hardening rule, sub-loading surface and super-loading surface. A fully coupled thermo-hydro-chemo-mechanical (THCM) model is applied to study the mutiphysical responses of GHBSs during hydrate production by depressurization. The simulation results of the two-layer model show that the mutiphysical responses are dependent on not only the different material properties of the two layers but also the difference between the hydrate dissociated and undissociated zones. Although depressurization is the driving factor of hydrate dissociation, the heat transfer from the clay layer is also a key factor in the hydrate dissociation. Hydrate dissociation results in the variation in the stiffness and strength of the GHBSs leading to stress and strain and strain redistribution. The yielding and structural failure of sediments mainly occur in the hydrate dissociated zone.

Sun, Y., Kang, S., Wang, S., He, L., Guo, W., Li, Q., Deng, S., 2019. Subcritical water extraction of Huadian oil shale at 300 °C. Energy & Fuels 33, 2106-2114.


In this work, Huadian oil shale was extracted by subcritical water at 300 °C over different time periods to better characterize the underground mining of oil shale in situ. The results revealed that the kerogen in the oil shale mostly transformed into bitumen through extraction over a long time period by subcritical water at 300 °C; however, a portion of the bitumen remained in the shale matrix. The yields of both bitumen 1 (the bitumen extracted by subcritical water) and bitumen 2 (the bitumen remaining in the shale matrix) reached maximums at approximately 250 h. It should take a long time for bitumen 2 to be released because the ability of the transporting substrates of subcritical water was insufficient, the solubility of bitumen 2 was poor, and tiny fractures were generated in the oil shale matrix at such a low temperature. The gas chromatography–mass spectrometry analysis showed that the major components of bitumen 1 and bitumen 2 were similar and consisted of n-alkanes, n-alkanoic acids, n-alk-2-ones, and isoprenoid alkane. Initially, kerogen decomposition produced a large number of n-alkanes with low molecular weights; however, as the reaction continued, comparatively higher-molecular-weight n-alkanes were obtained more. In addition, the bitumen underwent a secondary cracking in the subcritical water, resulting in its decreased yield over time, whereas the contents of gaseous C2–C6 hydrocarbons increased. The organic matter dissolved in the spent aqueous solution consisted of mainly paraffins, isoparaffins, cyclohexanone derivatives, and phenolic derivatives. The analysis of the oil shale residue showed that minerals were less reactive in the subcritical water except for feldspar and calcite and that mesopores developed in the oil shale with prolongated extraction time, as more bitumen diffused out and into the subcritical water at 300 °C.

Sundman, A., Koeksoy, E., Byrne, J.M., Kappler, A., Planer-Friedrich, B., Lohmayer, R., Halevy, I., Konhauser, K.O., 2019. Formation of green rust and elemental sulfur in an analogue for oxygenated ferro-euxinic transition zones of Precambrian oceans. Geology 47, 211-214.


For much of the Precambrian era, the bulk ocean was anoxic and Fe(II) rich (ferruginous), except for the first development of shallow ocean oxygenation and temporally/spatially restricted sulfide-rich waters (euxinia) along productive continental margins in the late Archean, which prevailed throughout much of the remaining Precambrian. There is little detail pertaining to transition zones between ferruginous, euxinic, and oxic seawater over the continental shelf that may have played an important role in shaping the composition of the underlying sediment. Here we present spectroscopic data on the Fe and sulfur mineralogy in the Arvadi Spring (Switzerland), a proposed analogue for such conditions. Our study reveals green rust, ferrihydrite, and lepidocrocite as the main Fe minerals. Because the reactivity of green rust differs from that of ferric hydroxides and Fe(II) sulfides, it is important to understand its role in the transfer of metals and nutrients from seawater to underlying sediments, if those sediments are to be used as chemical archives of paleo-seawater. We observed elemental sulfur (S0) as the dominant sulfur precipitate and found indications for its role in pyrite formation, implying that S0 could have had a similar role in Precambrian deposition of pyrite-poor or pyrite-rich sediments.


https://doi.org/10.2110/jsr.2019.8

Recent studies recognized distinct stromatolite provinces in Hamelin Pool, Western Australia, each with morphologically distinct stromatolite structures paired with characteristic shelf physiography. In the present paper, we couple detailed lithofacies mapping with Hamelin Pool bathymetry and consider physiography as a control of sedimentation processes, including stromatolite development. Bathymetric transects, derived from a high-resolution bathymetry map with depths from 0 to 11 meters, allow calculation of slope gradients in the provinces. As in other settings, bathymetry is linked to energy regimes, which in turn appear to be coupled with variations in stromatolite morphologies and associated lithofacies as follows: (1) low-gradient ramps with low-energy settings are associated with sheet mats and elongate-clustered stromatolites that exhibit regular spatial patterns, possibly indicative of self-organization; (2) low gradients coupled with high-energy settings resulting from strong winds result in seif stromatolites with pronounced directional bands; (3) medium to steep gradients coupled with medium to high energy are associated with individual and merged stromatolites, often with thin basal necks; (4) headlands and promontories where the topography deflects currents are associated with elongate-nested stromatolites; and (5) medium- to high-energy slopes typically found at promontory edges and shelf margins are dominated by blocky pavement. Observations linking stromatolite morphology to physiography in a modern microbial system provide insight into the long-lived debate about biology versus environment in controlling stromatolite morphology. When physiography leads to a high-energy regime, environmental controls are the main factor determining stromatolite morphology. In contrast, when physiography promotes a low-energy environment, the response of biological communities becomes the main driver of macroscale stromatolite morphology.

Sutherland, J.T.F., Moon, B., C., Stubbs, T., L., Benton, M., J., 2019. Does exceptional preservation distort our view of disparity in the fossil record? Proceedings of the Royal Society B: Biological Sciences 286, 20190091.


How much of evolutionary history is lost because of the unevenness of the fossil record? Lagerstätten, sites which have historically yielded exceptionally preserved fossils, provide remarkable, yet distorting insights into past life. When examining macroevolutionary trends in the fossil record, they can generate an uneven sampling signal for taxonomic diversity; by comparison, their effect on morphological variety (disparity) is poorly understood. We show here that lagerstätten impact the disparity of ichthyosaurs, Mesozoic marine reptiles, by preserving higher diversity and more complete specimens. Elsewhere in the fossil record, undersampled diversity and more fragmentary specimens produce spurious results. We identify a novel effect, that a taxon moves towards the centroid of a Generalized Euclidean dataset as its proportion of missing data increases. We term this effect ‘centroid slippage’, as a disparity-based analogue of phylogenetic stemward slippage. Our results suggest that uneven sampling presents issues for our view of disparity in the fossil record, but that this is also dependent on the methodology used, especially true with widely used Generalized Euclidean distances. Mitigation of missing cladistic data is possible by phylogenetic gap filling, and heterogeneous effects of lagerstätten on disparity may be accounted for by understanding the factors affecting their spatio-temporal distribution.



Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or double or cascade regulation. The closest and most variable connection exists between AphS, AphR, AphT, and BenR. We have identified a new LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs.

Sverjensky, D.A., 2019. Thermodynamic modelling of fluids from surficial to mantle conditions. Journal of the Geological Society 176, 348-374.


Carbon is subducted to depths where metamorphism liberates water-bearing fluids. The C-bearing fluids facilitate partial melting of the upper mantle, generating magmas that may erupt as arc volcanics. Degassing of the magmas releases CO2 and other volatile species to the atmosphere. Over geological time, this process contributes to the composition of the atmosphere and planetary habitability. Here I summarize the background needed to carry out theoretical geochemical modelling of fluids and fluid–rock interactions from surficial conditions into the upper mantle. A description of the general criteria for predicting equilibrium and non-equilibrium chemical reactions is followed by a summary of how the thermodynamic activities of species are related to measurable concentrations through standard states and activity coefficients. Specific examples at ambient conditions involving dilute water are detailed. The concept of aqueous speciation and how it can be calculated arises from this discussion. Next, I discuss how to calculate standard Gibbs free energies and aqueous activity coefficients at elevated temperatures and pressures. The revised Helgeson–Kirkham–Flowers equations of state are summarized and the revised predictive correlations for the estimation of equation of state coefficients in the Deep Earth Water (DEW) model are presented. Finally, the DEW model is applied to the solubility and speciation of aqueous aluminium.

Syed, F.I., Boukhatem, M., Al Kiyoumi, A.A., 2019. Lean HC gas injection pilots analysis and IPR back calculation to examine the impact of asphaltene deposition on flow performance. Petroleum Research 4, 84-95.


Gas injection is one of the most economical and effective approach to improve oil recovery. However, outcome of such approach is contingent to reservoir heterogeneities impacting gas override and fingering. Furthermore, injected fluid composition and its compatibility with the reservoir fluid potentially impact flow assurance issues such as asphaltene precipitation into the wellbore and surface facilities.

The objective of this paper is to examine the lesson learnt from a couple of field scale 5 spot patterned lean hydrocarbon gas injection pilots which were deployed in a heterogeneous carbonate formation of a giant field located offshore Abu Dhabi under secondary and tertiary drive mechanisms. Said pilots provides a valuable insight on production performance, pressure support, gravity override, fluid composition and evidence of asphaltene deposition that resulted in heavy production loss prior to the solvent treatment.

This paper presents the overall pilot performance including pattern recovery, fluid front movement, potential role of heterogeneity in gas breakthrough timings and the operational events to witness asphaltene deposition affecting the flow performance. The deposited asphaltene cake thickness was measured mechanically during routine tubing clearance check operation that was helpful in estimating production loss due to altered production tubing flow opening. Also an integrated approach is applied to confirm the AOP laboratory measurements with the actual deposits of asphaltene that were found in to the production tubing.

In order to confirm the effect of asphaltene deposition on inflow from near wellbore formation to the wellbore, a straightforward yet innovative nodal analysis approach was applied to study well performance using the calibrated and history matched well model. It was noticed that not only the outflow was altered because of asphaltene deposition into wellbore but also the inflow (productivity index) was seriously impacted potentially due to asphaltene deposition in near wellbore formation.

Szymczak-Żyła, M., Krajewska, M., Witak, M., Ciesielski, T.M., Ardelan, M.V., Jenssen, B.M., Goslar, T., Winogradow, A., Filipkowska, A., Lubecki, L., Zamojska, A., Kowalewska, G., 2019. Present and past-millennial eutrophication in the Gulf of Gdańsk (southern Baltic Sea). Paleoceanography and Paleoclimatology 34, 136-152.

https://doi.org/10.1029/2018PA003474

Eutrophication is manifested by increased primary production leading to oxygen depletion in near‐bottom water and toxic cyanobacteria blooms. This is an important contemporary problem of the Baltic Sea and many other coastal waters. The present eutrophication is mainly ascribed to anthropogenic activity. To compare the present trophic state with that during past millennia, two sediment cores (50 cm long and ~400 cm long covering ca. 5,500 years) were taken from the Gulf of Gdańsk (southern Baltic Sea). The core subsamples were analyzed for phytoplankton pigments (chlorophylls and their derivatives, and carotenoids). In addition, carbon (Ctot, Corg, and δ13C), 14C dating, grain size, diatoms, and selected metals in the cores were analyzed to determine conditions in the depositional environment. The results indicated that there were high primary production periods in the past, during the Littorina Sea and the Roman Climatic Optimum, accompanied by oxygen deficiency in the near‐bottom water, most probably caused by climate warming. The ratio of 132,173‐cyclopheophorbide‐a enol, a labile degradation product of chlorophyll‐a, to the sum of other chloropigments‐a (CPPB‐aE/ΣChlns‐a) is proposed as a new paleoredox proxy. Heterocystous cyanobacteria blooms of an intensity similar to or even greater than at present also occurred in past millennia and were connected with climate warming. Hence, eutrophication must have occurred in the past, which means that natural factors have a substantial influence on it.

Taheri-Shakib, J., Hosseini, S.A., Kazemzadeh, E., Keshavarz, V., Rajabi-Kochi, M., Naderi, H., 2019. Experimental and mathematical model evaluation of asphaltene fractionation based on adsorption in porous media: Dolomite reservoir rock. Fuel 245, 570-585.


In this study, a whole asphaltene sample was first aged with five dolomite core samples. Then the core samples were washed with toluene; this asphaltene was named the bulk sub-fraction. Thereafter, they were washed with tetrahydrofuran, so that the n-adsorbed sub-fraction was dissolved in solvent. At the last step, the core sample was washed with an azeotrope of methanol/chloroform, which corresponded to the h-adsorbed sub-fraction, and the residual asphaltenes within the porous media were irreversibly adsorbed. According to the elemental analysis of whole asphaltene and its sub-fractions, sulfur was the most abundant element in the molecular structure of asphaltene. The presence of sulfur near dolomite increased the interaction between asphaltene and the rock surface; thus, the h-adsorbed asphaltene had the highest sulfur content. Nitrogen and oxygen content did not show a clear trend in the sub-fractions; therefore, their placements in the molecule were examined using more precise tools, such as Fourier-transform infrared spectroscopy (FTIR). Oxygen was found in asphaltene fractions in the form of a carboxylic acid functional group. From the calculation of the value of the RO–H index, the h-adsorbed asphaltene had more ability to establish a hydrogen bond (RO–H = 26.88) than the other fractions. Furthermore, by calculating the aliphatic and aromaticity indices, the sub-fraction adsorbed to the dolomite surface (h-adsorbed) had the least aliphatic compounds and the highest amount of aromaticity among the sub-fractions. In addition, the h-adsorbed sub-fraction had shorter side alkyl chains than the bulk and n-adsorbed asphaltenes. Carbon number analysis was also performed to determine the number of carbons present in each molecule and to measure the molecular size of each asphaltene sub-fraction. The results showed that the C29+ fractions in the bulk sub-fraction were high (41.39%), while the C14–C26 and C15–C24 fractions had the highest frequencies in the n-adsorbed and h-adsorbed sub-fractions, respectively. A new mathematical model was tuned to determine the porosity and permeability of a resulting asphaltene deposition. The main reason for the high accuracy and innovation in the proposed relationship was the use of the fluid velocity parameter in the porous media and the volume of fluid injected into the core. In addition, the dependence of porosity and permeability reductions on parameters such as the ratio of the contribution of each asphaltene sub-fraction and the amount of the heteroatoms in each sub-fraction was studied for the first time.

Tajik, S., Shahrabadi, A., Rashidi, A., 2019. Silica-graphene nanohybrid supported MoS2 nanocatalyst for hydrogenation reaction and upgrading heavy oil. Journal of Petroleum Science and Engineering 177, 822-828.


Application of nanoparticles in enhanced heavy oil recovery has drawn numerous attentions in the last decade. The nanoparticles can act as carries for catalytic species, e.g., metals for in situ reactions, such as oxidation and hydrogenation, which are efficiently used to improve the heavy oil recovery process. Herein the facile ball-milling method is reported for the synthesis of silica-graphene nanohybrid supported molybdenum disulfide (MoS2) nanocatalyst with different weight percentages of MoS2 (silica-graphene/MoS2), which can be used for upgrading heavy crude oil. The morphological analyses show that adding nanohybrids containing graphene sheets in ball-milling process for the synthesis of silica-graphene/MoS2 increases the distance between crystalline plates in MoS2 and improves catalytic activity. Hydrogenation reactions of phenanthrene and crude oil were carried out at a total pressure of 60 bar (900 psi), at 200 °C. Reaction products were analyzed by a gas chromatograph-mass spectrometer. Furthermore, the effect of the amount of catalyst (10 wt% and 20 wt% of MoS2) loading on the supported in hydrogenation reactions is investigated. The silica-graphene/MoS2 containing 10 wt% MoS2 can significantly increase the API gravity of crude oil (up to 7.7°) and decrease its viscosity (up to 81%).

Tang, K., Wang, Y., Wang, X., 2019. Recent progress on signalling molecules of coral-associated microorganisms. Science China Earth Sciences 62, 609-618.

https://doi.org/10.1007/s11430-018-9332-1

Coral reefs have high primary productivity and are one of the most important ecosystems in the ocean. However, the health and stability of coral reefs are constantly threatened by climate change and human activities. The coral holobiont is a complex symbiosis between the coral animal, zooxanthellae, and the associated community of microorganisms including bacteria, archaea, viruses, etc. Coral-associated microorganisms are found to be important for the maintenance of coral health, and they are proposed to contribute to the acclimatization and adaptation of reef-building corals under rapid climate change. The coral-microbe interaction mediated by chemical signalling molecules is an important driving force for shaping the microbial communities. Herein, we summarize our current knowledge of the chemical signalling molecules involved in the interaction of the coral holobiont. Specifically, the cooperation and competition among microbes mediated by N-acyl homoserine lactones (AHLs), the interrelationship between microbes and hosts mediated by dimethylsulfoniopropionate (DMSP) and nitric oxide (NO), and the response of corals and microorganisms to reactive oxygen species (ROS) under environmental stresses are highlighted in this review. We further discuss the potential of manipulating the coral microbiome using signalling molecules to restore and protect coral reefs.

Temel, O., Karatekin, Ö., Gloesener, E., Mischna, M.A., van Beeck, J., 2019. Atmospheric transport of subsurface, sporadic, time-varying methane releases on Mars. Icarus 325, 39-54.


This study is devoted to the general circulation modeling (GCM) of methane transport in the Martian atmosphere. A localized source originating from a near-subsurface methane reservoir is considered in the GCM simulations, which are performed with a modified version of the Weather Research and Forecasting (WRF) model, MarsWRF. The localized strength of a methane source varies with time, based on a 1-D near-subsurface diffusive transport. Time-varying surface release scenarios are also compared with an instantaneous release scenario. After release from the surface, the methane transport is investigated in the GCM as a passive scalar over time scales varying between 15 and 60 days, much shorter than the photochemical lifetime. Different emission scenarios of various duration and source intensity, as well as multiple locations with different elevation and terrain complexity are considered, to reproduce the substantial concentrations of methane (up to 50 ppb) observed in the northern hemisphere of Mars in 2003 (Mumma et al., 2009). Among the scenarios considered, the observations are reproduced best for an emission scenario of 45 sols duration, during which a total amount of about 90,000 metric tons of methane is released. The results reveal that observed Mars methane plumes in the northern hemisphere of Mars by Mumma et al. (2009) can be reproduced using a localized, time-varying methane source, consistent with a near surface methane reservoir.

Tena-Garitaonaindia, M., Llamas, I., Toral, L., Sampedro, I., 2019. Chemotaxis of halophilic bacterium Halomonas anticariensis FP35 towards the environmental pollutants phenol and naphthalene. Science of The Total Environment 669, 631-636.


Chemotaxis can play an important role in bioremediation and substrate bioavailability. The bioremediation of hydrocarbons in saline environments can be carried out by technologies using halophilic bacteria. The aim of this study is to analyse chemotactic responses of the halophilic bacterium Halomonas anticariensis FP35T to environmental pollutants, as well as its catabolic potential for biotechnological use in bioremediation processes under saline conditions. Chemotaxis was detected and quantified using a modified Adler capillary assay. PCR amplification with degenerate primers for genes encoding ring-cleaving enzymes was used to characterize the catabolic versatility of FP35T. The results indicate that phenol (100–1,000 ppm) and naphthalene (100–500 ppm) are chemoattractants for H. anticariensis FP35T in a dose-dependent manner. These hydrocarbons were observed to act as chemoattractants for FP35T grown in a wide range of sea salt solutions (5–12.5% (w/v). However, the 7.5% (w/v) saline concentration was found to have the strongest chemotactic response. We also detected genes encoding ring-cleaving enzymes in the β-ketoadipate pathway for aromatic catabolism. These results suggest that H. anticariensis FP35T has the potential to catabolize aromatic compounds and to be used in bioremediation processes under saline conditions.

Termopoli, V., Famiglini, G., Palma, P., Piergiovanni, M., Rocio-Bautista, P., Ottaviani, M.F., Cappiello, A., Saeed, M., Perry, S., 2019. Evaluation of a liquid electron ionization liquid chromatography–mass spectrometry interface. Journal of Chromatography A 1591, 120-130.


Liquid Electron Ionization (LEI), is an innovative liquid chromatography-mass spectrometry (LC–MS) interface that converts liquid HPLC eluent to the gas-phase in a mass spectrometer equipped with an electron ionization (EI) source. LEI extends the electronic spectra libraries access to liquid chromatography, providing a powerful tool in the untargeted approacssh. Negligible matrix effects allow accurate quantitative information. The purpose of this research was to evaluate the main aspects concerning the interfacing process. These fundamental studies were necessary to understand the mechanism of LEI in details, and improve the interfacing process, especially regarding robustness and sensitivity. Hardware components were installed to prevent analytes precipitation, reduce thermal decomposition of sensitive compounds, and to stabilize the nano-flow delivery with different mobile-phase compositions. Particular attention was devoted to insulating the heated vaporization area from the LC part of the system. Experiments were performed to optimize the interface inner capillary dimensions, and other operative parameters, including temperature, gas and liquid flow rates. Test compounds of environmental interest were selected based on molecular weight, thermal stability, volatility, and polarity. Robustness was evaluated with a set of replicated injections and calibration experiments using a soil matrix as a test sample. MRM detection limits in the low-picogram range were obtained for five pesticides belonging to different classes in a soil sample. High-quality electron ionization mass spectra of a mixture of pesticides were also obtained.

Thakar, Y., Bhavsar, R., Swadia, M., Vinodkumar, M., Mason, N., Limbachiya, C., 2019. Electron interactions with astro chemical compounds. Planetary and Space Science 168, 95-103.


In present work electron induced processes with important astro-compounds found in the tholins of Titan are investigated. We report calculated total elastic cross sections Qel, total inelastic cross sections Qinel, total ionization cross sections Qion, total excitation cross sections ∑Qexc and total cross sections QT for hydrogen cyanide (HCN), cyanoacetylene (HCCCN), vinyl cyanide (CH2CHCN), methanimine (CH2NH) and ethanimine (CH3CHNH) on electron impact for energies from ionization

threshold to 5 keV. We have employed the Spherical Complex Optical Potential (SCOP) formalism to investigate elastic as well as inelastic processes and used Complex Scattering Potential – ionization contribution (CSP-ic) method to derive ionization cross sections. In absence of any theoretical or experimental data of ionization cross sections except for HCN and HCCCN, we have computed Q ion using the Binary- Encounter- Bethe (BEB) method for all these molecules and have found reasonable agreement. This is the maiden attempt to report various total cross sections for all these astro-molecules except HCN and HCCCN.

Thottathil, S.D., Reis, P.C.J., Prairie, Y.T., 2019. Methane oxidation kinetics in northern freshwater lakes. Biogeochemistry 143, 105-116.

https://doi.org/10.1007/s10533-019-00552-x

Understanding the drivers of aerobic methane (CH4) oxidation (MOX) is paramount in assessing the current and potential future CH4 emissions from freshwater aquatic systems. Regulation of MOX kinetics is a complex function of CH4 and oxygen (O2) concentrations. While MOX activity is usually proportional to the concentration of CH4 itself, the effects of O2 have been more conflicting, with maximum MOX rates often restricted to low O2 concentrations. Despite the complexity involved, MOX kinetics are often modelled as monotonic positive functions of both CH4 and O2 concentrations. We conducted a series of incubation experiments using natural and unamended water samples obtained from multiple depths in northern temperate lakes that vary widely and independently in their CH4 and O2 concentrations. Our results showed the expected positive effect of CH4 concentration and temperature but also demonstrated the strong inhibitory effects of O2 at high concentration. We then developed a general model describing the kinetics of MOX, simultaneously integrating the effects of CH4 concentration, temperature as well as the non-linear effect O2 on MOX activity. The model revealed an overall temperature dependency (activation energy = 0.49 ± 0.06 eV) much lower than reported for methanogenesis and an optimal O2 level around 15 μmol O2 L−1 where maximum MOX activity occurs, regardless of CH4 concentration and temperature. We further show that ignoring the inhibitory effect of O2 can lead to significant bias in calculating the expected MOX rates in different portions of the water column.

Tian, L., Tong, J., Xiao, Y., Benton, M.J., Song, H., Song, H., Liang, L., Wu, K., Chu, D., Algeo, T.J., 2019. Environmental instability prior to end-Permian mass extinction reflected in biotic and facies changes on shallow carbonate platforms of the Nanpanjiang Basin (South China). Palaeogeography, Palaeoclimatology, Palaeoecology 519, 23-36.


Shallow carbonate platforms exhibit major changes in faunal composition and facies types during the latest Permian and earliest Triassic. Although the microbialites that developed following the latest Permian mass extinction (LPME) have attracted wide attention, temporal variations in shallow-platform facies and faunas prior to the LPME have been less thoroughly studied. Here, we analyze diversity patterns and variation in skeletal composition in three Upper Permian sections from isolated carbonate platforms of the Nanpanjiang Basin. In addition to the well-known transition from fossil-rich Upper Permian limestones to fossil-poor Permian-Triassic boundary (PTB) microbialites, these sections exhibit several distinct changes that predate the LPME. First, foram faunas show a shift from non-fusulinid-dominated to fusulinid-dominated communities in the <1-m interval below the LPME horizon of each section, reflecting a shallowing trend over ~20–30 kyr preceding the mass extinction. Second, a “foram gap” and concurrent “detrital event” are observed below the LPME in all three sections, recording a rapid influx of detrital siliciclastics that predated the mass extinction by <60 kyr.

These features reflect a degree of marine environmental instability prior to the end-Permian mass extinction. The sudden influx of siliciclastics may represent an early perturbation to terrestrial ecosystems linked to incipient Siberian Traps magmatism, resulting in secondary effects in marine environments through increased sediment yields.



Considering the influence of reservoir on microbial growth and the competition of microbial community on nutrition, a mathematical model for microbial enhanced oil recovery considering the double-bacterial competition mechanism is established. The components of this mathematical model consist of oil, water, microbe 1, microbe 2, nutrients, metabolite1 and metabolite2. The equations of this numerical model take into account the decay and growth of microorganisms, nutrient consumption, metabolism production, chemotaxis, convection–dispersion, water viscosity increment, oil viscosity reduction, interfacial tension reduction, adsorption, and desorption. In this study, three numerical examples were performed to analyze the double-bacterial competition mechanism and the effects of product interaction on improving oil recovery through a simulator developed according to our mathematical model. We found that: (1) Under different double-bacterial growth models (symbiotic effect, repressive effect and no effect), there is a big difference in product concentration and oil displacement efficiency; (2) Double-bacterial growth model can better simulate actual reservoir application of microbial flooding technology than single microbial model; (3) Double-bacterial growth model with different products can increase oil recovery by up to 12.3% compared with water flooding.

Tirjoo, A., Bayati, B., Rezaei, H., Rahmati, M., 2019. Molecular dynamics simulations of asphaltene aggregation under different conditions. Journal of Petroleum Science and Engineering 177, 392-402.


The formation of organic sediments, especially asphaltene in reservoirs, wells and equipment, has a harmful effect on the oil production economy, which reduces oil production and can block oil production facilities. In order to investigate the asphaltene aggregation and solubility, a series of molecular dynamics simulations in different conditions were performed on two famous asphaltene based model, of M1 and VI. VI asphaltene has two high aliphatic side chains, whereas M1 asphaltene has only two methyl groups on its sides. The simulation results show that the solubility parameter increases with increasing number of aromatic rings and decreasing the number of carbon atoms in the side chain. The aggregation of asphaltene molecules in toluene, heptane and isopropyl benzene solvents and also in the mixture of solvents has been investigated. The results show that the aggregation of M1 asphaltene in toluene and isopropyl benzene is lower than that of VI asphaltene. The mixture isopropyl benzene-heptane is appropriate solvent for both asphaltenes M1 and VI which represents less interaction between asphaltene molecules. The effect of six types of inhibitors on the aggregation of asphaltene was investigated. Based on the simulation results, the aggregation of asphaltene with the presence of DETPMP inhibitor significantly decreases due to the delay in the growth of crystals and by increasing the concentration of all used inhibitors, their inhibitory properties were decreased.

Tokano, T., Lorenz, R.D., 2019. Modeling of seasonal lake level fluctuations of Titan's seas/lakes. Journal of Geophysical Research: Planets 124, 617-635.

https://doi.org/10.1029/2018JE005898

Abstract: Seasonal variations in lake levels of Titan's hydrocarbon seas/lakes are predicted by an ocean circulation model in an effort to understand the observed temporal changes in lake size or lack thereof. Three different ground permeabilities are assumed so as to change the relative importance of precipitation, evaporation, river runoff, and groundwater seepage for the lake methane budget. The lake level generally rises in the rainy season around the summer solstice and falls or stagnates during long dry periods in autumn and winter. The annual lake level range in the northern hemisphere amounts to 50–120 cm depending on geographic location and size of the lakes and ground permeability. If the hydraulic connection between Punga Mare and Kraken Mare is weak, the lake level range of Punga Mare amplifies at the expense of other seas and also establishes a large lake level difference between these two seas, which is not compatible with the observation by the Cassini spacecraft. On‐lake precipitation would cause the lake level of Ontario Lacus to vary seasonally by merely 15 cm, yet river runoff from the huge catchment area can increase the annual lake level range to several meters. The shrinkage of Ontario Lacus observed by Cassini is more likely to be caused by lakebed seepage than by evaporation. The ultimate cause of the difference in the seasonal behavior between northern and southern lakes may be the hemispheric asymmetry in precipitation, be it caused astronomically or topographically.

Plain Language Summary: Saturn's moon Titan has many hydrocarbon lakes in the polar region, but only one lake near the south pole has so far shown evidence of lake size change. In order to understand the possible difference in the temporal variation between the northern and southern lakes, we simulated numerically the seasonal lake level change of all major lakes on Titan. The lake level generally rises in spring and summer during the rainy season and falls in dry seasons due to evaporation. However, the magnitude of lake level variation strongly depends on the geographic location and size of the lakes as well as how the ground outside the lakes and lake bottom are made of. Large seas near the north pole experience moderate lake level changes of about 1 m as a response to spatially averaged precipitation and evaporation. Ontario Lacus in the southern hemisphere is located in a dry environment and rapidly grows after sporadic rainfall but also rapidly shrinks by leakage from the lake bottom. This difference ultimately reflects the north‐south asymmetry in Titan's climate.

Topper, T.P., Guo, J., Clausen, S., Skovsted, C.B., Zhang, Z., 2019. A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria. Nature Communications 10, Article 1366.

https://doi.org/10.1038/s41467-019-09059-3

Deuterostomes are a morphologically disparate clade, encompassing the chordates (including vertebrates), the hemichordates (the vermiform enteropneusts and the colonial tube-dwelling pterobranchs) and the echinoderms (including starfish). Although deuterostomes are considered monophyletic, the inter-relationships between the three clades remain highly contentious. Here we report, Yanjiahella biscarpa, a bilaterally symmetrical, solitary metazoan from the early Cambrian (Fortunian) of China with a characteristic echinoderm-like plated theca, a muscular stalk reminiscent of the hemichordates and a pair of feeding appendages. Our phylogenetic analysis indicates that Y. biscarpa is a stem-echinoderm and not only is this species the oldest and most basal echinoderm, but it also predates all known hemichordates, and is among the earliest deuterostomes. This taxon confirms that echinoderms acquired plating before pentaradial symmetry and that their history is rooted in bilateral forms. Yanjiahella biscarpa shares morphological similarities with both

enteropneusts and echinoderms, indicating that the enteropneust body plan is ancestral within hemichordates.

Tranchida, P.Q., Aloisi, I., Giocastro, B., Zoccali, M., Mondello, L., 2019. Comprehensive two-dimensional gas chromatography-mass spectrometry using milder electron ionization conditions: A preliminary evaluation. Journal of Chromatography A 1589, 134-140.


The present research is based on the use of comprehensive two-dimensional gas chromatography-quadrupole mass spectrometry (GC × GC-QMS), using “milder” electron ionization (EI) conditions. The term milder refers to the use of lower energy EI conditions (e.g., 20 eV), instead of the most common electron energy of 70 eV. The effects of using lower source temperatures were also evaluated. Within such an analytical context, GC × GC-QMS was applied to the analysis of a variety of different molecular-mass compounds with various polarities (sterols, linear alkanes, fatty acid methyl esters, vitamin E, squalene, a linear alcohol, and a group of fifteen pesticides). In general, the results attained indicate that milder EI conditions, and lower source temperatures, generate mass spectra with a higher relative abundance of ions at higher mass-over-charge (m/z) values, comprising the molecular ion, and reduced fragmentation at lower m/z values. The extent to which such a phenomenon occurred was obviously related to the chemical structure of each analyte. Spectral repeatability was also assessed, and was found to be satisfactory. Finally, with regard to analyte signal-to-noise ratios these were generally comparable in applications involving different electron ionization energies.



Significance: During the Holocene (11,600 y ago to present), northern peatlands accumulated significant C stocks over millennia. However, virtually nothing is known about peatlands that are no longer in the landscape, including ones formed prior to the Holocene: Where were they, when did they form, and why did they disappear? We used records of peatlands buried by mineral sediments for a reconstruction of peat-forming wetlands for the past 130,000 y. Northern peatlands expanded across high latitudes during warm periods and were buried during periods of glacial advance in northern latitudes. Thus, peat accumulation and burial represent a key long-term C storage mechanism in the Earth system.

Abstract: Glacial−interglacial variations in CO2 and methane in polar ice cores have been attributed, in part, to changes in global wetland extent, but the wetland distribution before the Last Glacial Maximum (LGM, 21 ka to 18 ka) remains virtually unknown. We present a study of global peatland extent and carbon (C) stocks through the last glacial cycle (130 ka to present) using a newly compiled database of 1,063 detailed stratigraphic records of peat deposits buried by mineral sediments, as well as a global peatland model. Quantitative agreement between modeling and observations shows extensive peat accumulation before the LGM in northern latitudes (>40°N), particularly during

warmer periods including the last interglacial (130 ka to 116 ka, MIS 5e) and the interstadial (57 ka to 29 ka, MIS 3). During cooling periods of glacial advance and permafrost formation, the burial of northern peatlands by glaciers and mineral sediments decreased active peatland extent, thickness, and modeled C stocks by 70 to 90% from warmer times. Tropical peatland extent and C stocks show little temporal variation throughout the study period. While the increased burial of northern peats was correlated with cooling periods, the burial of tropical peat was predominately driven by changes in sea level and regional hydrology. Peat burial by mineral sediments represents a mechanism for long-term terrestrial C storage in the Earth system. These results show that northern peatlands accumulate significant C stocks during warmer times, indicating their potential for C sequestration during the warming Anthropocene.

Trower, E.J., Lamb, M.P., Fischer, W.W., 2019. The origin of carbonate mud. Geophysical Research Letters 46, 2696-2703.

https://doi.org/10.1029/2018GL081620

Abstract: Carbonate mudstones are key geochemical archives for past seawater chemistry, yet the origin of carbonate mud remains a subject of continued debate and uncertainty. Prevailing hypotheses have settled on two mechanisms: (1) direct precipitation in the water column and (2) postmortem dispersal of mud‐sized algal skeletal components. However, both mechanisms conflict with geochemical observations in modern systems and are problematic in deep time. We tested the hypothesis that abrasion of carbonate sand during sediment transport might produce carbonate mud using laboratory experiments and a sediment transport model. We documented experimental mud production rates up to two orders f magnitude faster than rates estimated for other mechanisms. Combined with model calculations, these results illustrated that transport and abrasion of carbonate sand is a major source of carbonate mud.

Plain Language Summary: Carbonate mudstones are widely used as archives of ancient seawater chemistry, under the assumption that the compositions of mud‐sized (<62.5 μm in diameter) carbonate particles that make up these mudstones provide reliable records of seawater at the time the particles were formed and deposited. This assumption relies on understanding how carbonate mud forms—current ideas center on direct mineral precipitation from seawater and the disintegration of algae mineral skeletons—but these mechanisms conflict with some geochemical observations in modern systems. We used experiments to demonstrate that when carbonate sand grains are transported by currents, collisions cause mud‐sized carbonate particles to be released from grain surfaces via abrasion. The rapid rates of carbonate mud production observed in our experiments suggest that abrasion has been a significant source of carbonate mud throughout Earth history, which is important for interpreting geochemical records from carbonate mudstones because the material abraded from sand grains may not be instantaneous records of seawater chemistry.

Tsikalas, F., Eldholm, O., 2019. Malvinas (Falkland) Plateau structure versus Mjølnir crater: Geophysical workflow template for proposed marine impact craters. Meteoritics & Planetary Science 54, 544-557.


A diagnostic geophysical‐based template, supported by modelling, is suggested to be used prior to, or in combination with geological/drilling data, when proposing a marine impact crater. The latter refers to impacts occurring in a marine setting and resulting in structures that are currently partially or totally underwater. The methodology is based on the well‐documented Mjølnir crater in the Barents Sea. The template has been developed in conjunction with the recently proposed and debated impact

crater on the Malvinas (Falkland) Plateau in the South Atlantic. Despite their different sizes, their comparison adds to the ambiguous nature of the Malvinas structure and shows that the integrated analysis of seismic and potential field data and modelling is crucial for any interpretation of a marine impact crater without relevant geological information. The proposed workflow template utilizes all available geophysical data and is composed of a series of iterative steps, including a range of alternative nonimpact interpretations that must be discussed and accounted for. Subsequently, further iterative geophysical modelling is required to support and decipher the impact related processes. A more complex impact crater model and additional impact crater features can be resolved by physical property modelling. In all cases, a close spatial correspondence of the defined impact structure with potential field anomalies is a necessity to establish a causal relationship. We suggest that the diagnostic workflow template provides a methodology to be applied to future studies of the Malvinas structure, as well as to proposed marine (and, with minor adaptions, to nonmarine) impact craters in general.



To investigate the evolution of the hydraulic and elastic properties of reservoir rocks associated with CO2 mineralization in carbon capture and storage projects, we simulated the mineral precipitation process in a 3D model of natural sandstone, created from micro-CT scanned images, and a 3D model consisting of close-packed beads. Two different mineralization schemes were used: the first calculated pore filling by calcite by applying an advection-reaction equation to the fluid flow velocity field within the pore spaces of the rock models using a lattice Boltzmann simulation, and the second simulated pore filling by increasing the grain radius. We estimated the P-wave and S-wave velocities in the rock models using a dynamic wave propagation simulation and estimated the permeabilities using a lattice Boltzmann simulation. The simulation results showed that the elastic properties of the digital rocks were strongly influenced by mineralization around the grains, whereas their hydraulic properties were influenced by mineralization within the pore body. The elastic and hydraulic properties calculated from our rock models agree with those calculated using conventional rock physics theories, such as effective medium theory and the Kozeny-Carman equation, in terms of crack aspect ratio and tortuosity. Direct simulation using digital rocks enables us to explore the complex relations among the hydraulic and elastic parameters of rocks during CO2 mineralization. The relationships between permeability and seismic velocity are strongly influenced by mineralization types as well as rock types; nevertheless, permeabilities have a definite relationship with the P-wave to S-wave velocity ratio (Vp/Vs). By applying the rock modeling approach of this study to target reservoirs, permeability evolution due to CO2 mineralization could be evaluated on the basis of seismic velocities from geophysical monitoring data.

Tumiati, S., Malaspina, N., 2019. Redox processes and the role of carbon-bearing volatiles from the slab–mantle interface to the mantle wedge. Journal of the Geological Society 176, 388-397.


The valence of carbon is governed by the oxidation state of the host system. The subducted oceanic lithosphere contains considerable amounts of iron so that Fe3+/Fe2+ equilibria in mineral assemblages are able to buffer the (intensive) fO2 and the valence of carbon. Alternatively, carbon itself can be a carrier of (extensive) ‘excess oxygen’ when transferred from the slab to the mantle, prompting the oxidation of the sub-arc mantle. Therefore, the correct use of intensive and extensive

variables to define the slab-to-mantle oxidation by C-bearing fluids is of primary importance when considering different fluid/rock ratios. Fluid-mediated processes at the slab–mantle interface can also be investigated experimentally. The presence of CO2 (or CH4 at highly reduced conditions) in aqueous COH fluids in peridotitic systems affects the positions of carbonation or decarbonation reactions and of the solidus. Some methods to produce and analyse COH fluid-saturated experiments in model systems are introduced, together with the measurement of experimental COH fluids composition in terms of volatiles and dissolved solutes. The role of COH fluids in the stability of hydrous and carbonate minerals is discussed comparing experimental results with thermodynamic models and the message of nature.

Turney, C.S.M., McGregor, H.V., Francus, P., Abram, N., Evans, M.N., Goosse, H., von Gunten, L., Kaufman, D., Linderholm, H., Loutre, M.F., Neukom, R., 2019. Introduction to the special issue “Climate of the past 2000 years: regional and trans-regional syntheses”. Climate of the Past 15, 611-615.

https://www.clim-past.net/15/611/2019/

This PAGES (Past Global Changes) 2k (climate of the past 2000 years working group) special issue of Climate of the Past brings together the latest understanding of regional change and impacts from PAGES 2k groups across a range of proxies and regions. The special issue has emerged from a need to determine the magnitude and rate of change of regional and global climate beyond the timescales accessible within the observational record. This knowledge also plays an important role in attribution studies and is fundamental to understanding the mechanisms and environmental and societal impacts of recent climate change. The scientific studies in the special issue reflect the urgent need to better understand regional differences from a truly global view around the PAGES themes of “Climate Variability, Modes and Mechanisms”, “Methods and Uncertainties”, and “Proxy and Model Understanding”.

Uesugi, M., Ito, M., Yabuta, H., Naraoka, H., Kitajima, F., Takano, Y., Mita, H., Kebukawa, Y., Nakato, A., Karouji, Y., 2019. Further characterization of carbonaceous materials in Hayabusa-returned samples to understand their origin. Meteoritics & Planetary Science 54, 638-666.


Carbonaceous materials in the sample catcher of the Hayabusa spacecraft were assigned as category 3 particles. We investigated the category 3 particles with a suite of in situ microanalytical methods. Possible contaminants collected from the cleanrooms of the spacecraft assembly and extraterrestrial sample curation center (ESCuC) were also analyzed in the same manner as category 3 particles for comparison. Our data were integrated with those of the preliminary examination team for category 3 particles. Possible origins for the category 3 particles include contamination before and after the operation of the Hayabusa spacecraft.

Ullmann, P.V., Pandya, S.H., Nellermoe, R., 2019. Patterns of soft tissue and cellular preservation in relation to fossil bone tissue structure and overburden depth at the Standing Rock Hadrosaur Site, Maastrichtian Hell Creek Formation, South Dakota, USA. Cretaceous Research 99, 1-13.


Recovery of soft tissues and cells from fossil bones is becoming increasingly common, with structures morphologically consistent with vertebrate osteocytes, blood vessels, fibrous/collagenous

matrix, and potential intravascular contents now recognized from specimens dating back to the Permian. However, it largely remains unclear how bone tissue structure, early diagenetic regimes, and many other taphonomic variables influence or control the preservation potential of soft tissues in vertebrate fossils. To explore the influence of a few of these factors, we tested a suite of fossils from the Standing Rock Hadrosaur Site, a vast Edmontosaurus annectens bonebed in the Maastrichtian Hell Creek Formation of South Dakota, for preservation of cellular and tissue components. Demineralization of bone samples from each specimen yielded abundant microstructures morphologically consistent with vertebrate osteocytes, blood vessels, and collagenous matrix. This includes the first recovery of osteocytes and vessels from a fossil vertebral centrum and ossified tendons. Perhaps surprisingly, no correlation was found between soft tissue/cellular recovery and either bone tissue structure type (cortical vs. cancellous) or overburden depth at the time of discovery. A traditional taphonomic survey of the site, conducted in parallel and reported previously, affords a clear and detailed history of these remains, both pre- and postburial. Cumulative taphonomic evidence indicates the Edmontosaurus individuals died in a mass mortality event and their disarticulated remains were buried rapidly in a shallow floodplain pond during a crevasse splay event. Oxygenated flood waters and/or groundwater oxidized initially sideritic concretions to goethite during early diagenesis, facilitating rapid cementation of portions of the sediment that likely aided stabilization of soft tissues by shielding regions of the bones from prolonged exposure to pore fluids. Our findings support cancellous bone as a viable target for cellular analyses, corroborate previous propositions that iron-rich environments and rapid burial facilitate soft tissue preservation, and provide new details into early diagenetic environments conducive to such preservation.

Urrutia-Fucugauchi, J., Pérez-Cruz, L., Morgan, J., Gulick, S., Wittmann, A., Lofi, J., Party, I.-I.E.S., 2019. Peering inside the peak ring of the Chicxulub Impact Crater—its nature and formation mechanism. Geology Today 35, 68-72.

https://doi.org/10.1111/gto.12261

The IODP-ICDP Expedition 364 drilled into the Chicxulub crater, peering inside its well-preserved peak ring. The borehole penetrated a sequence of post-impact carbonates and a unit of suevites and clast-poor impact melt rock at the top of the peak ring. Beneath this sequence, basement rocks cut by pre-impact and impact dykes, with breccias and melt, were encountered at shallow depths. The basement rocks are fractured, shocked and uplifted, consistent with dynamic collapse, uplift and long-distance transport of weakened material during collapse of the transient cavity and final crater formation.

Vadsaria, T., Ramstein, G., Dutay, J.C., Li, L., Ayache, M., Richon, C., 2019. Simulating the occurrence of the last sapropel event (S1): Mediterranean Basin ocean dynamics simulations using Nd isotopic composition modeling. Paleoceanography and Paleoclimatology 34, 237-251.

https://doi.org/10.1029/2019PA003566

Sapropels are sediments rich in black, pelagic organic matter which occur mainly in the Eastern Mediterranean, documenting anoxic environments and high biological productivity. The quasiperiodicity of deposition of sapropels ‐over millions of years‐ relates to the Earth's precession cycle, which directly enhances the African monsoon, ultimately increasing freshwater input from the Nile. The last sapropel event, S1, occurred about 10,000 years ago (Early Holocene), when the Mediterranean region was warmer and wetter than today. Several modeling studies reflect the impact of this climate and a stronger Nile influx on Mediterranean oceanic circulation, but the regional models used lacked the spatial resolution necessary to simulate winter intermediate and deep

convection. Here, we investigate recently occurring changes in the convective areas in the Eastern Mediterranean, using a regional ocean–atmosphere coupled climate model of high spatial resolution, essential to the simulation of a realistic Mediterranean circulation for present‐day conditions. We focused on the thermohaline circulation and the simulation of neodymium isotopic composition to compare our modeling results to modern data and paleo‐proxies. A sensitivity experiment shows a radical response of the Mediterranean to enhanced Nile discharge, creating the appropriate conditions for sapropel formation. We thus demonstrate that increased discharge of the Nile River can trigger the shutdown of Eastern Mediterranean convection and create conditions favorable to the development of anoxic events.

Vakhin, A.V., Onishchenko, Y.V., Chemodanov, A.E., Sitnov, S.A., Mukhamatdinov, I.I., Nazimov, N.A., Sharifullin, A.V., 2019. The composition of aromatic destruction products of Domanic shale kerogen after aquathermolysis. Petroleum Science and Technology 37, 390-395.

https://doi.org/10.1080/10916466.2018.1547760

In this article we studied a sample of Domanic rock with high kerogen content obtained from Volga-Ural oil and gas basin. A laboratory modeling of the catagenesis process was carried out in order to establish the transformation mechanism of organic matter. The composition of liquid products resulting from kerogen pyrolysis was investigated. The kerogen fragments fall in aromatic hydrocarbons fraction. Alkyltoluenes also exist in saturated hydrocarbon fractions due to alkyl substitutes. The thermal influence changes the ratios of relative content of ortho-, para- and meta-isomers. Heavy aromatic hydrocarbons content increases by increasing temperature and kerogen macroelements ratio changed under thermal effect that is an indicator for maturation process of organic matter.

Valsala, R., Govindarajan, S.K., 2019. Co-colloidal BTEX and microbial transport in a saturated porous system: Numerical modeling and sensitivity analysis. Transport in Porous Media 127, 269-294.

https://doi.org/10.1007/s11242-018-1191-2

A large number of studies were carried out in the past to analyze the significance of colloids and microbes in remediating groundwater aquifers contaminated with petroleum hydrocarbons. However, the influence of the co-occurrence of colloid and microbe on the migration of petroleum hydrocarbons is still poorly understood. In the present study, an attempt is made to numerically investigate the impact of the co-occurrence of colloids and microbes on the transport of BTEX (benzene, toluene, ethylbenzene, and xylene). A finite-difference model is developed to analyze the co-transport of colloid, microbe, and BTEX within a saturated porous aquifer. The present model is formulated based on the assumption that the colloid migration within the aquifer is not affected by the presence of microbe and BTEX. The microbe presented in the manuscript is deemed to biodegrade the BTEX constituents aerobically. Hence, the modeling study also incorporates the migration of dissolved oxygen within the aquifer. The results obtained from the simulation study suggest that the co-occurrence of colloid and microbe causes significant retardation in the movement of dissolved BTEX constituents within the aquifer. It is also seen that the presence of colloid considerably enhances the biodegradation rate of BTEX within the aquifer. A sensitivity analysis is carried out to investigate the sensitivity of the concentration distribution of colloid, microbe, and BTEX to various flow and sorption parameters. The concentration level of colloid, microbe, and BTEX constituents is found to be sensitive to the variation in the flow and sorption parameters.

Vasiliev, I., Karakitsios, V., Bouloubassi, I., Agiadi, K., Kontakiotis, G., Antonarakou, A., Triantaphyllou, M., Gogou, A., Kafousia, N., de Rafélis, M., Zarkogiannis, S., Kaczmar, F., Parinos, C., Pasadakis, N., 2019. Large sea surface temperature, salinity, and productivity-preservation changes preceding the onset of the Messinian Salinity Crisis in the eastern Mediterranean Sea. Paleoceanography and Paleoclimatology 34, 182-202.

https://doi.org/10.1029/2018PA003438

Abstract: The Messinian Salinity Crisis (MSC; 5.97–5.33 Ma) is an enigmatic episode of paleoceanographic change, when kilometer‐thick evaporite units were deposited in the Mediterranean basin. Here we use geochemical (biomarker and isotope) data to reconstruct sea surface temperature, salinity, and productivity‐preservation changes in the Mediterranean basin just before the MSC. The proxy data indicate that the Mediterranean Sea was significantly saltier and colder between 6.415 and 6.151 Ma, than between 6.151 and 5.971 Ma. Salinity decrease at 6.151 Ma seems to be a relatively fast event just preceding the inception of a warming phase that lasted almost uninterrupted until the MSC onset. The water exchange with the Paratethys could have caused, along with the African rivers, an increased freshwater supply, resulting in normal marine Mediterranean waters between 6.151 and 5.971 Ma, despite the severe restriction of marine connections with the Atlantic at that time. Sea surface temperature changes determined a sharp drop in productivity and/or preservation of organic matter, marked by deposition of calcareous marls. Productivity and preservation were relatively high and constant until 6.01 Ma. Afterward, increased influx of terrestrial organic matter and probably enhanced water column stratification prevailed. Around 5.971 Ma, modifications in aquatic versus terrestrially derived biomarkers indicate changes in organic matter influx at the MSC onset.

Plain Language Summary: More than five million years ago, the Mediterranean Sea underwent astonishing changes in its hydrological budget leading to the formation of hypersaline water bodies and the deposition of a more than 1,000‐m salt giant. The way toward the hypersaline conditions of the Messinian Salinity Crisis (5.97–5.33 Ma) was marked by gradual closure of Mediterranean oceanic seaways. Data reveal that the Mediterranean Sea was 8‰ saltier and, in average, 1.2 °C colder between 6.415 and 6.151 Ma, than between 6.151 and 5.971 Ma. At 6.151 Ma, a salinity decrease from 47‰ toward normal marine of 39‰ was a fast event just preceding the inception of a warming lasting almost uninterrupted until the Messinian Salinity Crisis onset.

Veillard, C.M.A., John, C.M., Krevor, S., Najorka, J., 2019. Rock-buffered recrystallization of Marion Plateau dolomites at low temperature evidenced by clumped isotope thermometry and X-ray diffraction analysis. Geochimica et Cosmochimica Acta 252, 190-212.


Much debate exists on the extent to which early dolomites recrystallize and preserve the signature of their primary diagenetic setting. Here, we combine clumped isotopes thermometry with X-ray diffraction and thin section petrography to study dolomite recrystallization under shallow burial (<1 km) conditions. We analysed 26 dolomite samples from two Miocene carbonate platforms on the Marion Plateau, NE Australia. Marion Plateau dolomites provide an ideal case study to examine the effects of recrystallization because of the relative simplicity of the geological setting, with simple subsidence, and several episodes of early dolomitization by normal sea water. Results show that Marion Plateau dolomites are very rich in calcium and their formation temperature inferred from clumped isotopes T(Δ47dol) ranges between 12 and 35 °C. The apparent fluid composition (δ18Ow(app)) falls in the range of sea water composition, but a correlation between T(Δ47dol), δ18Odol, and δ18Ow(app) exists: the higher T(Δ47dol), the higher δ18Ow(app). T(Δ47dol) and δ18Ow(app) increase with depth, whereas δ18Odol and δ13Cdol tend to both decrease with depth. We interpret the correlation

between T(Δ47dol) and δ18Ow(app) as evidence of shallow burial recrystallization via dissolution/re-precipitation. Modelling of the T(Δ47dol), δ18Odol, and δ18Ow(app) indicates that the recrystallization happened at very low water to rock ratio. Carbon isotopes δ13C are not reset during recrystallization and are probably inherited from the dolomitization process. This study shows that dolomite recrystallization has the potential to affect T(Δ47dol) at depths shallower than previously demonstrated. It emphasizes the fact that high calcium dolomites (and possibly aragonite and high Mg-calcite) can have a range of T(Δ47dol) before entering the solid-state reordering realm, and that in deeper buried basins, the range of measured T(Δ47dol) could still to a large extent result from recrystallization via dissolution/re-precipitation processes.



Microalgae are considered one of the most promising microorganisms for sustainable production of food products. In order to maximize the biotechnological potential of microalgae, further information on their metabolism is still needed. Gas chromatography (GC) is advantageous for the metabolites analysis, since it allows the separation and detection of several organic compounds, among them volatiles, amino acids, organic acids, carbohydrates, fatty acids and sterols from different sample preparation, with high resolution and sensitivity. In addition to the monitoring and optimization of the microalgal bioprocesses, GC analyzes also aid in the characterization and verification of the biomass quality obtained at the end of the cultivation. Thus, the use of GC shows great potential of monitoring of important metabolites for development of microalgae bioprocesses.



Methane is one of the most important greenhouse gases emitted from natural and human activities. It is scarcely soluble in water; thus, it has a low bioavailability for microorganisms able to degrade it. In this work, the capacity of the fungus Fusarium solani to improve the solubility of methane in water and to biodegrade methane was assayed. Experiments were performed in microcosms with vermiculite as solid support and mineral media, at temperatures between 20 and 35 °C and water activities between 0.9 and 0.95, using pure cultures of F. solani and a methanotrophic consortium (Methylomicrobium album and Methylocystis sp) as a control. Methane was the only carbon and energy source. Results indicate that using thermally inactivated biomass of F. solani, decreases the partition coefficient of methane in water up to two orders of magnitude. Moreover, F. solani can degrade methane, in fact at 35 °C and the highest water activity, the methane degradation rate attained by F. solani was 300 mg m−3 h−1, identical to the biodegradation rate achieved by the consortium of methanotrophic bacteria.


https://doi.org/10.3176/oil.2019.1.06

This paper gives a historic overview of the innovation activities in the former Soviet Union, including the Estonian SSR, in the direct chemical processing of organic matter concentrates of Estonian oil shale kukersite (kukersite) as well as other sapropelites. The overview sheds light on the laboratory experiments started in the 1950s and subsequent extensive, triple-shift work on a pilot scale on nitric acid, to produce individual dicarboxylic acids from succinic to sebacic acids, their dimethyl esters or mixtures in the 1980s.

Vigneron, A., Alsop, E.B., Cruaud, P., Philibert, G., King, B., Baksmaty, L., Lavallee, D., Lomans, B.P., Eloe-Fadrosh, E., Kyrpides, N.C., Head, I.M., Tsesmetzis, N., 2019. Contrasting pathways for anaerobic methane oxidation in Gulf of Mexico cold seep sediments. mSystems 4, Article e00091-00018.

http://msystems.asm.org/content/4/1/e00091-18.abstract

Abstract: Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages.

Importance: Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.



Petroleum has been the world's major source of energy since the middle of the twentieth century, leading to positive changes but also social, political, and environmental problems worldwide. Oil contamination affects all ecosystems, and the remediation of polluted sites using environmentally friendly strategies is crucial. Here, we report an analysis of the patent documents of potential petroleum bioremediation techniques that use microbes to clean seawater. The patent search was performed using Orbit Intelligence®, SciFinder® and the Derwent World Patents Index®. A group of 500 patent documents were validated according to the search objective and carefully studied. Increases in patent deposits coincide with periods following widely reported oil spills, suggesting a relationship between media disclosure and stimulation of innovation activities. China leads the list of countries with patent applications in bioremediation with 152 deposits, followed by Russia with 133 and the US with 48. These three countries have completely different temporal deposit profiles, influenced by their historical, political, and economic scenarios. A total of 368 patents described degradation of the oil compounds exclusively by bacteria, 24 by fungi and yeasts, 1 by Archaea, 1 using a microalgal strain, and 32 by mixed consortia. The leading microbial genera found in the patents are Pseudomonas (114 patents), Bacillus (75), and Rhodococcus (60). In the top-10 list of microbial strains mostly cited/claimed, no genera are obligate hydrocarbonoclastic bacteria. This fact, together with the broad pattern found in the main International Patent Classification (IPC) codes, suggest that most of the documents are general bioremediation approaches and not focused on oil-polluted seawater. This work highlights the importance of stimulating the development of innovative environmentally friendly strategies focused on the degradation of oil hydrocarbons in marine ecosystems.

Vione, D., Albinet, A., Barsotti, F., Mekic, M., Jiang, B., Minero, C., Brigante, M., Gligorovski, S., 2019. Formation of substances with humic-like fluorescence properties, upon photoinduced oligomerization of typical phenolic compounds emitted by biomass burning. Atmospheric Environment 206, 197-207.


The irradiation under simulated sunlight of some phenolic compounds typically emitted in ambient air by biomass burning, namely vanillin and acetosyringone, yielded intermediates with humic-like fluorescence properties that can be assimilated to humic-like substances (HULIS). Evidence was obtained by ultra-high-resolution mass spectrometry of the occurrence of oligomerization processes up to the formation of trimeric species. In contrast, the irradiation of other biomass-burning compounds such as vanillic acid, m-cresol and guaiacol did not yield either HULIS-type fluorescence or oligomers. We suggest that the photolysis of biomass-burning compounds is a potential HULIS source in the atmosphere, if the relevant substrates undergo photoinduced oligomerization reactions.



Petroleum-bearing fluid inclusions are small encapsulations of oil and gas that offer an invaluable opportunity to better constrain the evolution of petroleum systems. Insights into palaeo fluid compositions complement observations on present day fluid compositions, which represent only the end-point of complex cumulative processes throughout basin history. In this contribution, we review a wide range of approaches used to extract geochemical information from petroleum inclusions, and how these can be used to better constrain petroleum systems. These techniques can be grouped into

optical, spectrographic and thermometric non-destructive methods, or destructive chemical analyses of bulk samples or individual inclusions.

Typically optical methods documenting the distribution and visual properties of petroleum inclusions are used to provide petrographic context for subsequent specialised geochemical analyses of petroleum inclusions. Additional non-destructive techniques such as Raman spectroscopy can then be applied to provide some further insights into the composition of the trapped fluids, although the complex nature of petroleum generally requires direct access to the fluid for a more complete understanding of geochemical aspects. A variety of destructive techniques have been developed, initially to analyse bulk samples released by mechanical crushing and more recently through ablation type techniques that allow the composition of individual inclusions to be characterised.

Screening geochemical techniques that utilise mechanical crushing of bulk samples to analyse petroleum inclusions using mass spectrometry without prior chromatographic separation have become routine analyses. Other geochemical techniques more geared towards detailed molecular information such as biomarkers utilise chromatographic separation prior to mass spectrometry. Evaluation of the isotopic composition of petroleum inclusions is also possible for both bulk samples and compound specific analyses.

The use of lasers to open individual inclusions allows the released contents to be analysed by thermal extraction-gas chromatography-mass spectrometry (GC-MS), or mass spectrometric mapping of minerals using Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), a surface-sensitive analytical method that uses ion beams to ablate into minerals.

The continued evolution of techniques to analyse the incredibly small volume of hydrocarbons trapped within fluid inclusions has progressed to a point where there is little that can be done to evaluate a live oil or gas sample that cannot be achieved for a fluid inclusion sample. The full power for tracing petroleum systems is, however, only realised where there is an effective integration of fluid inclusion data with a more conventional approach to petroleum systems analysis.

Vozka, P., Kilaz, G., 2019. How to obtain a detailed chemical composition for middle distillates via GC × GC-FID without the need of GC × GC-TOF/MS. Fuel 247, 368-377.


The method presented in this research allows the development of detailed chemical composition of hydrocarbon mixtures (petroleum and non-petroleum based) in the range of C6 to C33 (69 to 475 °C) via comprehensive two-dimensional gas chromatography (GC × GC) with a flame ionization detector (FID). This method displays the protocol of obtaining a detailed chemical analysis via the classification using only 24 standard compounds without the need for a GC × GC with time-of-flight mass spectrometry (TOF/MS). The column configuration used was a reversed phase, composed of a series of a mid-polar or a polar as the primary column and a non-polar secondary column. Results were expressed as wt% for each main hydrocarbon class divided into each carbon number. Hydrocarbon classes of interest were n-paraffins, isoparaffins, mono-, di-, and tricycloparaffins, alkylbenzenes, cycloaromatics (naphthene-containing aromatic compounds), alkylnaphthalenes, biphenyls, three fused benzene rings aromatics (phenanthrenes and anthracenes), and pyrenes. This method was validated by the use of GC-FID, ASTM D1319, D6591, and standard compound mixture.

Vuitton, V., Yelle, R.V., Klippenstein, S.J., Hörst, S.M., Lavvas, P., 2019. Simulating the density of organic species in the atmosphere of Titan with a coupled ion-neutral photochemical model. Icarus 324, 120-197.


We present a one-dimensional coupled ion-neutral photochemical kinetics and diffusion model to study the atmospheric composition of Titan in light of new theoretical kinetics calculations and scientific findings from the Cassini–Huygens mission. The model extends from the surface to the exobase. The atmospheric background, boundary conditions, vertical transport and aerosol opacity are all constrained by the Cassini–Huygens observations. The chemical network includes reactions between hydrocarbons, nitrogen and oxygen bearing species. It takes into account neutrals and both positive and negative ions with masses extending up to 116 and 74 u, respectively. We incorporate high-resolution isotopic photoabsorption and photodissociation cross sections for N2 as well as new photodissociation branching ratios for CH4 and C2H2. Ab initio transition state theory calculations are performed in order to estimate the rate coefficients and products for critical reactions. Main reactions of production and loss for neutrals and ions are quantitatively assessed and thoroughly discussed. The vertical distributions of neutrals and ions predicted by the model generally reproduce observational data, suggesting that for the small species most chemical processes in Titan’s atmosphere and ionosphere are adequately described and understood; some differences are highlighted. Notable remaining issues include (i) the total positive ion density (essentially HCNH+) in the upper ionosphere, (ii) the low mass negative ion densities (CN−, C3N−/C4H

−) in the upper atmosphere, and (iii) the minor oxygen-bearing species (CO2, H2O) density in the stratosphere. Pathways towards complex molecules and the impact of aerosols (UV shielding, atomic and molecular hydrogen budget, nitriles heterogeneous chemistry and condensation) are evaluated in the model, along with lifetimes and solar cycle variations.

Waage, M., Portnov, A., Serov, P., Bünz, S., Waghorn, K.A., Vadakkepuliyambatta, S., Mienert, J., Andreassen, K., 2019. Geological controls on fluid flow and gas hydrate pingo development on the Barents Sea margin. Geochemistry, Geophysics, Geosystems 20, 630-650.

https://doi.org/10.1029/2018GC007930

Abstract: In 2014, the discovery of seafloor mounds leaking methane gas into the water column in the northwestern Barents Sea became the first to document the existence of nonpermafrost‐related gas hydrate pingos (GHPs) on the Eurasian Arctic shelf. The discovered site is given attention because the gas hydrates occur close to the upper limit of the gas hydrate stability, thus may be vulnerable to climatic forcing. In addition, this site lies on the regional Hornsund Fault Zone marking a transition between the oceanic and continental crust. The Hornsund Fault Zone is known to coincide with an extensive seafloor gas seepage area; however, until now lack of seismic data prevented connecting deep structural elements to shallow seepages. Here we use high‐resolution P‐Cable 3‐D seismic data to study the subsurface architecture of GHPs and underlying glacial and preglacial deposits. The data show gas hydrates, authigenic carbonates, and free gas within the GHPs on top of gas chimneys piercing a thin section of low‐permeability glacial sediments. The chimneys connect to faults within the underlying tilted and folded fluid and gas‐hydrate‐bearing sedimentary rocks. Correlation of our data with regional 2‐D seismic surveys shows a spatial connection between the shallow subsurface fluid flow system and the deep‐seated regional fault zone. We suggest that fault‐controlled Paleocene hydrocarbon reservoirs inject methane into the low‐permeability glacial deposits and near‐seabed sediments, forming the GHPs. This conceptual model explains the existence of climate‐sensitive gas hydrate inventories and extensive seabed methane release observed along the Svalbard‐Barents Sea margin.

Plain Language Summary: Gas hydrates (concentrated hydrocarbon gases in cages of ice) are stable within high pressure and low temperature. At boundary conditions, minor increases in ocean temperature may trigger gas hydrate decay and the possibility that gas hydrates may dissociate due to future warming causes particular awareness. We present observations of a hydrate system expressed as ≤450‐m wide and ≤10‐m high gas hydrate pingos (seabed mounds bearing gas hydrates). The geological conditions controlling the formation of these shallow gas hydrate accumulations have not been previously investigated. Along a ~700‐km region that coincides with a regional fault system, the Hornsund Fault Zone, more than 1,200 seeps releasing gas from the seafloor have been observed. Linkage of this fault zone to the methane hotspots has been hypothesized but never supported by empirical data. Combining new and published data, we postulate the major preconditions for GHP development: geologically constrained focused release of methane from 55–65 million‐year‐old rocks, modern gas hydrate stability conditions, and a drape of muddy bottom sediments favorable for heaving due to hydrate growth. We observe a clear relationship between this methane system and the regional fault system, which potentially demonstrates a typical scenario of fault‐controlled methane migration across the Svalbard‐Barents Sea margin.

Wade, L., 2019. Did Black Death strike sub-Saharan Africa? Science 363, 1022.


In the 14th century, the Black Death swept across Europe, Asia, and North Africa, killing up to 50% of the population in some cities. But archaeologists and historians have assumed that the plague bacterium Yersinia pestis, carried by fleas infesting rodents, didn't make it across the Sahara Desert. Now, some researchers point to new evidence from archaeology, history, and genetics to argue that the Black Death likely did sow devastation in medieval sub-Saharan Africa. Sites in West Africa suddenly shrank or were abandoned in the second half of the 14th century, and the oldest living relative of the Black Death strain survives in pockets in East and Central Africa. But to clinch the case, researchers need to find ancient DNA from the pathogen in the region.

Walder, B.J., Berk, C., Liao, W.-C., Rossini, A.J., Schwarzwälder, M., Pradere, U., Hall, J., Lesage, A., Copéret, C., Emsley, L., 2019. One- and two-dimensional high-resolution NMR from flat surfaces. ACS Central Science 5, 515=523.


Determining atomic-level characteristics of molecules on two-dimensional surfaces is one of the fundamental challenges in chemistry. High-resolution nuclear magnetic resonance (NMR) could deliver rich structural information, but its application to two-dimensional materials has been prevented by intrinsically low sensitivity. Here we obtain high-resolution one- and two-dimensional 31P NMR spectra from as little as 160 picomoles of oligonucleotide functionalities deposited onto silicate glass and sapphire wafers. This is enabled by a factor >105 improvement in sensitivity compared to typical NMR approaches from combining dynamic nuclear polarization methods, multiple-echo acquisition, and optimized sample formulation. We demonstrate that, with this ultrahigh NMR sensitivity, 31P NMR can be used to observe DNA bound to miRNA, to sense conformational changes due to ion binding, and to follow photochemical degradation reactions.

Wang, C., Huang, Z., Xing, Z., Chen, Y., Yu, J., Liu, F., Yuan, M., 2019. Direct determination of ultra-trace polycyclic aromatic hydrocarbons in water by liquid chromatography coupled with online solid phase extraction. Chinese Journal of Chromatography 37, 239-245.

http://www.chrom-china.com/EN/abstract/abstract14650.shtml

A method was developed for the direct determination of 16 ultra-trace polycyclic aromatic hydrocarbons (PAHs) in water by liquid chromatography (LC) coupled with online solid phase extraction (online SPE). The water sample was centrifuged at a high speed to remove the particulate matter and prepared into an aqueous solution containing 40% (v/v) methanol. A 2 mL-sample was directly injected into the online SPE flow path. Online purification and enrichment of the samples were carried out on the SPE column (Acclaim PA , 50 mm×4.6 mm, 3 μm). The PAHs eluted from Ⅱthe SPE column were transferred to the analytical flow path by valve switching, and were separated on a Hypersil Green PAHs column (150 mm×3 mm, 3 μm). Water and acetonitrile were used as the mobile phases. The flow rates of 1.0 mL/min and 0.4 mL/min were used in the extraction and balance processes, respectively. The flow rate of 0.6 mL/min was used to separate the PAHs in the analytical flow path. Acenaphthylene without a fluorescent signal was detected at the ultraviolet absorption wavelength of 220 nm, while other PAHs were measured by the fluorescence signal via the special excitation/emission wavelength program. The entire analysis could be completed within 37 min. The linear correlation coefficients of the 16 PAHs were greater than 0.996. The limits of detection of the PAHs were 0.14-12.50 ng/L (S/N=3) with only 0.38 ng/L for benzo(a)pyrene (B(a)P). The recoveries of PAHs at spiked levels of 10, 40 and 200 ng/L in the water samples were 76.1%-134.9%. The RSDs (n=3) were 0.3%-16.6%. Furthermore, the recoveries and RSDs (n=3) of B(a)P were 71.8%-92.7% and 3.9%, respectively. The proposed method is simple, rapid, solvent-saving, stable and sensitive, and can meet the ultra-trace analysis requirements of the PAHs (especially B(a)P) in various water samples

Wang, C., Wang, Z., Kong, Y., Zhang, F., Yang, K., Zhang, T., 2019. Most of the northern hemisphere permafrost remains under climate change. Scientific Reports 9, Article 3295.

https://doi.org/10.1038/s41598-019-39942-4

Degradation of cryospheric components such as arctic sea ice and permafrost may pose a threat to the Earth’s climate system. A rise of 2 °C above pre-industrial global surface temperature is considered to be a risk-level threshold. This study investigates the impacts of global temperature rises of 1.5 °C and 2 °C on the extent of the permafrost in the Northern Hemisphere (NH), based on the 17 models of Coupled Model Intercomparison Project Phase 5 (CMIP5). Results show that, when global surface temperature rises by 1.5 °C, the average permafrost extent projected under Representative Concentration Pathway (RCP) scenarios would decrease by 23.58% for RCP2.6 (2027–2036), 24.1% for RCP4.5 (2026–2035) and 25.55% for RCP8.5 (2023–2032). However, uncertainty in the results persists because of distinct discrepancies among the models. When the global surface temperature rises by 2 °C, about one-third of the permafrost would disappear; in other words, most of the NH permafrost would still remain even in the RCP8.5 (2037–2046) scenario. The results of the study highlight that the NH permafrost might be able to stably exist owing to its relatively slow degradation. This outlook gives reason for hope for future maintenance and balance of the cryosphere and climate systems.

Wang, F., Yin, S., 2019. Hydrocarbon generation potential of the C-P continental source rocks in the Qinshui Basin. Petroleum Science and Technology 37, 208-214.

https://doi.org/10.1080/10916466.2018.1533865

The hydrocarbon generation potential of continental source rocks in the Carboniferous-Permian (C-P) coal-bearing stratum in the Qinshui Basin were systematically analyzed in this paper. Ro of the C-P

source rocks is mainly distributed between 1.5% and 2.5%. The coal rock belongs to a typical type III organic matter, while the mudstone mainly contains type III organic matter and a small proportion of type II2 organic matter. Moreover, The geochemical characteristics of the source rock kerogen was analyzed in detail. Finally, an evaluation standard for hydrocarbon generation potential of the C-P continental source rocks was proposed.



1H-pyrrole-2,5-diones, or maleimides, are degradation products or derivatives from tetrapyrrole pigments found in petroleum, soils, sediments and sedimentary rocks; among them, 2-methyl-3-n-propyl (Me,n-Pr) and 2-methyl-3-isobutyl (Me,i-Bu) maleimide are mainly sourced from the bacteriochlorophylls of green phototrophic sulfur bacteria (Chlorobiaceae). In this study, the maleimides fractions were extracted from crude oil with mixed sources and geneses, and the gas chromatography-mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) were used for analysis and identification. The results show that three different sets of maleimides occur in China’s lacustrine oil, and there are significant differences in the maleimide components of mixed-genesis crude oil. Abundant Me,n-Pr and Me,i-Bu maleimides are mainly distributed in the crude oil derived from the upper source rocks in Member 4 of Shahejie Formation, Bohai Bay Basin with saline-water permanent stratification, while both are undeveloped in the crude oil under brackish or fresh water conditions. Meanwhile, Me,n-Pr and Me,i-Bu maleimides can be used to identify the occurrence of light-permeable stagnant water zone for oil-source correlations. Thus, maleimides are expected to become a new kind of biomarkers in hydrocarbon geochemistry.

Wang, G., Zhan, R., Percival, I.G., 2019. The end-Ordovician mass extinction: A single-pulse event? Earth-Science Reviews 192, 15-33.


The end-Ordovician mass extinction (EOME) is widely interpreted as consisting of two pulses associated with the onset and demise of the Gondwana glaciation, respectively, with the second pulse eradicating the distinctive, glacially related Hirnantian benthic biota (HBB). A global review of occurrence data of latest Ordovician benthic marine organisms reveals that virtually all warm-water benthic assemblages previously assigned to the HBB comprise two distinct and clearly postglacial faunas, both younger (middle and late Hirnantian, respectively) than the cool-water Hirnantia fauna (latest Katian to early Hirnantian). The newly recognised three Transitional Benthic Faunas (i.e., TBFs 1–3) can be closely tied to graptolite, conodont, and chitinozoan biozonations, the Hirnantian Isotope Carbon Excursion (HICE), and the glaciation, thereby providing an integrated, much higher-resolution timescale for understanding the tempo and nature of the EOME. At this finer resolution, we postulate a more profound impact of the first pulse of the EOME than hitherto envisaged, as evidenced by opportunistic expansion of the Hirnantia fauna globally and the complete absence of metazoan reefs in its immediate aftermath. We also argue, based on high-quality data from well-documented benthic groups in South China (i.e., brachiopods, tabulate and rugose corals, trilobites, and sponges), that the magnitude of the second pulse of the EOME caused by the deglaciation has been overestimated because the two postglacial faunas (i.e., TBFs 2–3) were part of a subsequent recovery phase of marine ecosystems rather than contributing to biodiversity decline. Thus, it is more plausible to reinterpret the EOME as a single-pulse, rapid event that was followed by a prolonged

initial recovery intermittently impeded by climatic shocks through the Hirnantian, prior to the onset of a progressive reestablishment of marine ecosystems during the early Silurian (Rhuddanian and Aeronian) associated with an overall amelioration of climatic conditions.

Wang, H., Wu, W., Chen, T., Yu, J., Pan, J., 2019. Pore structure and fractal analysis of shale oil reservoirs: A case study of the Paleogene Shahejie Formation in the Dongying Depression, Bohai Bay, China. Journal of Petroleum Science and Engineering 177, 711-723.


In the exploration and development of shale gas, the evaluation of reservoir microscopic pore structure is of great significance. In order to study the pore size distribution, pore networks, seepage capacity and heterogeneity of shale reservoirs more effectively, mercury intrusion capillary pressure (MICP) and the fractal theory were carried out on a suite of the shale samples of the Dongying Depression, Bohai Bay, China. The results demonstrate that shale is characterized by complex and heterogeneous microcosmic pore structure. The pore throat size could be divided into four types: micropores (25–100 nm), mesopores (100–1000 nm), macropores (1000-rⅡ apex nm, rapex is the pore throat radius corresponding to the maximum point in the plot of mercury saturation versus the mercury saturation divided by capillary pressure) and macropores (>rⅠ apex nm). The pore throat radii of shale from the Dongying Depression are mostly mesopores and macropores . Micropores and Ⅱmacropores are the controlling factors of porosity, whereas permeability is dominated primarily by Ⅱmacropores . The fractal dimension of pore throat are clearly separated into two segments: D1 and ⅡD2, corresponding to large pores (>rapex) and small pores (<rapex), respectively. There are no apparent relationships between D1 and the pore structure parameters, whereas D2 are strongly related to the maximum mercury saturation, entry pressure, average pore throat radius and maximum pore throat radius. These relationships enable D2 to represent the complexity of shale. The mercury capillary curves can be divided into three types based on the shape of the curves: type , type , type . Ⅰ Ⅱ ⅢAccording to these types of pore structure, reservoirs can be classified into three categories. The good reservoirs (type ) are characterized by dominant macropores and mesopores volumes, a large Ⅰporosity and permeability and a low fractal dimension. Medium reservoirs (type ) have a low oil Ⅱreservoir potential due to the developed mesopores and micropores. The type pore system is a poorⅢ reservoir that is inadequate for shale oil. Our analyses suggest that MICP coupled with the fractal theory is a powerful tool to evaluate the porous structure of shale.

Wang, J., Hilton, R.G., Jin, Z., Zhang, F., Densmore, A.L., Gröcke, D.R., Xu, X., Li, G., West, A.J., 2019. The isotopic composition and fluxes of particulate organic carbon exported from the eastern margin of the Tibetan Plateau. Geochimica et Cosmochimica Acta 252, 1-15.


Erosion of organic carbon from the terrestrial biosphere and sedimentary rocks plays an important role in the global carbon cycle across a range of timescales. Over geological timescales (>104 years), erosion and burial of particulate organic carbon (POC) from the terrestrial biosphere (POCbiosphere) is an important CO2 sink, while oxidation of organic carbon derived from sedimentary rocks (petrogenic, POCpetro) releases CO2 to the atmosphere. Over decadal to millennial timescales, the balance between POCbiosphere production and degradation affects atmospheric CO2 concentrations. To better constrain the controls on erosional carbon transfers, here we quantify POCbiosphere and POCpetro fluxes in a mountain range with relatively low runoff, the Longmen Shan, which drains the eastern margin of the Tibetan Plateau. We measure total organic carbon content ([OC total]) and the carbon isotopic compositions (13C/12C expressed as δ13C; 14C/12C expressed as fraction modern or Fmod) of

organic matter in suspended sediments collected from six gauging stations on the Min Jiang, a tributary of the Yangtze River, from 2005 to 2012. We find that POCpetro has a large range of δ13C, from −26.2‰ to −13.2‰. This POCpetro mixes with POCbiosphere to set the δ13C of POC in river sediments. Binary mixing models reveal the possibility of aged POCbiosphere at two gauging stations which drain the high elevations of the eastern Tibetan Plateau, with modelled biospheric Fmod values of 0.82 ± 0.09 and 0.84 ± 0.08. This is consistent with prior suggestions of aged biospheric carbon being eroded from the plateau.

The annual POCpetro yields range from 0.04 ± 0.02 tC km−2 yr−1 to 1.69 ± 0.56 tC km−2 yr−1 across the five study catchments, with basin average yield that appears to be linked to catchment average slope as a likely proxy for erosion rate. Here, the variability in the petrogenic organic carbon content of rocks masks the signal of the weathering and oxidation of this rock-derived organic carbon. The annual POCbiosphere yields range from 0.21 ± 0.04 tC km−2 yr−1 to 3.33 ± 0.57 tC km−2 yr−1. These values are towards the lower end of those measured in mountain ranges around the world, which we suggest not only reflects the relatively low erosion rates of the Longman Shan, but also the low annual runoff (<1 m yr−1). Across this region, the river POCbiosphere discharge is related to the intensity of runoff events. Our data suggest that a wetter (and/or stormier) climate could increase the erosional export of POCbiosphere in this tectonically-active mountain range. Depending on the fate of POCbiosphere downstream in larger river systems, this could act as carbon-cycle climate feedback over geological timescales.

Wang, J., Hua, M., Cai, C., Hu, J., Wang, J., Yang, H., Ma, F., Qian, H., Zheng, P., Hu, B., 2019. Spatial-temporal pattern of sulfate-dependent anaerobic methane oxidation in an intertidal zone of the East China Sea. Applied and Environmental Microbiology 85, Article e02638-02618.


Abstract: Methane is a primary greenhouse gas which is responsible for global warming. The sulfate-dependent anaerobic methane oxidation (S-AOM) process catalyzed by anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB) is a vital link connecting the global carbon and sulfur cycles, and it is considered to be the overriding methane sink in marine ecosystem. However, there have been few studies regarding the role of S-AOM process and the distribution of ANME archaea in intertidal ecosystem. The intertidal zone is a buffer zone between sea and land and plays an important role in global geochemical cycle. In the present study, the abundance, potential methane oxidation rate, and community structure of ANME archaea in the intertidal zone were studied by quantitative PCR, stable isotope tracing method and high-throughput sequencing. The results showed that the potential S-AOM activity ranged from 0 to 0.77 nmol 13CO2 g−1 (dry sediment) day−1. The copy number of 16S rRNA gene of ANME archaea reached 106 ∼ 107 copies g−1 (dry sediment). The average contribution of S-AOM to total anaerobic methane oxidation was up to 34.5%, while denitrifying anaerobic methane oxidation accounted for the rest, which implied that S-AOM process was an essential methane sink that cannot be overlooked in intertidal ecosystem. The simulated column experiments also indicated that ANME archaea were sensitive to oxygen and preferred anaerobic environmental conditions. This study will help us gain a better understanding of the global carbon-sulfur cycle and greenhouse gas emission reduction and introduce a new perspective into the enrichment of ANME archaea.

Importance: The sulfate-dependent anaerobic methane oxidation (S-AOM) process catalyzed by anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB) is a vital link connecting the global carbon and sulfur cycles. We conducted a research into the spatial-temporal pattern of S-AOM process and the distribution of ANME archaea in coastal sediments collected from the intertidal zone. The results implied that S-AOM process was a methane sink that cannot be

overlooked in the intertidal ecosystem. We also found that ANME archaea were sensitive to oxygen and preferred anaerobic environmental conditions. This study will help us gain a better understanding of the global carbon-sulfur cycle and greenhouse gas emission reduction and introduce a new perspective into the enrichment of ANME archaea.

Wang, J., Wang, C., Han, X., 2019. Tutorial on lipidomics. Analytica Chimica Acta 1061, 28-41.


The main stream of lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about lipidomics and to provide readers with some core ideas and the most important approaches for studying the field.



In order to improve the current recovery factor of unconventional reservoirs and take it to the next level (10–20%), gas Huff and Puff is a very promising enhanced oil recovery technology used currently. Many laboratory works and field pilot tests have been conducted recently. However, most of the research work is based on CO2 as an injected gas. Few of them were built upon the more realistic lean gas Huff and Puff process. From the feedback of lean gas Huff and Puff pilot in Eagle Ford, the field response is always beyond analysis and reservoir simulation forecast. Methane, the main component of lean gas, and its adsorption and desorption effects on the unconventional resources are pronounced due to nanopore confinement effects and a much larger surface area than conventional reservoirs. On the other hand, the minimum miscibility pressure of lean gas in Eagle Ford is high (>4000 psi), which makes gas phase and liquid phase still separate in a long period of Huff and Puff process before reservoir pressure is elevated high enough to developing the supercritical state. Therefore, relative permeability hysteresis – gas trapping effect in nature, should be also very significant on gas EOR performance for unconventional resources. To our best knowledge, there are no such studies about the lean gas adsorption and gas trapping for Huff and Puff process of unconventional reservoir reported so far. In this study, these two mechanisms are systematically analyzed and quantified in a compositional reservoir simulation study. The gas EOR dependence on permeability is also studied and the resulting gas injectivity problem is answered, trying to explore the real problem encountered in the pilot practice.

Wang, P.-H., Correia, K., Ho, H.-C., Venayak, N., Nemr, K., Flick, R., Mahadevan, R., Edwards, E.A., 2019. An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. The ISME Journal 13, 1042-1055.

https://doi.org/10.1038/s41396-018-0333-4

Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium

ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate–pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.

Wang, S.-J., Rudnick, R.L., Gaschnig, R.M., Wang, H., Wasylenki, L.E., 2019. Methanogenesis sustained by sulfide weathering during the Great Oxidation Event. Nature Geoscience 12, 296-300.

https://doi.org/10.1038/s41561-019-0320-z

The Great Oxidation Event following the end of the Archaean eon (~2.4 Ga) was a profound turning point in the history of Earth and life, but the relative importance of various contributing factors remains an intriguing puzzle. Controls on methane flux to the atmosphere were of particular consequence; too much methane would have inhibited a persistent rise of O2, but too little may have plunged Earth into severe and prolonged ice ages. Here, we document a shift in the weathering reactions controlling the ocean-bound flux of nickel—an essential micronutrient for the organisms that produced methane in Precambrian oceans—by applying Ni stable isotope analysis to Mesoarchaean and Palaeoproterozoic glacial sediments. Although Ni flux to the ocean dropped dramatically as Ni content of the continental crust decreased, the onset of sulfide weathering delivered a small, but vital, flux of Ni to the oceans, sustaining sufficient methane production to prevent a permanent icehouse, while allowing O2 to rise.

Wang, T., Burne, R.V., Yuan, A., Wang, Y., Yi, Z., 2019. The evolution of microbialite forms during the Early Triassic transgression: A case study in Chongyang of Hubei Province, South China. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 209-220.


The widespread development of microbialites in shallow areas of the Tethys Ocean at the start of the Early Triassic reflects the deterioration of marine ecosystems in the aftermath of the extinction that marked the demise of the majority of Palaeozoic marine faunas. Here we present a study of the evolving microbialite forms and associated biotic assemblages of this pioneering microbialite interval from exposures at Chongyang, Hubei Province, China. This research provides a perspective on the effects of eustatic transgression on marine ecosystems as water depths increased at the beginning of Mesozoic, through the study of the changing forms, microfacies and distribution of microbialites. Microbialite forms evolved from stratiform stromatolites to a sequence of tabular thrombolites (with an intercalated layer of columnar stromatolites), followed by domical thrombolites that were overlain, in turn, by oolites. The stratiform stromatolites contain poorly preserved remains of calcified cyanobacteria, but microfossils with chambered structure can also be seen. Metazoan fossils increased from the base of the overlying tabular thrombolite, reflecting increasing biodiversity with deepening

of seawater. The occurrence of columnar stromatolites within the tabular thrombolite may indicate a temporary sea-level shallowing. Foraminiferans and other metazoans are absent within the columnar stromatolites, but spherical cyanobacterial remains are extremely abundant. Well-preserved calcified cyanobacteria may reflect an absence of metazoan predation and/or carbonate supersaturation of seawater. As water deepened, domical thrombolites developed and the more complex seafloor relief created varied niches between and within the domes that harboured more ecologically diverse communities. During the process of transgression within the microbialite interval, carbon isotopes exhibit a negative relationship with biodiversity, implying that upwelling of anoxic deep-ocean water, if associated with the negative excursion of carbon isotope values, did not inhibit the diversification of benthic organisms at least on shallow carbonate platforms in the period immediately after the end-Permian mass extinction.

Wang, T., Tian, S., Li, G., Sheng, M., Ren, W., Liu, Q., Tan, Y., Zhang, P., 2019. Experimental study of water vapor adsorption behaviors on shale. Fuel 248, 168-177.


Understanding water distribution behaviors plays an essential role in shale gas development due to the hydraulic fracturing technology. In this study, water vapor adsorption isotherms were measured for Upper Triassic Yanchang and Lower Silurian Longmaxi samples at 288.15 K, 298.15 K and 308.15 K to investigate the adsorption behaviors of water on shale. For a description of adsorption process, a Dent’s model provides an estimate of primary and secondary adsorption sites of water adsorption. The effects of temperature, shale mineralogy, and water distribution were discussed. The results show that temperature has a negative effect on water vapor adsorption. Adsorption capacities of primary and secondary sites decrease with increasing temperature. Water vapor adsorption capacity is tightly associated with clay content, whereas water vapor adsorption has no significant relationship with total organic carbon (TOC). Normalized water vapor adsorption content also has no significant relationship with TOC, which indicates no obvious correlation between water vapor adsorption and TOC content. The inter-crystal pores of clay minerals provide significant specific surface for gas adsorption in shale. At low relative pressure, a large number of water molecules adsorb on the primary sites. At high relative vapor pressure, most of the primary sites have been occupied, so that the secondary adsorption sites will be utilized. Therefore, due to relative weak binding energies in secondary adsorption sites, water cluster are formed in micro-pores of shale. As relative vapor pressure increases, capillary condensation gradually predominates over the adsorption. The study will reveal mechanism of water adsorption and distribution characteristics on shale and provide some foundation for geological reserve estimation and shale gas recovery prediction.

Wang, X., Cawood, P.A., Zhao, H., Zhao, L., Grasby, S.E., Chen, Z.-Q., Zhang, L., 2019. Global mercury cycle during the end-Permian mass extinction and subsequent Early Triassic recovery. Earth and Planetary Science Letters 513, 144-155.


The end-Permian mass extinction (EPME) at ∼252 Ma was the most severe extinction in the Phanerozoic. Marine ecosystems devastated by the EPME had a highly prolonged recovery, and did not substantially recover until after the Smithian–Spathian substage boundary (SSB) of the Lower Triassic (5 to 9 Ma after the EPME). While the Siberian Traps large igneous province (STLIP) has been invoked as the driver of the mass extinction, there remains controversy as to the cause of the protracted Early Triassic recovery; although renewed STLIP volcanism has been suggested. These previous studies though have drawn conclusions based on geochemical records of sediments

deposited in northern latitude settings. To investigate the relationship between STLIP and extinction/recovery processes on a global base, we examined mercury chemostratigraphy, including mercury concentrations and isotopes, from high southern latitude and equatorial sections that span the Late Permian Changhsingian to Early Triassic Spathian substage successions; the Guryul Ravine section, Kashmir in northern India, and the Chaohu section in southern China. Organic and inorganic carbon-isotope data define the EPME horizon in the Chaohu section and the SSB in the Guryul Ravine section, respectively. Hg/TOC values are dramatically elevated approaching the EPME horizon and maintain high values until the lower Isarcicella Isarcica conodont zone, the base of which is believed to be the end of the mass extinction. In the stratigraphically overlying beds, Hg/TOC generally displays lower values with slight fluctuations through the two sections. These fluctuations are likely related to the increased terrestrial Hg influx associated with strong chemical weathering in the Early Triassic, as shown by a positive correlation between the contents of Hg and Al, and by less positive Δ199Hg values in Early Triassic samples. Our data, presenting the first Southern Hemisphere Hg record from Guryul Ravine, in combination with previous results, indicates that anomalous high mercury deposition at the EPME occurred globally. The generally positive Δ199Hg values at this time reflects atmospheric-derived Hg, consistent with a volcanic Hg source which we suggest indicates global impact of STLIP eruption. In contrast, there is no evidence for a global Hg/TOC anomaly during the protracted Early Triassic biotic recovery, suggesting that potentially renewed STLIP volcanism had only a northern hemisphere influence on the global Hg cycle. This more limited impact, may still have played a role in the delayed Early Triassic recovery.

Wang, X., Cawood, P.A., Zhao, L., Chen, Z.-Q., Lyu, Z., Ma, B., 2019. Convergent continental margin volcanic source for ash beds at the Permian-Triassic boundary, South China: Constraints from trace elements and Hf-isotopes. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 154-165.


Volcanic activity around the time of the Permian-Triassic boundary (PTB) has been proposed as a trigger for the associated biocrisis. Multiple claystone beds are prominent near the PTB sections in South China. Twenty one PTB ash beds from three sections at Shangsi, Jianshi and Meishan in South China were sampled and analyzed. Volcanic ash geochemistry indicate dacite and rhyolite compositions. Zircons from the ash layers yield comparatively low Nb/Hf and high Th/Nb ratios, falling in the range of arc/orogenic-related settings. Zircon Hf-isotope compositions show that εHf(t) values vary from −11.7 to 1.8, indicating involvement of both juvenile and ancient crustal components. The ash beds (SS27a, JS129, JS130, JS133,MS25, MS26) near the biotic extinction horizon display a large variation in εHf (t) and relatively positive average values, indicating input of juvenile mantle or crust, and implying rapid transit through the older basement of the South China Craton. Spatial and temporal distribution of ash beds from thirty one PTB sections worldwide reveal that volcanic ash beds occur mainly in, or proximal to, the Tethys region and were sourced locally. Integration of Hf-isotope and trace-element compositions from magmatic zircons suggests that the PTB volcanism occurred along the convergent continent margin in, or near, southwestern South China as a result of the closure of the Paleo-Tethys Ocean.

Wang, X., Sheng, J.J., 2019. Multi-scaled pore network modeling of gas-water flow in shale formations. Journal of Petroleum Science and Engineering 177, 899-908.


Multiphase flow is commonly encountered within shale reservoirs, however, the previous studies are more focused on single phase flow. Due to the extremely low permeability of shale formations, the

experimental measurements are not capable to be performed. Attempts are made by applying the techniques of digital rock analysis and pore network modeling to investigate the multiphase flow mechanisms in shale reservoirs. This work follows this way. Firstly, a stochastic pore network generation algorithm and a two-phase flow simulation method are presented. This algorithm is applied and validated in Berea sandstone. By applying the proposed algorithm, the organic and inorganic pore networks are generated for shale formations, then the multi-scaled pore network is established after upscaling the organic pores to an organic path. Finally, the gas-water flow is simulated within this established multi-scaled pore network and some analysis and discussions are conducted. The results imply that the characteristics of pore systems in shale formations pose an extreme impact on the gas-water flow mechanisms, especially the proportion of organic pores and pore-throat aspect ratio.

Wang, X., Wang, X., Pan, Z., Yin, X., Chai, P., Pan, S., Yang, Q., 2019. Abundance and distribution pattern of rare earth elements and yttrium in vitrain band of high-rank coal from the Qinshui basin, northern China. Fuel 248, 93-103.


Vitrain bands are clean and contain less ash than the bulk coal. A comprehensive study on rare earth elements and yttrium (REY) in vitrain may provide insights into the REY affinity. In this study, abundance and distribution pattern of REY in bulk coal, vitrain band and HCl-HF demineralized vitrain band was investigated. The coal studied in the present work was low-ash (ash yields ranging from 4.13 to12.86%, with 8.59% as the average), high-rank (anthracite to semi-anthracite, with volatile matter yields of 7.52–13.42%, 9.58% on average) coal of Permian Shanxi Formation, collected from the Sihe and Zhaozhuang mines, southern Qinshui Basin. The major minerals identified by powder XRD are illite and kaolinite, with small amount of ankerite, chlorite, calcite, siderite and pyrite. In comparison to the bulk coal, vitrain band displays a lower REY content and smaller compositional range. The bulk coal has N-, H- and L-type REY patterns based on Seredin-Dai’s classification, while the REY distribution for the vitrain band is commonly characterized by an H-type pattern. Moreover, the LaN/LuN ratio in the vitrain band is usually lower than that in the bulk coal. This probably suggests that the organic component has a higher HREY association than LREY compared to the inorganic part. The limited impact of HCl-HF demineralization on content and distribution pattern of REY in vitrain band probably reflects the weak acid solubility of REY in the vitrain band. The sequential chemical extraction procedure reveals that the clays and the residual organics, which have a stronger association with LREY and HREY respectively, are the dominant carriers of total REY in the studied bulk coals.

Wang, X., Xia, K., Yang, X., Tang, C., 2019. Growth strategy of microbes on mixed carbon sources. Nature Communications 10, Article 1279.

https://doi.org/10.1038/s41467-019-09261-3

A classic problem in microbiology is that bacteria display two types of growth behavior when cultured on a mixture of two carbon sources: the two sources are sequentially consumed one after another (diauxie) or they are simultaneously consumed (co-utilization). The search for the molecular mechanism of diauxie led to the discovery of the lac operon. However, questions remain as why microbes would bother to have different strategies of taking up nutrients. Here we show that diauxie versus co-utilization can be understood from the topological features of the metabolic network. A model of optimal allocation of protein resources quantitatively explains why and how the cell makes the choice. In case of co-utilization, the model predicts the percentage of each carbon source in

supplying the amino acid pools, which is quantitatively verified by experiments. Our work solves a long-standing puzzle and provides a quantitative framework for the carbon source utilization of microbes.

Wang, X., Zhu, Y., Lash, G.G., Wang, Y., 2019. Multi-proxy analysis of organic matter accumulation in the Upper Ordovician–Lower Silurian black shale on the Upper Yangtze Platform, south China. Marine and Petroleum Geology 103, 473-484.


There is no doubt that organic matter plays an important role in shale gas accumulation and storage. Thus, successful evaluation and production strategies of organic-rich shale deposits require an understanding of the range of factors that contribute to the accumulation and preservation of organic matter in these deposits. This paper reports results of a multi-faceted study of two Ordovician–Silurian transition sections of the Upper Yangtze Platform of South China. Organic and inorganic geochemical data are used to reconstruct paleoenvironmental changes across this critical interval of Earth history and to identify those factors that were most important to organic matter accumulation. Deposition of organic-rich shale of the Katian lower Wufeng Formation was favored by rising sea level and diminished clastic sediment content. Black shale of the upper Wufeng preceded Hirnantian glaciation whereas the overlying lower Longmaxi Formation accumulated in association with a post-glacial rise of sea level as well as the peak of Caledonian tectonism. The carbonaceous deposits appear to reflect the combined effects of elevated primary productivity as suggested by Si/Al and Ti/Al ratios, especially in the upper Wufeng, and consequent depletion of water column oxygen (preservation). Consideration of the relationships of redox-sensitive trace element concentrations and total organic carbon content suggest that bottom water conditions fluctuated between anoxic and euxinic during this period, perhaps related to rapid oscillations of sea level. Moreover, the basin appears to have remained connected with the global ocean in spite of Caledonian uplift of bordering areas. Thus, black shale sedimentation on the Upper Yangtze Platform at the Ordovician-Silurian boundary reflects the interplay of climate change and tectonism and their influences on sea level, clastic sediment content, and paleo-productivity.

Wang, Y., Liu, L., Sheng, Y., Wang, X., Zheng, S., Luo, Z., 2019. Investigation of supercritical methane adsorption of overmature shale in Wufeng-Longmaxi Formation, southern Sichuan Basin, China. Energy & Fuels 33, 2078-2089.


Accurately determining the gas sorption capacity of a specific shale reservoir is critical for further assessment of shale gas reserves. A series of high-pressure methane adsorption measurements were conducted at 60 °C with a pressure of up to 30 MPa for Wufeng-Longmaxi shales from the southern Sichuan Basin, which is considered as the most promising shale-gas target in China, to evaluate the fitting quality of different excess adsorption models and to determine the effect of organic matter content, maturity, mineralogy, and pore structure on the gas adsorption capacity. Both the Langmuir- and supercritical Dubinin–Radushkevich (SDR)-based adsorption models are closely fitted with the measured excess adsorption amount. However, the freely fitted SDR model is considered to be the most reasonable model, in which the adsorbed-phase density is always lower than the liquid methane density at the boiling point (0.424 g/cm3) and the average relative error (ARE) is relatively small. Adsorbed-phase density is a key parameter for calculating absolute adsorption isotherms. For a specific shale, a lower constant adsorbed-phase density applied in the adsorption model would result in higher absolute adsorption capacity. For the Langmuir-based model, the actual absolute adsorption

capacity would be underestimated when adsorption experiments were only conducted at the low-pressure range (0–15 MPa). The methane adsorption capacities show a great positive correlation with the total organic carbon (TOC) content. The TOC-normalized adsorption capacities have a negative relationship with maturity at an overmature stage. The clay content shows a positive correlation with the TOC-normalized adsorption capacities, indicating that clays also make some contribution to methane sorption on these organic-rich shales. Furthermore, methane adsorption in overmature shales is mainly controlled by the structure of the pore <20 nm in size, revealing that the adsorbed methane is occupied not only in micropores but also in fine mesopores.


https://doi.org/10.1038/s41564-019-0364-2

Methanogenesis and anaerobic methane oxidation through methyl-coenzyme M reductase (MCR) as a key enzyme have been suggested to be basal pathways of archaea. How widespread MCR-based alkane metabolism is among archaea, where it occurs and how it evolved remain elusive. Here, we performed a global survey of MCR-encoding genomes based on metagenomic data from various environments. Eleven high-quality mcr-containing metagenomic-assembled genomes were obtained belonging to the Archaeoglobi in the Euryarchaeota, Hadesarchaeota and different TACK superphylum archaea, including the Nezhaarchaeota, Korarchaeota and Verstraetearchaeota. Archaeoglobi WYZ-LMO1 and WYZ-LMO3 and Korarchaeota WYZ-LMO9 encode both the (reverse) methanogenesis and the dissimilatory sulfate reduction pathway, suggesting that they have the genomic potential to couple both pathways in individual organisms. The Hadesarchaeota WYZ-LMO4–6 and Archaeoglobi JdFR-42 encode highly divergent MCRs, enzymes that may enable them to thrive on non-methane alkanes. The occurrence of mcr genes in different archaeal phyla indicates that MCR-based alkane metabolism is common in the domain of Archaea.

Wang, Y., Zhang, D., Hu, Y.Z., 2019. X-ray computed tomography characterization of soil and rock mixture under cyclic triaxial testing: the effects of confining pressure on meso-structural changes. Environmental Earth Sciences 78, 185.

https://doi.org/10.1007/s12665-019-8161-z

The mechanical meso-damage mechanism of soil and rock mixture (SRM) subjected to cyclic loading is very significant to evaluate the stability of construction and building structures composed of SRM. However, to date, few experiments have been done to investigate the physical mesoscopic damage evolution in SRM. In this work, cyclic triaxial tests were conducted on soil and rock mixture samples with rock block percentage of 40%, under confining pressures (CPs) of 60 kPa, 120 kPa, and 200 kPa using in situ X-ray computed tomography technique. The effects of confining pressure on the meso-structural changes have been visualized and investigated by CT image analysis. For the SRM samples, hysteresis loop on the cyclic stress–strain curves presents different pattern that is caused by the differential applied CP. The hysteresis loop area first decreased and then increased with plastic deformation increasing for samples under a CP of 60 kPa and 120 kPa; however, it shows monotonously decreasing trend under a CP of 200 kPa. In addition, after extracting cracks from the original CT images, it shows that the damage initiation moment of SRM is different even though with the same stress amplitude. The crack geometric parameters, however, decreased under larger confining pressure mainly due to the restriction of rock block movement. The stress dilatancy characteristics of SRM under various CPs also presented different trend from the volumetric change

analysis on the CT images. The interlocking among rock blocks restricts the development of localized bands under high CP, and the ability to resist cyclic damage improves with the increase of CP.

Wang, Z., 2019. Reservoir formation conditions and key efficient exploration & development technologies for marine shale gas fields in Fuling area, South China Acta Petrolei Sinica 40, 370-382.


Although shale gas resources are abundant in China, commercial discoveries have not been made before the discovery of Fuling shale gas field. Sinopec has done lots of theoretical and technological studies on marine shale gas development in China. Research shows shale gas has dynamic accumulations with early preservation and late reconstruction and proposes high-quality shale developed in deep-water shelf as the base and good preservation conditions as the key factor for shale gas accumulation. Key technologies and facilities were developed for geophysical survey of shale gas, design and optimization of shale gas development, drilling and completion of horizontal wells, and fracturing stimulation. As the first and largest shale gas field in China, the discovery and successful development of Fuling shale gas filed has made China the first country to achieve large-scale development of shale gas after North America. By August 2017, Fuling shale gas field had declared 6 008.14×108m3 proven reserves, 76.8×108m3 production capacity and 133.9×108m3 cumulative production. The construction of Fuling shale gas field with high level, high speed and high quality has been a good example of shale gas development in China. Its successful experiences can be used to other fields and play an important role in optimizing energy structure and improving environment.

Wang, Z., Fu, R., Ji, J., Chen, B., 2019. Simultaneous determination of chlorogenic acid and cynaroside contents in Lonicerae Japonica Flos by high resolution sampling two-dimensional liquid chromatography. Chinese Journal of Chromatography 37, 201-206.

http://www.chrom-china.com/CN/abstract/article_14644.shtml

An innovative analytical method based on high resolution sampling two-dimensional liquid chromatography (HiRes 2D-LC) was established for determination of chlorogenic acid and cynaroside in Lonicerae Japonica Flos. A C18 column was used in the first dimension (1D)-LC separation with acetonitrile and 0.4% (v/v) phosphoric acid aqueous solution as mobile phases. Five heart cuts of chlorogenic acid and four heart cuts of cynaroside were stored in 2D-LC interface, which was a 5-position-10-port valve equipped with two multiple heart-cutting valves. The stored cuts were sequentially separated in the second dimension (2D)-LC. The 2D separation was carried out on an SB-Phenyl column with acetonitrile and 0.5% (v/v) acetic acid aqueous solution as mobile phases. The results showed that chlorogenic acid peaks in the 1D were well separated, whereas cynaroside peaks in the 1D were co-eluted with interferences. The above two targets were accurately quantified through a high resolution sampling mode based on continuous slice cuts of the whole target peaks. The method had good linearity, recovery and repeatability. The HiRes 2D-LC system could be used to improve separation and quantification of (un)targets in traditional Chinese medicine samples.

Wang, Z., Shi, B., Wen, Z., Tong, X., Song, C., He, Z., Liu, X., 2019. Shale oil and gas exploration potential in the Tanezzuft Formation, Ghadames Basin, North Africa. Journal of African Earth Sciences 153, 83-90.


The Silurian Tanezzuft Formation ‘hot shale’ in North Africa is a high-quality source rock and a major contributor to the oil and gas reserves of the Paleozoic Ghadames Basin. This hot shale has similar sedimentary characteristics to those of the Silurian Longmaxi Formation shale in the Sichuan Basin in China, which is a proven prolific source of shale gas. In this study, the oil and gas accumulation conditions and sedimentary characteristics of the Tanezzuft shale are compared with those of the commercially exploited Longmaxi shale and the Marcellus and Barnett shales (North America), and criteria for shale oil and gas potential in the Tanezzuft shale are established from these commercially exploited shales. For the Tanezzuft shale, the net pay thickness of effective source rock, total organic carbon, thermal maturity and burial depth, and the locations of faults in the Ghadames Basin are analyzed and mapped. The distributions of these variables are then used to predict the distribution of shale oil and gas with respect to the established criteria. It is shown that the Tanezzuft shale has significant potential for the production of shale oil and gas; in particular, the northeastern and southwestern slopes of the Ghadames Basin are the most favorable in terms of prospective shale oil and gas exploration.

Wang, Z., Xie, T.-T., Yan, X., Xue, S., Chen, J.-W., Wu, Z., Qiu, Y.-K., 2019. Gradual gradient two-dimensional preparative liquid chromatography system for preparative separation of complex natural products. Chromatographia 82, 543-552.

https://doi.org/10.1007/s10337-018-3652-8

A low-cost and gradual gradient online two-dimensional preparative liquid chromatography system was developed for the preparative separation of compounds of interest from complex natural products. Medium-pressure liquid chromatography (MPLC) was applied as the first dimension and preparative high-performance liquid chromatography (HPLC) was employed as the second dimension. Two trapping columns and a makeup pump were also used. Each of the two dimension columns was packed with reversed-phase ostadecyl-silca (ODS), and eluted by an isocratic pump with a gradient mixing device, in which the solvent of the first and the second dimensions were gradiently changed to fit the demand of the sample elution. The instrument operation and the performance of this MPLC × preparative HPLC system were evaluated via gram-scale isolation of a crude methanol extract of toad venom from Bufo bufo gargarizans. As a result, in a single 2D separation run (345 min), 18 bufadienolides (1–18) were isolated from 0.5 g crude extract, and the purity of each compound was higher than 90%. We anticipate that this improved low-cost preparative 2D-LC system has broad applications for the simultaneous isolation and purification of multiple components from other complex sample matrices.


https://doi.org/10.1007/s10533-019-00555-8

In the last 40 years, large areas of the Mau forest, the largest contiguous tropical montane forest in East Africa, have been cleared for agriculture. To date, there are no empirical data on how this land use change affects carbon dioxide (CO2) fluxes from soil respiration and soil methane (CH4) fluxes. This study reports measured annual soil CO2 and CH4 fluxes from the native Mau forest and previously forested lands converted to smallholder grazing land, smallholder and commercial tea plantations and eucalyptus plantations. Fluxes were measured weekly from August 2015 to August

2016 using the static chamber method. Grazing lands had the highest (p = 0.028) cumulative respiratory CO2 fluxes (25.6 ± 2.9 Mg CO2

–C ha−1 year−1), whereas lowest fluxes were observed in commercial tea plantations (5.6 ± 0.5 Mg CO2

–C ha−1 year−1). Soil respiratory CO2 fluxes were positively correlated with soil pH, but negatively correlated with soil C:N ratio. Annual soil fluxes were explained by soil pH, bulk density and the interaction between soil pH and C:N ratio. Most soils were sinks for atmospheric CH4 across all land use types. Methane uptake was highest for native forest sites (− 3.08 ± 0.35 to − 5.84 ± 0.61 kg CH4

–C ha−1 year−1) and for eucalyptus plantations (− 3.43 ± 0.19 kg CH4

–C ha−1 year−1). Uptake decreased significantly with increasing land use intensity (smallholder tea plantations: − 1.42 ± 0.09 kg CH4

–C ha−1 year−1, commercial tea plantations: − 1.44 ± 0.29 kg CH4

–C ha−1 year−1). Soils of smallholder grazing lands had the lowest CH4 uptake rates (− 0.36 ± 0.25 kg CH4

–C ha−1 year−1). Annual CH4 uptake was negatively correlated with mean annual soil water-filled pore space (p < 0.01) and bulk density (p = 0.003) and decreased with increasing soil inorganic NH4

+ concentrations (p = 0.03). Annual soil CH4 can be explained by mainly soil water content and bulk density and these factors are related to gas diffusion. Our study shows that converting tropical montane forests to managed land use types affects soil CO2 and CH4 fluxes. Specifically, the CH4 sink strength in managed land use types of these montane tropical soils was reduced to less than half of the sink strength in the native forest. Soil respiratory CO2 fluxes were also altered by land use with grazing lands emitting 3–4 times more CO2 than the other land use types.

Ward, L.M., Rasmussen, B., Fischer, W.W., 2019. Primary productivity was limited by electron donors prior to the advent of oxygenic photosynthesis. Journal of Geophysical Research: Biogeosciences 124, 211-226.

https://doi.org/10.1029/2018JG004679

Abstract: To evaluate productivity on the early Earth before the advent of oxygenic photosynthesis, we integrated estimates of net primary production by early anaerobic metabolisms as limited by geological fluxes of key electron donor compounds, phosphate, and fixed nitrogen. These calculations show that productivity was limited by fluxes of electron donor compounds to rates that were orders of magnitude lower than today. Results suggest that ferrous iron provided a minor fuel for net primary productivity compared to molecular hydrogen. Fluxes of fixed nitrogen and phosphate were in excess of demands by the electron donor‐limited biosphere, even without biological nitrogen fixation. This suggests that until life learned to use water as an electron donor for photosynthesis, the size and productivity of the biosphere were constrained by the geological supply of electron donors and there may not have been much ecological pressure to evolve biological nitrogen fixation. Moreover, extremely low productivity in the absence of oxygenic photosynthesis has implications for the potential scale of biospheres on icy worlds such as Enceladus and Europa, where photosynthesis is not possible and life would be unable to escape electron donor limitation.

Plain Language Summary Life on Earth today is fueled by oxygenic photosynthesis—the process performed by plants, algae, and Cyanobacteria that takes water, light, and carbon dioxide and produces sugar and oxygen. The raw materials for this process are abundant, so productivity :is limited by nutrients such as phosphorous and fixed nitrogen. Oxygenic photosynthesis evolved midway through Earth history, and it has long been unclear how productive the biosphere was earlier in time. Here we considered the compounds necessary for early metabolisms that may have fueled life on the early Earth—including iron and hydrogen compounds that fuel earlier “anoxygenic” photosynthesis. We determined that it was these “electron donor” compounds such as ferrous iron and molecular hydrogen that were most limiting on the early Earth and that the slow geological supply of these compounds resulted in a biosphere that was 1,000‐fold less productive than it is today. The innovation of using water as an electron donor allowed oxygenic photosynthesis to dominate primary production and made the Earth as productive as it is today. This impacts how productive we can

expect life on other planets to be, and assumptions about when certain biochemical processes like those involving the cycling of nitrogen evolved.



Sediments in the hyper-arid core of the Atacama Desert are a terrestrial analogue to Mars regolith. Understanding the distribution and drivers of microbial life in the sediment may give critical clues on how to search for biosignatures on Mars. Here, we identify the spatial distribution of highly specialised bacterial communities in previously unexplored depth horizons of subsurface sediments to a depth of 800mm. We deployed an autonomous rover in a mission-relevant Martian drilling scenario with manual sample validation. Subsurface communities were delineated by depth related to sediment moisture. Geochemical analysis indicated soluble salts and minerology that influenced water bio-availability, particularly in deeper sediments. Colonization was also patchy and uncolonized sediment was associated with indicators of extreme osmotic challenge. The study identifies linkage between biocomplexity, moisture and geochemistry in Mars-like sediments at the limit of habitability and demonstrates feasibility of the rover-mounted drill for future Mars sample recovery.

Wei, H., Jiang, X., 2019. Early Cretaceous ferruginous and its control on the lacustrine organic matter accumulation: Constrained by multiple proxies from the Bayingebi Formation in the Bayingebi Basin, inner Mongolia, NW China. Journal of Petroleum Science and Engineering 178, 162-179.


The greenhouse climate in the Cretaceous period promoted widespread organic-rich marine/lacustrine black shales or mudrocks. Organic matter (OM) accumulation is generally affected by preservation conditions and surface water primary productivity. The detail of organic-rich mudrock formation in lacustrine system still remains enigmatic. The widespread OM-rich mudrocks in the Cretaceous period as petroleum source rocks in many large terrestrial petroliferous basins in China offer an opportunity to explore the mechanism of lacustrine OM accumulation. Fe speciation, CSFe system, pyrite morphology, pyrite-sulfur isotopic composition, elements, and biomarkers in the Bayingebi Formation from a drill core in the Bayingebi Basin, Inner Mongolia, NW China are used to constrain redox conditions, OM source and primary productivity in a lacustrine system. Our results show that the dark-gray mudrocks in the Bayingebi Formation were deposited in ferruginous and stratified water-column in the Bayingebi Basin. The biomarkers suggest a mixed organic matter source of algae, bacteria and high plant with a low algal contribution. The surface-water primary productivity during the deposition of the Bayingebi Formation was low and shows a weak correlation with total organic carbon (TOC) content. The OM accumulation in early Cretaceous lacustrine system was mainly controlled by redox conditions. Ferruginous anoxic conditions in lacustrine system may have high potential for hydrocarbon source rocks owing to the reduction of oxygen decomposition.

Weiss, A.M., Martindale, R.C., 2019. Paleobiological traits that determined scleractinian coral survival and proliferation during the Late Paleocene and Early Eocene hyperthermals. Paleoceanography and Paleoclimatology 34, 252-274.

https://doi.org/10.1029/2018PA003398

Abstract: Coral reefs are particularly sensitive to environmental disturbances, such as rapid shifts in temperature or carbonate saturation. Work on modern reefs has suggested that some corals will fare better than others in times of stress and that their life history traits might correlate with species survival. These same traits can be applied to fossil taxa to assess whether life history traits correspond with coral survival through past intervals of stress similar to future climate predictions. This study aims to identify whether ecological selection (based on physiology, behavior, habitat, etc.) plays a role in the long‐term survival of corals during the late Paleocene and early Eocene. The late Paleocene‐early Eocene interval is associated with multiple hyperthermal events that correspond to rises in atmospheric pCO2 and sea surface temperature, ocean acidification, and increases in weathering and turbidity. Coral reefs are rare during the late Paleocene and early Eocene, but despite the lack of reef habitat, corals do not experience an extinction at the generic level and there is little extinction at the species level. In fact, generic and species richness increases throughout the late Paleocene and early Eocene. We show that corals with certain traits (coloniality, carnivorous, or suspension feeding diet, hermaphroditic brooding reproduction, living in clastic settings) are more likely to survive climate change in the early Eocene. These findings have important implications for modern coral ecology and allow us to make more nuanced predictions about which taxa will have higher extinction risk in present‐day climate change.

Plain Language Summary\: Climate change is negatively impacting corals and reefs today. In order for us to plan for future reef survival, we must learn how corals will respond to these stresses. Past intervals of climate change can provide valuable information about what happens to reefs when the environment changes quickly and how, or if, they recover. We explore the Paleocene and Eocene Stages, which contain a series of high‐temperature events called hyperthermals. We look at the specific traits of the corals at this time, for example, what type of food they ate, how they reproduced, whether they could share resources with one another in a colony, and calculate whether these traits made the corals more likely to survive during this time period. Corals have a relationship with algae that photosynthesize food for the coral, which helps the corals build large skeletons. We show that corals that do not depend on these photosymbionts for food are colonial or live in special habitats and have a better chance of surviving climate change events over long timescales. This research is important for future predictions of coral reef response to climate change; past events, like the one studies, can identify the types of corals that will likely perform best. This information can help scientists figure out how to best protect coral reefs.

Wells, M., McGarry, J., Gaye, M.M., Basu, P., Oremland, R.S., Stolz, J.F., 2019. Respiratory selenite reductase from Bacillus selenitireducens strain MLS10. ournal of Bacteriology 201, e00614-00618.

http://jb.asm.org/content/201/7/e00614-18.abstract

Abstract: The putative respiratory selenite [Se(IV)] reductase (Srr) from Bacillus selenitireducens MLS10 has been identified through a polyphasic approach involving genomics, proteomics, and enzymology. Nondenaturing gel assays were used to identify Srr in cell fractions, and the active band was shown to contain a single protein of 80 kDa. The protein was identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a homolog of the catalytic subunit of polysulfide reductase (PsrA). It was found to be encoded as part of an operon that contains six genes that we designated srrE, srrA, srrB, srrC, srrD, and srrF. SrrA is the catalytic subunit (80 kDa), with a twin-arginine translocation (TAT) leader sequence indicative of a periplasmic protein and one putative 4Fe-4S binding site. SrrB is a small subunit (17 kDa) with four putative 4Fe-4S binding sites, SrrC (43 kDa) is an anchoring subunit, and SrrD (24 kDa) is a chaperon protein. Both SrrE (38 kDa) and SrrF (45 kDa) were annotated as rhodanese domain-containing proteins. Phylogenetic analysis

revealed that SrrA belonged to the PsrA/PhsA clade but that it did not define a distinct subgroup, based on the putative homologs that were subsequently identified from other known selenite-respiring bacteria (e.g., Desulfurispirillum indicum and Pyrobaculum aerophilum). The enzyme appeared to be specific for Se(IV), showing no activity with selenate, arsenate, or thiosulfate, with a Km of 145 ± 53 μM, a Vmax of 23 ± 2.5 μM min−1, and a kcat of 23 ± 2.68 s−1. These results further our understanding of the mechanisms of selenium biotransformation and its biogeochemical cycle.

Importance: Selenium is an essential element for life, with Se(IV) reduction a key step in its biogeochemical cycle. This report identifies for the first time a dissimilatory Se(IV) reductase, Srr, from a known selenite-respiring bacterium, the haloalkalophilic Bacillus selenitireducens strain MLS10. The work extends the versatility of the complex iron-sulfur molybdoenzyme (CISM) superfamily in electron transfer involving chalcogen substrates with different redox potentials. Further, it underscores the importance of biochemical and enzymological approaches in establishing the functionality of these enzymes.


https://doi.org/10.1155/2019/3717239

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.

White, A.J., Stevens, L.R., Lorenzi, V., Munoz, S.E., Schroeder, S., Cao, A., Bogdanovich, T., 2019. Fecal stanols show simultaneous flooding and seasonal precipitation change correlate with Cahokia’s population decline. Proceedings of the National Academy of Sciences 116, 5461-5466.


Significance: Our article examines the relationship between the population size of Cahokia, one of the most significant archaeological sites in North America, and evidence for major flooding and drought events. We use changes in the concentrations of fecal molecules contained in lake sediment as a proxy of population change and directly compare these variations with paleoenvironmental data from the same sediment core. These data show that a shift to decreased summer precipitation and a Mississippi River flood occurred circa 1150 CE, coinciding with a decline in the region’s population and a major climate transition. Our study highlights the importance of multiple, concurrent environmental stressors in combination with societal tensions as contributors to sociopolitical change.

Abstract: A number of competing hypotheses, including hydroclimatic variations, environmental degradation and disturbance, and sociopolitical disintegration, have emerged to explain the dissolution of Cahokia, the largest prehistoric population center in the United States. Because it is likely that Cahokia’s decline was precipitated by multiple factors, some environmental and some societal, a robust understanding of this phenomenon will require multiple lines of evidence along with a refined chronology. Here, we use fecal stanol data from Horseshoe Lake, Illinois, as a population proxy for Cahokia and the broader Horseshoe Lake watershed. We directly compare the fecal stanol data with oxygen stable-isotope and paleoenvironmental data from the same sediment cores to evaluate the role of flooding, drought, and environmental degradation in Cahokia’s demographic decline and sociopolitical reorganization. We find that Mississippi River flooding and warm season droughts detrimental to agriculture occurred circa (ca.) 1150 CE and possibly generated significant stress for Cahokia’s inhabitants. Our findings implicate climate change during the Medieval Climatic Anomaly to Little Ice Age transition as an important component of population and sociopolitical transformations at Cahokia, and demonstrate how climate transitions can simultaneously influence multiple environmental processes to produce significant challenges to society.

Winkler, A.J., Myneni, R.B., Alexandrov, G.A., Brovkin, V., 2019. Earth system models underestimate carbon fixation by plants in the high latitudes. Nature Communications 10, Article 885.

https://doi.org/10.1038/s41467-019-08633-z

Most Earth system models agree that land will continue to store carbon due to the physiological effects of rising CO2 concentration and climatic changes favoring plant growth in temperature-limited regions. But they largely disagree on the amount of carbon uptake. The historical CO2 increase has resulted in enhanced photosynthetic carbon fixation (Gross Primary Production, GPP), as can be evidenced from atmospheric CO2 concentration and satellite leaf area index measurements. Here, we use leaf area sensitivity to ambient CO2 from the past 36 years of satellite measurements to obtain an Emergent Constraint (EC) estimate of GPP enhancement in the northern high latitudes at two-times the pre-industrial CO2 concentration (3.4 ± 0.2 Pg C yr−1). We derive three independent comparable estimates from CO2 measurements and atmospheric inversions. Our EC estimate is 60% larger than the conventionally used multi-model average (44% higher at the global scale). This suggests that most models largely underestimate photosynthetic carbon fixation and therefore likely overestimate future atmospheric CO2 abundance and ensuing climate change, though not proportionately.


https://doi.org/10.1007/s10533-019-00548-7

Submerged rice cultivation is characterized by redox fluctuations and results in the formation of paddy soils, often accompanied by soil organic carbon (SOC) accumulation. The impact of redox fluctuations and the underlying soil type on the fate of organic carbon (OC) in paddy soils are unknown. Hence, we mimicked paddy soil development in the laboratory by exposing two soil types with contrasting mineral assemblages (Alisol and Andosol) to eight anoxic–oxic cycles over 1 year. Soils regularly received 13C-labeled rice straw. As control we used a second set of samples without straw addition as well as samples under static oxic conditions with and without straw. Headspaces were analyzed for carbon dioxide and methane as well as their δ13C signatures, whereas soil solutions were analyzed for redox potential, pH, dissolved iron, and dissolved organic carbon (DOC and DO13C). At the end of the experiment, when eight redox cycles were completed, mineral-associated organic matter (MOM) was isolated by density fractionation and characterized for δ13C, non-cellulosic carbohydrates, and lignin-derived phenols. Moreover, changes in the soil’s microbial community structure were measured. For both soil types, headspace data confirmed less respiration in straw-amended soils with redox fluctuation than in those under static oxic conditions. The δ13C data revealed that, irrespective of soil type, straw carbon allocation into MOM was larger in soils with redox fluctuation than in those with static oxic conditions. A net increase in MOM after the one-year incubation, however, was only observed in the respective Andosol, probably due to abundant reactive minerals capable of OC uptake. In the Alisol, straw OC most likely exchanged initial MOM. A potential for lignin accumulation in the MOM of soils incubated with straw and redox fluctuation was observed for both soil types. Lignin and carbohydrates suggest a plant origin of MOM formed under redox fluctuation. The initially similar bacterial community composition of the Alisol and Andosol changed differently under redox fluctuation. The stronger change in the Alisol indicates less protective microbial habitats. In summary, the overall turnover of straw OC in soils under redox fluctuation seems to be independent of soil type, while net accumulation of SOC as well as the evolution of the bacterial community structure may in part depend on soil type, suggesting an impact of the soil’s mineral composition.



Water-soluble organic compounds (WSOCs) are a complex mixture of organic components with a variety of chemicals structures that may have significant impacts on the formation process and health hazards of atmospheric fine particles. In this study, the molecular characteristics of WSOCs in PM2.5 were investigated using ultrahigh resolution mass spectrometry. In total 7389 compounds in PM2.5 water extracts were identified, including CHO±, CHOS±, CHON±, CHONS±, CH+, CHS+, CHN+ and CHNS+ species. CHO± and CHON± were the major components in PM2.5 water extracts. S-containing compounds detected in both ionization modes were observed with distinct molecular characteristics. Selective partitioning of WSOCs between PM2.5 water extracts and polydimethylsiloxane (PDMS, log DPDMS = 0.51–3.87) coating phases was found, which was significantly correlated with molecular characteristic (i.e. double-bond equivalent, number of O and H atoms, O/C ratios, and aromaticity equivalent). The extent of accumulation for negatively charged compounds was generally lower, which related to the existence of polar functional groups, such as hydroxyl, carboxyl, nitrate, and sulfate, as observed by MS/MS fragmentation analysis.



Solvent recovery from diluted bitumen and froth treatment tailings, produced during the bitumen recovery process for mined oil sands, requires an understanding of the thermodynamic equilibrium and kinetics of solvent dissolution in bitumen. Thermodynamic properties of solvent in bitumen having various asphaltene contents are needed in order to model and improve the solvent recovery process. In this work, the thermodynamic properties of light hydrocarbons in bitumen were investigated using an inverse gas liquid chromatography (IGC) method. Bitumen containing different amounts of asphaltenes (0 wt%, 2.6 wt%, 9.9 wt%, 36.9 wt%, and 53.7 wt%) were used as the stationary phase of the chromatographic column, while light hydrocarbons were injected into mobile phase. The specific retention volumes of the hydrocarbons in bitumen, Vg

o, were measured at different temperatures (333.2 K–393.2 K). Thermodynamic properties of these light hydrocarbons in bitumen, including infinite dilution activity coefficient, γ∞, enthalpy of solution, ΔHo, heat capacity changes, ΔCp

o, Gibbs energy change, ΔGo, as well as entropy of solution change, ΔSo, were then calculated based on thermodynamic principles and data obtained from IGC measurements.

Wu, L., Horsfield, B., 2019. Initial insights into releasing bound biomarkers from kerogen matrices using microscale sealed vessel catalytic hydrogenation (MSSV-HY). Organic Geochemistry 130, 22-32.


Microscale Sealed Vessel pyrolysis (MSSV) is a microanalytical technique originally developed for artificially maturing sedimentary organic matter and examining the bulk compositional relationships between kerogen and petroleum. Here, we explore the possibility of modifying the standard MSSV pyrolysis approach to increase biomarker release from macromolecular matrices. This is termed microscale sealed vessel catalytic hydrogenation, or MSSV-HY. Tetralin is employed as hydrogen donor and dispersed sulfide molybdenum as catalyst. Using two kerogen concentrates, one of low maturity (vitrinite reflectance: 0.6 %Ro) and the other over-mature (1.8 %Ro), from the Dalong Mudstone (Permian, Sichuan Basin), the effects of tetralin and catalyst alone and as mixtures, and the tetralin/kerogen ratio on biomarker release have been investigated, and optimum conditions identified. A comparison of results with those of HyPy enabled the utility of the method to be assessed. Biomarkers were generated from the over-mature sample and preserved using MSSV-HY, whereas they were absent in MSSV products. Biomarkers released from the low maturity sample using MSSV were devoid of extended hopanes, and dominated by C27 steranes, whereas the MSSV-HY products were rich in Tm, the extended hopanes, and with C27–C29 regular steranes. MSSV-HY products showed some similarities to HyPy products. The steranes from MSSV-HY were very similar to those from HyPy; although some differences in hopane distributions were discernable (e.g., the abundances of Ts and C30 hopane) due to varied contribution of occluded OM in the HyPy and MSSV-HY analyses. This proof of concept study has shown that off-line MSSV-HY shows great promise as a means for releasing bound biomarkers and reducing secondary cracking because of catalyst associated pressure increase in the MSSV tubes. Its currently planned area of operation is in petroleum systems.

Wu, L., Wang, P., Geng, A., 2019. Later stage gas generation in shale gas systems based on pyrolysis in closed and semi-closed systems. International Journal of Coal Geology 206, 80-90.


As a self-contained source-reservoir petroleum system, shale gas plays have different generation mechanisms from conventional natural gas plays, especially with respect to the effects of residual

hydrocarbons on shale gas generation. In this study, closed-system pyrolysis experiments were conducted on a suite of residual shales obtained by the semi-closed pyrolysis of shales from the Neoproterozoic Xiamaling Formation under various conditions. The effects of oil expulsion on the geochemical characteristics of residual organic matter (both bitumen and kerogen) in shale and on shale gas generation in the high maturity stage were investigated. The results indicated that shales with high oil expulsion efficiencies should be depleted in the aliphatic fractions in residual shale. In contrast, most of the aliphatic fractions should remain in shales with low oil expulsion efficiencies. Additionally, oil expulsion can further affect the chemical and isotopic compositions of the gas generated at later stages of thermal maturation. With increasing oil expulsion efficiency, C1, C2, C3, C1–5, and C2–5 gas yields and gas wetness decrease, while C1, C2, and C3 carbon isotopic values become heavier.

Wu, W., Wang, H., Yu, J., Pan, J., 2019. Geochemical characteristics of the Carboniferous-Permian source rocks in Western Henan, China. Petroleum Science and Technology 37, 519-527.

https://doi.org/10.1080/10916466.2018.1547750

55 source rock samples in the Carboniferous-Permian strata, southern Northern China basin were analyzed in this paper to obtain the sedimentary characteristics, organic matter abundance, kerogen type and thermal maturity and the unconventional oil and gas prospects. The results demonstrated that the source rocks were all dominated by the evolution of the sedimentary environment. High thermal evolution resulted in low S1, whereas poor preservation caused by strong tectonic activities resulted in low S2. The units of the southern North China Basin with weak tectonic activity and good preservation conditions may be the main areas for future unconventional gas exploration.

Wu, X., Xing, L., Jiang, Y., Zhang, X., Xiang, R., Zhou, L., 2019. High-resolution reconstruction of sedimentary organic matter variability during the Holocene in the mud area of the Yellow Sea using multiple organic geochemical proxies. Quaternary International 503, 178-188.


As a result of terrestrial input and local circulation, an area containing continuously deposited mud with abundant organic matter (OM) has formed in the Yellow Sea (YS) off the Shandong Peninsula, China, during the Holocene. The understanding of temporal variations in sedimentary organic matter (SOM) from this mud area helps to evaluate the influences of Yellow River discharge and marine productivity on the burial of organic matter in the YS. In this study, multiple organic geochemical proxies were used to reconstruct Holocene changes in SOM in a sediment core (A02C) recovered from the mud area of the YS. Higher total organic carbon (TOC) and biomarker contents during the early Holocene relative to the middle and late Holocene are attributed to sea-level fluctuations. The δ13C values of TOC (δ13CTOC) range from −21.8‰ to −23.5‰, becoming more positive from the bottom to the top of the core. TMBR' (terrestrial and marine biomarker ratio) values vary from 0.43 to 0.80, with a decreasing trend during the Holocene. The decrease in TOM contribution was related to elevated sea-level, shifting of the mouth of the Yellow River, and weakening of the East Asian Winter Monsoon (EAWM) during the Holocene. A mixing model with three end-members, based on δ13CTOC and TMBR', reveals that the contribution of soil OM (average 42%) is higher than that of plant OM (average 17%). Simultaneous decreases in the plant OM fraction and the marine OM fraction occurred around 10.3, 8.2, 5.9, 4.2, and 2.8 kyr BP, corresponding to drift-ice events in the North Atlantic. Spectral analyses also reveal that all three OM fractions exhibit 1015-year periodicity and that the soil and plant OM fractions display 1420-year periodicity, consistent with the 1000-year cycle of solar activity and the 1500-year cycle of the Kuroshio Current (KC), respectively.


https://doi.org/10.1080/10916466.2018.1539752

The abundant acyclic isoprene alkanes, including norpristane (2, 6, 10-tetramethyltetradecane), pristane (2, 6, 10, 14-tetramethylpentadecane), phytane (2, 6, 10, 14-tetramethylhexadecane) and their diastereomers, were detected and separated by GC-MS/MS in the coal sample of the Junggar Basin. Furthermore, the optimized condition of separation were discussed in terms of column type, length, and column temperature program. The results showed that the separation degree (R) of their diastereomers (i.e., 6(R)10(S)), 6(S)10(S)?+?6(R)10(R)) of norpristane, pristane and phytane reached 0.6, 0.8 and 0.9, respectively. It indicated that the method was versatile, simple, rapid and efficient to separate the diastereomers of acyclic isoprene alkanes.



Semi-closed hydrous pyrolysis experiments were conducted to investigate the isotopic evolution of shale gas produced from continental organic-rich shales with increasing thermal maturity and prospecting potential. The δ13C values of methane, ethane, propane and n-butane became heavier with increasing thermal maturity and showed good relationships with vitrinite reflectance (VR). Gases expelled from type-I, type-II, and type-III kerogens followed the normal carbon sequence (δ13CC1 < δ13CC2 < δ13CC3 < δ13CnC4) and the hydrogen isotopic sequence (δ2HC1 < δ2HC2 < δ2HC3 < δ2HnC4 < δ2HiC4) among the alkanes at VRs lower than 2.14% Ro, 2.42% Ro, and 1.87% Ro respectively. The isotopically reversed gases (δ13CC1 < δ13CC2 < δ13Cnc4 < δ13CC3) were observed in type-I kerogen with a VRs above 2.14% Ro and in type-II kerogen with a VR above 2.42% Ro. In type-III kerogen, isotopically reversed gases (δ13CC1 < δ13CnC4 < δ13CC3 < δ13CC2) were observed with a VR above 2.94% Ro. These results suggest four stages in the stable carbon isotope reversal of ethane, propane, and n-butane with increasing maturity. The isotopically reversed gases (δ13CC1 < δ13CC2 < δ13CnC4 < δ13CC3) may represent lower maturity and higher productivity shale gas than the isotopically reversed gases (δ13CC1 < δ13CnC4 < δ13CC3 < δ13CC2), indicating that continental type-I kerogen has the highest potential productivity for shale gas, and continental type-III kerogen has the lowest. Stable hydrogen isotope composition did not respond to the stable carbon isotope reversal in isotopically reversed gases. We suggest that indigenous generation and mixing may be the dominant mechanisms responsible for the stable carbon isotope reversal, and adsorption/desorption during hydrocarbon expulsion may promote the stable isotope reversal under semi-closed conditions. Overall, these results suggest that this study is an important contribution to continental shale gas exploration.

Xi, K., Cao, Y., Lin, M., Liu, K., Wu, S., Yuan, G., Yang, T., 2019. Applications of light stable isotopes (C, O, H) in the study of sandstone diagenesis: A review. Acta Geologica Sinica - English Edition 93, 213-226.

https://doi.org/10.1111/1755-6724.13769

This article reviews the applications of light stable isotope, including carbon, oxygen and hydrogen, in the studies on origin and formation temperature of authigenic carbonate, quartz and clay minerals. Theoretical knowledge and analytical methods for major light stable isotopes are introduced in detail. Negative and positive δ13C values indicate significant differences on the origin of carbonate cements. The δ18O value is an effective palaeotemperature scale for authigenic minerals formation. Various fractionation equations between δ18O and temperature are proposed for carbonate cements, quartz cements and clay minerals, whose merit and demerit, applicable conditions are clarified clearly. Clumped isotope analysis can reconstruct the temperature of carbonate precipitation with no requirement on the δ18O of initial waters, which makes temperature calculation of carbonate cements formation more convenient and accurate. Hydrogen and oxygen isotopes mainly reflect the origin of diagenetic fluid for clay mineral formation, providing reliable evidence for diagenetic environment analysis. This work aims at helping researchers for better understanding the applications of light stable isotope in sandstone diagenesis.



Short-chain chlorinated paraffins (SCCPs), with 10–13 carbon atoms, are persistent organic pollutants under the Stockholm Convention because they are persistent, toxic, and bioaccumulative. However, little information is available on CPs with <10 carbon atoms. C9-CPs were identified and quantified in environmental matrices in this study. The occurrences and sources of C9-CPs in environmental samples were investigated by determining C9-CPs in technical CP products and environmental matrices, including indoor air and sediment, by GC×GC‒ECNI‒TOFMS. Quantitative structure-property relationship modeling revealed C9-CPs have high octanol-water partition coefficients (log Kow 5.99), octanol-air partition coefficients (log Koa 7.24), and bioaccumulation factors (log BAF 4.07), indicating C9-CPs are semivolatile and could bioaccumulate. C9-CPs were detected in different fish (at 3.4–153 ng/g dw), confirming they can bioaccumulate. C9-CPs were found in soil (at 3.0–25.6 ng/g dw) and biota (at 7.5–57.8 ng/g dw) from the Antarctic, demonstrating they can undergo long-range transport and are global pollutants. This is the first comprehensive study reporting the sources, occurrences, and fates of C9-CPs in the environment, laying foundations for further evaluation of C9-CPs and their inclusion as candidate persistent organic pollutants under the Stockholm Convention.



The aim of this work was to study the production of bioemulsifier by Rhodococcus erythropolis OSDS1, and the improvement of crude oil depletion efficiency using a consortium of petroleum hydrocarbon degraders and OSDS1. The results showed that R. erythropolis OSDS1 produced highly stable bioemulsifier under various salinity (0–35 g/L NaCl) and pH (5.0–9.0) conditions; more than 90% of the initial emulsification activity was retained after 168 h. Emulsification capacity of the bioemulsifier on different petroleum hydrocarbons was diesel > mineral oil/crude oil > gasoline. A mixed bacterial consortium combining OSDS1 and four other petroleum hydrocarbon degraders was constructed. GC–MS results revealed that the constructed consortium achieved 85.26% depletion

efficiency of crude oil in 15 days, which was significantly higher than that of individual strains. During the process, alkane hydroxylase gene (alkB) was successfully amplified from the consortium, confirming presence of crude oil degrading enzymes.

Xiao, H., Li, M., Liu, J., Mao, F., Cheng, D., Yang, Z., 2019. Oil-oil and oil-source rock correlations in the Muglad Basin, Sudan and South Sudan: New insights from molecular markers analyses. Marine and Petroleum Geology 103, 351-365.


Oil-oil and oil-source rock correlations for nineteen crude oils and eight mudstone extracts from four sub-basins in the Muglad Basin were achieved by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Based on the characteristics of biomarker compositions and hierarchical cluster analysis, an outlier crude oil has been discovered in the Muglad Basin. The majority of discovered oils have similar geochemical characteristics and belong to an established oil family. This oil family has relatively higher (C19+C20)/C23TT and C24TeT/C26TT ratios, small amounts of long-chain tricyclic terpanes with a dominance of C21TT among C19C23TT homologues, a lower abundance of C28 regular steranes with abundant C30 4α-methylsteranes, an unusually higher content of diasteranes and diahopanes. These biomarker ratios indicate the mixed inputs of aquatic plankton and terrigenous organic matter deposited under oxic to sub-oxic, and fresh to brackish water sedimentary environments. This oil family belongs to source rocks of the Abu Gabra Formation as proven by oil-source rock correlation. In contrast, the distribution characteristics of tricyclic and tetracyclic terpanes, C28 regular steranes, C30 4α-methylsteranes, diasteranes and diahopanes are all significantly different than those of the established oil family in the well Kela-1 oil (2563 m) within the Darfur Group reservoir. The geochemical signatures indicate that their related source rock is an algal dominated organic matter input, deposited in sub-oxic condition, and brackish to saline sedimentary environment. Moreover, the composition and characteristics of molecular markers of the well Kela-1 oil are highly consistent with those of the two mudstone samples from the Darfur Group. This clearly demonstrates that the Darfur Group mudstones are the potential source rocks for the outlier crude oil. Identification of the outlier crude oil shows that the Darfur Group mudstones have a certain potential regarding hydrocarbons resources that could provide petroleum companies an impetus to enhance their exploration efforts.

Xiao, J., Fan, L., Wu, D., Xu, Y., Lai, D., Martin, W.F., Zhu, R., Zhang, C., 2019. Archaea, the tree of life, and cellular evolution in eukaryotes. Science China Earth Sciences 62, 489-506.

https://doi.org/10.1007/s11430-018-9326-1

The early history of life harbours many unresolved evolutionary questions, none more important than the genomic origin and cellular evolution of eukaryotes. An issue central to eukaryote origin concerns the position of eukaryotes in the tree of life and the relationship of the host lineage that acquired the mitochondrion some two billion years ago to lineages of modern-day archaea. Recent analyses indicate that the host lineage branches within the Archaea, prompting the search for novel archaeal lineages that can improve our understanding of the cellular evolution of eukaryotes. Here we give a brief review of the studies on Archaea, the tree of life and the cellular evolution of eukaryotes, which is followed by an overview of recent progress fueled by new genomic technologies and recent status of archaeal research in China. Future directions for the study of early evolution are considered.

Xiao, Q., Sun, Y., He, S., Liu, J., Zhu, C., 2019. Thermal stability of 2-thiadiamondoids determined by pyrolysis experiments in a closed system and its geochemical implications. Organic Geochemistry 130, 14-21.


The abundance of 2-thiadiamondoids is currently utilized to assess the extent of thermochemical sulfate reduction (TSR). However, these compounds are ultimately degraded to small molecules with increasing temperature in deep hot reservoirs, resulting in uncertainty in their use as a proxy to evaluate the extent of TSR. In this study, the thermal stability of 2-thiadiamondoids was determined from variations in their abundance upon pyrolysis at different temperatures using an oil enriched in thiadiamondoids. The results demonstrated that these compounds were generally stable at Easy%Ro ≤ 1.0, followed by partial destruction at Easy%Ro = 1.3–2.0 and intensive decomposition at Easy%Ro ≥ 2.0–2.3, suggesting the potential underestimation of the TSR extent at the highly mature to over mature stages. The thermal stability of 2-thiadiamondoids and diamondoids strongly depended on their cage numbers, which presented an increasing trend with higher cage numbers. However, diamondoids were far more stable than 2-thiadiamondoids and were still thermally stable even up to Easy%Ro = 1.8–2.3. The thermal stability of dibenzothiophenes (DBTs) showed a decreasing trend with increases in alkyl substituted carbon numbers. They were thermally stable at Easy%Ro ≤ 1.0–1.8 and can be seriously cracked at Easy%Ro ≥ 1.8–3.0. The C0-DBT and C1-DBTs were more stable than thiadiamondoids, but C3-DBTs showed the opposite trend. The thermal stability of gasoline range hydrocarbons showed a trend of CH4 > C2H6 > C3H8 > C4–5. CH4 and C2H6 were much more stable than diamondoids, while C3–5 hydrocarbons were only thermally stable at Easy%Ro ≤ 1.8–2.3 and severely degraded at Easy%Ro ≥ 2.6–3.0. The C3H8 and 2-cage diamantanes, C4–5 compounds and 1-cage adamantanes had a similar thermal stability. Therefore, to accurately assess the TSR extent should be made using thiadiamondoids, diamondoids and C0–1-DBTs, even gasoline range hydrocarbons, rather than thiadiamondoids alone, if gases are well preserved within petroleum reservoirs in the subsurface.

Xie, J., Chu, Y., Shi, Y., Han, X., Li, X., Wang, L., Guo, Y., 2019. Studies of chromatographic separation and self-emulsification of crude oil. Petroleum Science and Technology 37, 220-225.

https://doi.org/10.1080/10916466.2018.1536711

The crude oil in Zhundong Oilfield has good self-emulsification phenomenon. In order to reveal the mechanism, the crude oil was divided into saturated hydrocarbon, unsaturated hydrocarbon, resin and asphalt by chromatographic method, and their contents are 40.09%, 11.19%, 48.05% and 0.67%, respectively. The effects of the petroleum components on self-emulsification were investigated. The results show that the resin has the most important effect on emulsification and plays the role of emulsifier. The saturated hydrocarbon and unsaturated hydrocarbon act as the basic oil and cannot be emulsified with the injection water without the resin emulsifier. Moreover, the resin content is very important, only when it is in a proper proportion, the system can be well self-emulsified. This work is useful for water flooding.

Xie, J., Liang, Y., Zou, Q., Wang, Z., Li, X., 2019. Prediction model for isothermal adsorption curves based on adsorption potential theory and adsorption behaviors of methane on granular coal. Energy & Fuels 33, 1910-1921.


In this study, adsorption tests of methane on granular coal were performed to investigate the effects of various factors (temperature, particle size, pressure, and water content) on the adsorption behaviors. Using the experimental results, a new model was built for predicting isothermal adsorption curves by optimizing the saturated vapor pressure parameter in the adsorption potential theory. The predicted isothermal adsorption curves indicate that different coal samples have different saturated vapor pressure parameters. The fitting accuracy of different vapor pressure parameters was determined, for which the functions were also established. Thus, the optimal vapor pressure parameters for coal samples with different particle sizes were obtained and used to build a prediction model for the isothermal adsorption curves. To verify the accuracy, the model was used to predict the isothermal adsorption curve under the temperature of 308 K. The results were then compared with the experimental values measured at the corresponding temperature. Good agreement was found, thus verifying the veracity and accuracy of the model. Hence, the results of this study may provide a new method to predict the isothermal adsorption curves of coal at different temperatures.



In China, low-rank coalbed methane (CBM) resources are in the early stage of exploration. The evolution of pore structure for these coals around the first coalification jump is incomplete. Here systematic experiments were conducted to analyze the reservoir of low-rank coal (lignite and subbituminous coal) from China's major low-rank basins, thus revealing the pore structure evolution of low-rank coal in China. Scanning electron microscopy (SEM) demonstrates that there are obvious differences in the pore types of different rank coals. Well-developed cell lumina provides a large amount of macropore space in coals with Ro < 0.5%. After coal metamorphism and physical compaction, the volume and number of plant tissue pores are reduced, resulting in a significant reduction in macropores. The Fourier transform infrared spectroscopy (FTIR) spectral characteristics indicate that the evolution of chemical structure also has an effect on the pore structure of coal. Due to the low proportion of aromatic nuclei, the high proportion of functional groups and long side chains, when Ro is <0.5%,the spatial structure of coal reservoir is “loose”, resulting in a large surface area. With increasing coal maturity, the side chains gradually decompose and the length decreases, and the aromatic nuclei increase so that the structure becomes more “compact”. With increasing coal rank, the pore size distribution changes significantly. The peak shape of the NMR T2 spectrum shows a series of complex changes from trimodal to bimodal to trimodal and finally to bimodal, indicating that the pore size distribution undergoes continuous changes. With the continuous coalification and physical compaction, the porosity decreases rapidly with vitrinite reflectance increases from 0.42–0.68%, and the adsorption capacity shows an increasing trend with the increase of coal rank under the control of moisture content, pore type, and specific surface area. Understanding the evolution of pore structure in the early stage of coalification will provide a scientific reference and foundation for exploration and development of low-rank CBM.

Xiong, Y., Guilbaud, R., Peacock, C.L., Cox, R.P., Canfield, D.E., Krom, M.D., Poulton, S.W., 2019. Phosphorus cycling in Lake Cadagno, Switzerland: A low sulfate euxinic ocean analogue. Geochimica et Cosmochimica Acta 251, 116-135.


Low sulfate, euxinic water-column conditions were a common feature of many Precambrian and Phanerozoic periods of ocean anoxia. The cycling of phosphorus in anoxic marine environments

exerts a fundamental control on primary productivity, organic carbon production and burial, and hence ultimately oxygen production, but the dynamics of the phosphorus cycle in low sulfate, euxinic settings are largely unknown. Here, we provide a detailed geochemical investigation of phosphorus cycling in the low sulfate, euxinic Lake Cadagno, Switzerland, which is considered a prime analogue for ancient euxinic oceans. We find evidence for extensive recycling of phosphorus from the sediments back to the water column, stimulated by the microbial release of phosphorus from organic matter and Fe (oxyhydr)oxide minerals. Consistent with previous studies of modern and ancient anoxic settings, this regenerated flux maintains high concentrations of phosphorus in the water column, thus promoting a positive productivity feedback. However, the low-sulfate condition of the overlying water column, combined with the rapid removal of sulfide (as pyrite) from porewaters, promotes formation of Fe(II) phosphate minerals (e.g., vivianite) close to the sediment-water interface. This, in turn, modulates the extent of phosphorus recycling back to the water column, and contrasts with modern fully marine euxinic settings, where the higher concentrations of dissolved sulfate promote sulfide formation to greater depths, thus limiting Fe(II) phosphate formation close to the sediment-water interface. The prevalence of low-sulfate conditions during past euxinic episodes suggests that the operation of this near-surface sedimentary trap for recycled phosphorus would have limited the positive P-driven productivity feedback, promoting only a moderate degree of P recycling. Furthermore, the precise magnitude of this recycled P flux would, on a global scale, have been dependent on changes in the size of Earth’s marine sulfate reservoir through time. Thus our findings have major implications for rates of P-driven productivity and organic carbon burial in ancient euxinic settings, which have not previously been factored into reconstructions of Earth’s oxygenation history.

Xu, H., Peng, X., Bai, S., Ta, K., Yang, S., Liu, S., Jang, H.B., Guo, Z., 2019. Precipitation of calcium carbonate mineral induced by viral lysis of cyanobacteria: evidence from laboratory experiments. Biogeosciences 16, 949-960.


Viruses have been acknowledged as being important components of the marine system for the past 2 decades, but their role in the functioning of the geochemical cycle has not been thoroughly elucidated to date. Virus-induced rupturing of cyanobacteria is theoretically capable of releasing intracellular bicarbonate and inducing the homogeneous nucleation of calcium carbonate; however, experiment-based support for virus-induced calcification is lacking. In this laboratory study, both water carbonate chemistry and precipitates were monitored during the viral infection and lysis of host cells. Our results show that viral lysis of cyanobacteria can influence the carbonate equilibrium system remarkably and promotes the formation and precipitation of carbonate minerals. Amorphous calcium carbonate (ACC) and aragonite were evident in the lysate, compared with the Mg(OH)2 (brucite in this paper) precipitate in noninfected cultures, implying that a different precipitation process had occurred. Based on the carbonate chemistry change and microstructure of the precipitation, we propose that viral lysis of cyanobacteria can construct a calcification environment where carbonate is the dominant inorganic carbon species. Numerous virus particles available in lysate may coprecipitate with the calcium carbonate. The experimental results presented in this study demonstrate both the pathway and the outcome with respect to how viruses influence the mineralization of carbonate minerals. It is suggested that viral calcification offers new perspectives on mechanisms of CaCO3 biomineralization and may play a crucial role within the Earth system.

Xu, J., Cui, Z., Nie, K., Cao, H., Jiang, M., Xu, H., Tan, T., Liu, L., 2019. A quantum mechanism study of the C-C bond cleavage to predict the bio-catalytic polyethylene degradation. Frontiers in Microbiology 10, 489. doi: 410.3389/fmicb.2019.00489.


The growing amount of plastic waste ending up in landfills and in the oceans has become a global concern. Particularly, polyethylene (PE) and polystyrene (PS) are considered as notably recalcitrant to biodegradation due to the carbon-carbon backbone that is highly resistant to enzymatic degradation via oxidative reactions. The present research investigated the catalytic mechanism of P450 monooxygenases by quantum mechanics to determine the bio-catalytic degradation of PE or PS. The findings indicated that the oxygenase-induced free radical transition caused the carbon-carbon backbone cleavage of aliphatic compounds. This work provides a fundamental knowledge of the biodegradation process of PE or PS at the atomic level and facilitates predicting the pathway of plastics' biodegradation by microbial enzymes.

Xue, X., Jiang, H., Ouyang, F., Zhou, X., 2019. Molecular reconstruction of naphtha by maximum information entropy method. Petroleum Science and Technology 37, 535-542.

https://doi.org/10.1080/10916466.2018.1550496

Naphtha is the feedstock for steam cracking and catalytic reforming of aromatics. Based on the molecular library and 42 groups of practical data including the properties of density, potential aromatic content, the weight fractions of PNA and carbon number distribution, a molecular reconstruction model for naphtha was established by maximum information entropy method. The content of 451 components for naphtha were estimated. The molecular composition generated by the simulation is in good agreement with the practical data. The model can provide the referential value for the steam cracking and catalytic reforming of aromatics processes at molecular level.

Yamagata, K., Nagai, K., Miyamoto, H., Anzai, M., Kato, H., Miyamoto, K., Kurosaka, S., Azuma, R., Kolodeznikov, I.I., Protopopov, A.V., Plotnikov, V.V., Kobayashi, H., Kawahara-Miki, R., Kono, T., Uchida, M., Shibata, Y., Handa, T., Kimura, H., Hosoi, Y., Mitani, T., Matsumoto, K., Iritani, A., 2019. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging. Scientific Reports 9, Article 4050.

https://doi.org/10.1038/s41598-019-40546-1

The 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. Here we recovered the less-damaged nucleus-like structures from the remains and visualised their dynamics in living mouse oocytes after nuclear transfer. Proteomic analyses demonstrated the presence of nuclear components in the remains. Nucleus-like structures found in the tissue homogenate were histone- and lamin-positive by immunostaining. In the reconstructed oocytes, the mammoth nuclei showed the spindle assembly, histone incorporation and partial nuclear formation; however, the full activation of nuclei for cleavage was not confirmed. DNA damage levels, which varied among the nuclei, were comparable to those of frozen-thawed mouse sperm and were reduced in some reconstructed oocytes. Our work provides a platform to evaluate the biological activities of nuclei in extinct animal species.



Magnetotactic bacteria (MTB) play an important role in biogeochemical cycles of iron and remanent magnetization acquisition of sediments. It is generally considered that magnetite-producing MTB prefer chemical conditions in the oxic-anoxic transition zone (OATZ). We studied the distribution of fossil MTB magnetite (magnetofossils) and microbes phylogenetically related to MTB within deep-sea surface sediments across the OATZ. Transmission electron microscope (TEM) observations and rock-magnetic proxies show that magnetofossils commonly occur both within the OATZ and above it, even at the top of surface oxidized layers, and that the proportion of magnetofossils with a teardrop morphology increases within the OATZ. Consistent results were obtained from the pyrosequencing of 16S rRNA gene fragments. Operational taxonomic units (OTUs) related to Nitrospirae and OP3 MTB, which produce teardrop-shape magnetosomes, were detected only within the OATZ, whereas OTUs related to alphaproteobacterial MTB, which produce equant or elongated magnetite particles, were distributed above the OATZ. These results suggest that magnetofossil morphology can be used to detect past OATZs, and that some MTB lineages can occur ubiquitously in marine sediments rather than being limited within the OATZ. Our results imply that the timing of remanent magnetization acquisition may depend on the inhabiting MTB lineages.

Yan, H.-L., Li, Z.-K., Wang, Z.-C., Lei, Z.-P., Ren, S.-B., Pan, C.-X., Tian, Y.-J., Kang, S.-G., Yan, J.-C., Shui, H.-F., 2019. Characterization of soluble portions from cellulose, hemicellulose, and lignin methanolysis. Fuel 246, 394-401.


Methanolysis of the three biomass components was conducted to afford soluble portions (SPs) and residues. Cellulose has the highest SP yield, followed by hemicellulose and lignin. The relatively volatile or less polar species in the SPs were analyzed with a gas chromatograph/mass spectrometer (GC/MS) and the polar species were identified with a negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer (FTICRMS). According to analysis with GC/MS, sugars, esters, and phenols are the predominant compounds in cellulose- and hemicellulose-, and lignin-derived SPs, respectively. The analysis with FTICRMS shows that the molecular masses in the SPs range from 100 to 500 u and those in cellulose-/hemicellulose-derived SPs dominate from 250 to 300 u but in lignin-derived SP concentrates from 300 to 350 u. The identified compounds were assigned to On class species with double bond equivalent (DBE) values of 1–14 and carbon atom numbers of 5–35. The most abundant class species in cellulose-, hemicellulose-, and lignin-derived SPs are O5, O5, and O2, respectively. The van Krevelen diagrams of On class species suggest that primary species in lignin-derived SP are mainly located in a relatively narrow region with atomic ratio of O/C 0.0–0.3 and atomic ratio of H/C 1.0–1.3, while those in cellulose- and hemicellulose-derived SPs are principally located in a wider region with atomic ratio of O/C 0.2–0.8 and atomic ratio of H/C 0.8–1.5. The oxygen atom numbers of O4−O10 class species was negatively correlated with the average DBE value, which indicates a cyclic structure or double bond will be generated (opened or saturated) with the removal (addition) of oxygen atoms.

Yan, M., Bai, Y., Li, S.-G., Lin, H.-F., Yan, D.-J., Shu, C.-M., 2019. Factors influencing the gas adsorption thermodynamic characteristics of low-rank coal. Fuel 248, 117-126.


Low-temperature nitrogen and isothermal adsorption experiments were conducted on six typical low-rank coal samples from the Fukang mining area, Xinjiang, PR China. Using different temperatures, the effects of the coal’s pore structure on gas adsorption and other thermodynamic characteristics were analyzed. The Clausius–Clapeyron equation was used to calculate the isosteric heat of

adsorption, and the standard adsorption equilibrium constant was derived to calculate the adsorption free-energy and entropy. The relationships between pore structure characteristics and gas adsorption thermodynamic parameters were investigated. The results showed that the adsorption free-energy and enthalpy of the coal samples decreased with an increase in temperature. Adsorption heat and adsorption entropy were affected by an increase in pore volume and specific surface area. The specific surface area and transition pore volume exhibited quadratic relationships with the free-energy and total pore volume, whereas the mesopore volume exhibited a positive linear relationship with the adsorption free-energy. No prominent relationships among average pore diameter, adsorption heat, adsorption free-energy, and adsorption entropy were observed. No correlation was identified between micropore volume and adsorption free-energy. Fractal dimension was linearly and positively related to the adsorption heat and entropy but had no effect on the free-energy.

Yan, R., Kappler, A., Muehe, E.M., Knorr, K.-H., Horn, M.A., Poser, A., Lohmayer, R., Peiffer, S., 2019. Effect of reduced sulfur species on chemolithoautotrophic pyrite oxidation with nitrate. Geomicrobiology Journal 36, 19-29.

https://doi.org/10.1080/01490451.2018.1489915

We compared the response at neutral pH of some denitrifiers to different electron donors such as reduced sulfur (pyrite, S(0), and marcasite) and reduced Fe. Chemolithoautotrophic oxidation of pyrite with nitrate as electron acceptor was not possible when the pyrite was in a pure crystalline form, whereas oxidation of synthesized FeS2 of low crystallinity and of S(0) with nitrate as electron acceptor was possible. Neither nitrite nor sulfate was formed when Fe(II)-oxidizing strain Acidovorax sp. BoFeN1 was tested. Microbial reduction of nitrate appears to be induced via S oxidation but not via Fe oxidation.

Yang, H., Chen, Z.-Q., Kershaw, S., Liao, W., Lü, E., Huang, Y., 2019. Small microbialites from the basal Triassic mudstone (Tieshikou, Jiangxi, South China): Geobiologic features, biogenicity, and paleoenvironmental implications. Palaeogeography, Palaeoclimatology, Palaeoecology 519, 221-235.


We report small microbialites from the calcareous mudstone slightly above the Permian–Triassic boundary (PTB) in the Tieshikou section, southern Jiangxi Province, South China. The newly found microbialite is a bowl-like structure, which contrasts with the surrounding calcareous mudstone. The small microbialite is composed of columnar forms and fan-shaped structures. Mini-columnar structures resemble mini stromatolites. In plane view, most branches are patchy or strip-shaped, with clotted structures, resembling that of a thrombolite. Fan-shaped cement precipitates are comprised of multiple crystal fans that have a radiating texture and that show distinct growth laminae. The radiating fabrics are represented by rod-shaped filaments under SEM, which are interpreted as calcified trichomes/filaments. Prominent micropores occur within the rods, and they may be the plane views of multiple sheaths of the false branching zone of trichomes. Thus, both the columnar forms and radiating fans are probably microbial in origin. Moreover, three types of nano-sized structures: intraparticle micropores, fibrous biofilms, and filamentous sheaths are also pronounced in both the columnar structures and cement fans of the Tieshikou microbialite, all suggestive of biogenicity. These well-preserved fibrous biofilms probably represent calcified extracellular polymeric substances (EPS), and linear sheaths are interpreted as the traces of bacterial activities during the precipitation of dolomite crystals. The Tieshikou microbialite therefore shares similar biogenetic mechanisms with other PTB microbialites. The combination of the absence of pyrite framboids, slightly negative carbon isotope values, and an association with abundant ammonoids, bivalves, and gastropods

indicates oxic conditions during the growth of the Tieshikou microbialite. Moreover, the nodular preservational state resembles widely distributed nodular mudstones or muddy limestones of the Lower Triassic successions worldwide. This implies that nodular mudstone or argillaceous limestones may also have been deposited in microbe-rich environments, in which terrigenous supply was abundant.

Yang, M., Bell, T.G., Brown, I.J., Fishwick, J.R., Kitidis, V., Nightingale, P.D., Rees, A.P., Smyth, T.J., 2019. Insights from year-long measurements of air–water CH4 and CO2 exchange in a coastal environment. Biogeosciences 16, 961-978.


Air–water CH4 and CO2 fluxes were directly measured using the eddy covariance technique at the Penlee Point Atmospheric Observatory on the southwest coast of the United Kingdom from September 2015 to August 2016. The high-frequency, year-long measurements provide unprecedented detail on the variability of these greenhouse gas fluxes from seasonal to diurnal and to semi-diurnal (tidal) timescales. Depending on the wind sector, fluxes measured at this site are indicative of air–water exchange in coastal seas as well as in an outer estuary. For the open-water sector when winds were off the Atlantic Ocean, CH4 flux was almost always positive (annual mean of ∼0.05 mmol m−2 d−1) except in December and January, when CH4 flux was near zero. At times of high rainfall and river flow rate, CH4 emission from the estuarine-influenced Plymouth Sound sector was several times higher than emission from the open-water sector. The implied CH4 saturation (derived from the measured fluxes and a wind-speed-dependent gas transfer velocity parameterization) of over 1000 % in the Plymouth Sound is within range of in situ dissolved CH4 measurements near the mouth of the river Tamar. CO2 flux from the open-water sector was generally from sea to air in autumn and winter and from air to sea in late spring and summer, with an annual mean flux of near zero. A diurnal signal in CO2 flux and implied partial pressure of CO2 in water (pCO2) are clearly observed for the Plymouth Sound sector and also evident for the open-water sector during biologically productive periods. These observations suggest that coastal CO2 efflux may be underestimated if sampling strategies are limited to daytime only. Combining the flux data with seawater pCO2 measurements made in situ within the flux footprint allows us to estimate the CO2 transfer velocity. The gas transfer velocity and wind speed relationship at this coastal location agrees reasonably well with previous open-water parameterizations in the mean but demonstrates considerable variability. We discuss the influences of biological productivity, bottom-driven turbulence and rainfall on coastal air–water gas exchange.

Yang, Y., Zhang, D., Lan, B., Abdusalih, N., Feng, Z., 2019. Peat δ13Ccelluose-signified moisture variations over the past ∼2200 years in the southern Altai Mountains, northwestern China. Journal of Asian Earth Sciences 174, 59-67.


A ∼2200-year moisture history of the southern Altai Mountains (i.e., Chinese Altai) was established based on peat δ13Ccelluose data obtained at Yushenkule (YSKL) Peat. Generally speaking, the moisture record from YSKL Peat exhibits a “cool-wet” DACP (Dark Age Cold Period from ∼500 to ∼800 CE), a “warm-dry” MWP (Medieval Warm Period from ∼800 to ∼1200 CE), a “cool-wet” LIA (Little Ice Age from ∼1200 to ∼1900 CE), and a “warm-dry” CWP (Current Warm Period since ∼1900 CE). But, RWP (Roman Warm Period from prior to ∼100 CE to ∼500 CE) is an exception (i.e., “warm-wet”). If the heat-water combinations within those major temperature-change events are further examined, the “warm-dry/cool-wet” generalization collapses. The comparisons between the

variations in the peat δ13Ccelluose-based moisture obtained from YSKL Peat and the variations of reconstructed climatic variables in the referenced sequences suggest that the moisture variations in the Altai Mountains have been basically controlled by the precipitation that was primarily modulated by the NAO variations.


https://doi.org/10.1080/10916466.2018.1558240

We report detailed microscopic studies of asphaltenes aggregation onset during waterflooding of petroleum reservoirs. To achieve this objective, a series of simulations are performed on asphaltenic-oil miscibilized with water at high pressure and temperature through molecular dynamics. Results of this simulation onset are applicable to asphaltenes behavior in real crude oils. Our simulation results illustrate that the aggregation onset in waterflooding generally follows three sequential steps: (i) Asphaltene-water interaction; (ii) Water bridging; (iii) Face-to-face stacking. Then, asphaltene-water and water-water hydrogen-bonding network surround every aggregate boosting the intensity of aggregation onset. We intend to utilize such understanding of these details in our predictive and preventive measures of arterial blockage in oil reservoirs during waterflooding.



Gas hydrates and deep-sea cold seeps are of interest to industry and academia for several reasons, including their implications for offshore geohazards and unconventional resources, and for global climate change and carbon cycling. Guangzhou Marine Geological Survey (GMGS) implemented its fifth gas hydrate drilling expedition in the QiongDongNan Sea Area (QDN-SA) of the northern South China Sea (SCS) from June to September 2018. Multidisciplinary investigations, including Logging While Drilling (LWD), pressure and non-pressure coring, gas composition analyses, in situ temperature and permeability measurements, pore water geochemical analyses, and a regional seismic survey, reveal a complex distribution of gas hydrate within a vertical chimney structure. LWD profiles record high resistivity anomalies and high P-wave velocity variations at 9–174 mbsf, suggesting the coexistence of free gas and gas hydrate in the sediment column throughout the investigated gas chimney. Hydrate-bound and void gas is an admixture of methane (70.1%–98.3%) and heavier hydrocarbons (C2H6: 0.16%–17.59%, C3H8: 0.05%–9.88%, i-C4H10: <0.001%–2.06%, n-C4H10: <0.001%–0.85%, i-C5H12: <0.001%–0.12%, n-C5H12: <0.001%–0.02%), indicating a thermogenic origin for the gas. Based on the high content of C2+ hydrocarbons in the gas composition, it is suggested that sII/sH gas hydrate exists in the study area. The gas chimney is interpreted to provide efficient pathways for fluid migration from an intermediate gas reservoir below the BSR to the gas hydrate stability zone (GHSZ). Gas hydrate crystallization decreases the permeability of the sediment, impeding fluid flowing into the upper sediment layers. Bivalve fragments embedded within carbonate rocks were recovered at the seafloor and multiple levels at two main sediment levels of 3mbsf and ∼54mbsf, indicating recurrent seepage activity.

Yekeen, N., Padmanabhan, E., Idris, A.K., Chauhan, P.S., 2019. Nanoparticles applications for hydraulic fracturing of unconventional reservoirs: A comprehensive review of recent advances and prospects. Journal of Petroleum Science and Engineering 178, 41-73.


The application of horizontal drilling and hydraulic fracturing stimulations for improving hydrocarbon productivity from low-permeable reservoirs is a well-established practice. However, the development of fracturing fluids that can maintain excellent rheological properties at reservoir conditions, as well as, minimize damage to the formation is still very challenging. There has been increasing interest in recent years in the improvement of the hydraulic fracturing stimulation through the application of nanotechnology. We review the current status of nanoparticles applications for hydraulic fracturing treatments of the unconventional reservoirs, highlighting the mechanisms and applications, the findings, the technical challenges and directions for future studies. The review literature demonstrated the promising applications of nanomaterials for improving the rheology of viscoelastic surfactant fluid, foam-based fluid and polymer-based fracturing fluid using nano-crosslinker and bio-polymer nano-composite. Results of previous studies showed that the unique properties of nano-materials, such as their smaller sizes, high specific surface area, magnetic properties, superior strength and stability could be exploited in the development of downhole nano-sensors, nano-proppants, gel breakers and fluid loss control agents. More work will be required to understand the cross-linking mechanisms of nano-crosslinkers and the mechanisms governing the enhancement in fracturing fluid viscosity in presence of nanoparticles at reservoir conditions. The potential applications of generally used nanoparticles such as, aluminum oxide (Al2O3), Copper oxide (CuO), carbon nanotubes and low cost nanoparticles such as calcium carbonate (CaCO3), silicon dioxide (SiO2) and fly-ash nanoparticles in unconventional reservoirs need to be further researched. Moreover, more emphasize should be place on nanoparticles performance at reservoir conditions, influence of nanoparticles agglomeration, economic feasibility, as well as environmental and health hazards of nanoparticles applications. The improved hydrocarbon recovery from the unconventional reservoirs through wettability alterations and interfacial tension reduction by nanofluids, and the use of nanoparticles-enhanced combined fracturing fluid systems present exciting future opportunities.



Current evidence suggests domestications of the dog were incipient developments in many areas of the world. In southwest Asia this process took place in the Late Epipalaeolithic Natufian (∼14,500–11,600 cal BP) with the earliest evidence originating from the Mediterranean zone of the southern Levant. This paper presents new data for the importance of early domestic dogs to human groups in the region beyond this ‘core’ area where the Late Pleistocene and Early Holocene environment is usually thought of as less favourable for human occupation. By the Pre-Pottery Neolithic A it is demonstrated that dogs were living alongside humans in significant numbers. Most discussions of early domestic dogs assume that these animals would have facilitated the hunting of larger prey following the innate behavioural traits of their wolf ancestors. This paper suggests that the benefits of hunting with dogs could also extend to the capture of smaller prey. An increase in the hunting of such animals, as part of the broad-spectrum revolution, was not necessarily a response limited to resource reduction in the Late Pleistocene and factors such as new hunting methods need consideration.

Yi, H., Xia, G., Li, G., Yi, F., Zhang, S., Cai, Z., Jiao, H., Wu, C., 2019. The carbon isotope fluctuations across the Lower–Middle Jurassic boundary and the paleoclimate changes. Acta Geologica Sinica - English Edition 93, 244-245.

https://doi.org/10.1111/1755-6724.13789

No abstract

Yi, J., Bao, H., Zheng, A., Zhang, B., Shu, Z., Li, J., Wang, C., 2019. Main factors controlling marine shale gas enrichment and high-yield wells in South China: A case study of the Fuling shale gas field. Marine and Petroleum Geology 103, 114-125.


The marine shale in South China is characterized by multiple layers, a wide distribution, and a large amount of resources. However, the characterization of the enrichment degree of marine shale gas and the main factors affecting the enrichment and high-yield wells are still unclear, which seriously affects the process of shale gas exploration and development in South China. We integrated a large amount of drilling data, core analysis data, seismic data as well as gas testing results from Fuling shale gas field to study the shale gas-bearing properties. The results suggest that any single parameter is insufficient to accurately characterize the gas-bearing properties. Consequently, we propose to integrate multiple parameters, including total hydrocarbon values, gas content, gas saturation, porosity/pore diameters, formation pressure coefficient and resistivity, to comprehensively evaluate shale gas content and determine the origins of shale gas enrichment for the lower section of Wufeng-Longmaxi Formation in the Fuling shale gas field. We infer that the depositional environment and shale reservoir characteristic are the major factors affecting the stratigraphic variation of shale gas enrichment. The differences of structural deformation and uplift and erosion in the later period are the main factors leading to differential enrichment in the lateral direction. In factors affecting high-yield well, the completion parameters such as the lateral placement and lateral length of horizontal wells are the major factors affecting the test production.

Yin, Y., Wang, J., 2019. Enhanced biohydrogen production from macroalgae by zero-valent iron nanoparticles: Insights into microbial and metabolites distribution. Bioresource Technology 282, 110-117.


In this work, effect of Fe0 nanoparticles (Fe0 NPs) on macroalgae fermentation was explored. Hydrogen production was significantly enhanced by 6.5 times comparing with control test, achieving 20.25 mL H2/g VSadded with addition of 200 mg/L Fe0 NPs. In-depth analysis of substrate conversion showed that both hydrogen generation and acids accumulation were promoted with Fe0 NPs supplementation. Microbial analysis demonstrated that both hydrogen-producing strains belonging to genus Clostridium and Terrisporobacter sp. favorable for acids formation were enriched with Fe0 NPs supplementation, while species Acinetobacter lwoffii beneficial to organics mineralization was eliminated. Complex substrate compositions resulted in more prevalent cooperative relationships among species in the system. This study suggested that Fe0 NPs plays a crucial role in macroalgae fermentation by affecting the microbial distribution, subsequently influencing the products distribution and energy conversion.

You, Y., Wang, X., Han, X., Jiang, X., 2019. Kerogen pyrolysis model based on its chemical structure for predicting product evolution. Fuel 246, 149-159.


A kerogen pyrolysis model based on chemical structure using modified chemical percolation devolatilization (CPD) is proposed and aims to predict product distribution of kerogen and oil shale pyrolysis. Five representative structural units including aliphatic bridge, aromatic cluster, aromatic ether, alkyl and oxygen-containing bridge are selected to build kerogen network model according to its structural characteristics. Kerogen pyrolysis involves in four processes including initial cracking, aliphatic chain reaction, aromatization and condensation expressed by eight chain reactions. Specific volatile products are attributed to various fragments from kerogen network and classified into seven types on the basis of structural features, which allows model to provide product composition. Oil shale is simplified as a linear combination of kerogen and minerals. Model predictions for kerogen and oil shale are compared with experiment data in fixed bed and thermogravimetry analysis. In conclusion, model reflects kerogen pyrolysis based on its structural characteristics and provides reasonable prediction on product distribution.

Young, S.A., Kleinberg, A., Owens, J.D., 2019. Geochemical evidence for expansion of marine euxinia during an early Silurian (Llandovery–Wenlock boundary) mass extinction. Earth and Planetary Science Letters 513, 187-196.


Repeated biotic crises have become the hallmark for the Silurian with the three most significant marine turnover events being related to dramatic global environmental perturbations. Causal mechanisms linking these marine extinction events with positive carbon isotope (δ13C) excursions, paleoceanographic change, and climate remain poorly constrained. Here, we examine the positive δ13C excursion across the Llandovery/Wenlock boundary, and the associated Ireviken extinction event. This positive δ13C excursion has been interpreted to reflect a major change in global oceanographic-climate state and enhanced organic carbon burial. New geochemical data from two paleocean basins have been analyzed to determine local and global redox conditions using carbon- and sulfur-isotopes (δ34S), and iodine (I/Ca+Mg) proxies. The high-resolution δ13C and δ34S data from both sections show positive excursions indicative of global perturbations to each of these elemental cycles, with minimal temporal offsets between the two systems. Numerical box modeling of δ13C and δ34S data indicates that these isotopic shifts can be generated by significant increases in the burial of organic carbon and pyrite, which are most likely due to enhanced burial under euxinic (anoxic and sulfidic) conditions. Independently, I/(Ca+Mg) values point to locally anoxic bottom waters in the distal and deeper basinal setting in Nevada before, during, and after the Ireviken positive δ13C excursion. I/(Ca+Mg) values in the proximal shelf setting in Tennessee show relatively oxic waters during the onset of peak δ13C values, after which bottom-water oxygen concentrations dropped throughout the remainder of the excursion. This multiproxy paleoredox dataset provides the first direct evidence for local and global expansion of reducing marine conditions coincident with the Silurian biotic event and positive δ13C excursion. Integration of these geochemical data for local- and global-scale changes in marine redox conditions with the paleontological data and evidence for eustatic sea-level rise points toward a shoaling of anoxic and/or euxinic waters onto the shelf as a driver for the Ireviken extinction event.

Yu, Q., Chen, J., Qin, W., Cheng, S., Zhang, Y., Ahmad, M., Ouyang, W., 2019. Characteristics and secondary formation of water-soluble organic acids in PM1, PM2.5 and PM10 in Beijing during haze episodes. Science of The Total Environment 669, 175-184.


Water-soluble organic acids are widely involved in various atmospheric physicochemical processes and appear as an important fraction of atmospheric aerosols. Nineteen water-soluble organic acids in 12-h PM1, PM2.5 and PM10 samples collected in urban Beijing during haze episodes in winter and spring of 2017 were identified to investigate their characteristics and secondary formation mechanism. The molecular distributions of water-soluble organic acids as well as the high ratio of phthalic acid (Ph)/azelaic acid (C9) indicated severe aromatic secondary organic aerosol pollution during the haze episodes, especially in winter. The diurnal patterns, size distributions, and concentration ratios of specific organic acids were investigated to reveal the pollution characteristics and possible sources of major organic acids in particulate matter in Beijing during haze events. Multiple linear regression was used to tentatively quantify the relative contributions of photochemical oxidation and aqueous-phase oxidation to the formation of total water-soluble organic acids in PM1, PM2.5 and PM10 during haze episodes. The formation mechanism of sulfate and nitrate was also investigated for comparison. Different from the secondary formation of sulfate, the secondary formation of water-soluble organic acids showed enhanced contribution of gas-phase photochemical oxidation though the aqueous-phase oxidation was the dominant process. Capsule Molecular analyses of organic acids in PM1, PM2.5 and PM10 in Beijing during haze periods revealed their pollution characteristics, possible sources and formation mechanism.


https://doi.org/10.1080/10916466.2018.1547752

This research uses Illumina high-throughput sequencing method showing that dominant phylum of dried oily wastewater reservoirs (DOWRs) in oilfield were Proteobacteria, Actinobacteria, Bacteroidetes, and Carbohydrate Metabolism presented a major proportion of metabolic activity. Core microorganism analysis showed that Mycobacterium, Altererythrobacter, Dietzia, Pseudoxanthomonas, Melioribacter were the key genus, which were important in maintaining the microbial construction and function, and which can be treated as the key bio-stimulation community.

Yu, X., Chen, K., Li, S., Wang, Y., Shen, Q., 2019. Lipidomics differentiation of soft-shelled turtle strains using hydrophilic interaction liquid chromatography and mass spectrometry. Journal of Chromatography B 1112, 11-15.


Hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC-MS) was used as an accurate and sensitivity technique to separate and characterize the phospholipids in three strains of soft-shelled turtles. Under the optimized experimental parameters, the lipidomic profiles were successfully acquired, and a total of 55 phospholipid molecular species were identified. The principal component analysis (PCA) was applied to normalize the relative amounts of the phospholipid molecular species and revealed the differences among three strains of soft-shelled turtle, including Qingxi Huabie (QXH, GS-01-003-2008), Zhexin Wubie (ZXW, GS-02-005-2015), and Zhewu Erhao (ZWE, unregistered). Comparing with other methods, HILIC-MS is rapid, efficient and suitable in determining and visualizing phospholipids. This method also can be used for authenticating different strains of soft-shelled turtles.

Yu, Y., Katsoyiannis, A., Bohlin-Nizzetto, P., Brorström-Lundén, E., Ma, J., Zhao, Y., Wu, Z., Tych, W., Mindham, D., Sverko, E., Barresi, E., Dryfhout-Clark, H., Fellin, P., Hung, H., 2019. Polycyclic aromatic hydrocarbons not declining in Arctic air despite global emission reduction. Environmental Science & Technology 53, 2375-2382.


Two decades of atmospheric measurements of polycyclic aromatic hydrocarbons (PAHs) were conducted at three Arctic sites, i.e., Alert, Canada; Zeppelin, Svalbard; and Pallas, Finland. PAH concentrations decrease with increasing latitude in the order of Pallas > Zeppelin > Alert. Forest fire was identified as an important contributing source. Three representative PAHs, phenanthrene (PHE), pyrene (PYR), and benzo[a]pyrene (BaP) were selected for the assessment of their long-term trends. Significant decline of these PAHs was not observed contradicting the expected decline due to PAH emission reductions. A global 3-D transport model was employed to simulate the concentrations of these three PAHs at the three sites. The model predicted that warming in the Arctic would cause the air concentrations of PHE and PYR to increase in the Arctic atmosphere, while that of BaP, which tends to be particle-bound, is less affected by temperature. The expected decline due to the reduction of global PAH emissions is offset by the increment of volatilization caused by warming. This work shows that this phenomenon may affect the environmental occurrence of other anthropogenic substances, such as more volatile flame retardants and pesticides.

Yuan, Y., Rezaee, R., 2019. Fractal analysis of the pore structure for clay bound water and potential gas storage in shales based on NMR and N2 gas adsorption. Journal of Petroleum Science and Engineering 177, 756-765.


Fractal dimension (D) is a critical parameter to estimate the heterogeneity of complex pore structure in shale gas reservoirs. To quantify the fractal dimension of various pore types and evaluate their implications on shale effective porosity and gas storage capacity in potential, we performed fractal analysis based on experimental results of low-field nuclear magnetic resonance (LF-NMR) and low-pressure N2 gas adsorption (LP-N2-GA) in Permian Carynginia shales. By comparing the calculated fractal dimensions based on the two approaches, we analyzed the 'surface fractal dimension' for ineffective pores occupied by clay bound water (CBW) and the 'volume fractal dimension' for effective pores (Deff) holding removable fluids for the first time in shales. The NMR-based CBW pore fractal dimension (Dcbw) is linear positively correlated with the fractal dimension of micropore surface (D1) (R2 = 0.91) and the volume of CBW (R2 = 0.58), while negatively correlated with effective porosity (R2 = 0.58). The NMR-based effective pore fractal dimension (Deff) is linear positively correlated with the fractal dimension of meso/macropore volume (D2) (R2 = 0.82) and presents a good positive correlation with gas storage capacity (R2 = 0.80). The results indicate that CBW largely complicates the fractal geometry of nanoscaled pore network and potentially resist effective fluid flows in shales. The pore surface of higher heterogeneity (higher D1) associates with larger surficial CBW retention and would further block the effective pore space for fluid transport. The meso/macropore volumes of higher complexity (higher D2) is intimate with the larger heterogeneity in effective pores for the higher potential of hydrocarbon storage capacity in gas shales.

Zacs, D., Perkons, I., Bartkevics, V., 2019. Evaluation of analytical performance of gas chromatography coupled with atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry (GC-APCI-FT-ICR-MS) in the target and non-targeted analysis of brominated and chlorinated flame retardants in food. Chemosphere 225, 368-377.


A new analytical method was established and validated for the analysis of eighteen halogenated flame retardants (HFRs)in food products. Gas chromatography (GC) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) employing atmospheric pressure chemical ionization (APCI) was used for the identification and quantitation of contaminants. Intra-laboratory validation of the method was performed with respect to recovery, repeatability, linear calibration ranges, instrumental and method limits of quantitation (i-LOQ and m-LOQ), and trueness was verified where possible by analysis of reference materials (RMs). The validation results indicated recoveries of analytes between 59 and 115%, the repeatability in terms of relative standard deviations (RSDs) in the range of 5–15% and linearity with correlation coefficients of ≥0.99 between the i-LOQ and 250 pg injected on-column. The method i-LOQs ranged from ∼1 pg to ∼5 pg injected on-column, while m-LOQs were in the range of 0.002–0.04 ng g−1 sample. The measured values for RMs agreed with the provided values, giving the accuracy of obtained concentrations in the range of 92–133% with RSD range of 2–15% and were in agreement with the results obtained with the reference method based on magnetic sector GC-HRMS. For the majority of the compounds, the method met a limit of quantification criterion stated in the Commission Recommendation, 2014/118/EU on monitoring BFRs in food. The developed method was demonstrated to be suitable for qualitative screening of suspect target contaminants presented in the samples by the post-run treatment of raw data and confirmation by isotope cluster analysis.


https://doi.org/10.1002/jssc.201801071

Abstract Porous monoliths are well-known stationary phases in high-performance liquid chromatography and capillary electrochromatography. Contrastingly, their use in other types of separation methods such as gas or supercritical fluid chromatography is limited and scarce. In particular, very few studies address the use of monolithic columns in supercritical fluid chromatography. These are limited to silica-based monoliths and will be covered in this review together with an underlying reason for this trend. The application of monoliths in gas chromatography has received much more attention and is well documented in two reviews by Svec and Kurganov published in 2008 and 2013, respectively. The most recent studies, covered in this review, build on the previous findings and on further understanding of the influence of preparation conditions on porous properties and chromatographic performance of poly(styrene-co-divinylbenzene), polymethacrylate, and silica-based monolithic columns while expanding to polymer-based monoliths with incorporated metal organic frameworks and to vinylized hybrid silica monoliths. In addition, the potential application of porous layer open tubular monolithic columns in low-pressure gas chromatography will be addressed.

Zavodny, E., McClure, S.B., Welker, M.H., Culleton, B.J., Balen, J., Kennett, D.J., 2019. Scaling up: Stable isotope evidence for the intensification of animal husbandry in Bronze-Iron Age Lika, Croatia. Journal of Archaeological Science: Reports 23, 1055-1065.


The Bronze-Iron Age transition in Lika, Croatia is characterized by a seemingly rapid and significant transformation in sociopolitical organization. New hillfort centers were presumably supported by the intensification and specialization of economic activities to a larger degree than in previous periods,

though Lika's challenging environment and topography likely made large-scale agriculture and livestock keeping difficult. We present new stable carbon and nitrogen isotope values for domesticated and wild fauna from hillforts and caves dating from the Middle Bronze to Early Iron Ages to examine changing sociopolitical and economic organization during this time. Our results suggest animal husbandry was carried out across multiple spatial and organizational scales to take advantage of finite resources, from the centralized movement of cattle and ovicaprid herds across greater swaths of the landscape to the continued management of pigs by individual households.

Zeng, F., Yang, H., 2019. Temperature changes reconstructed from branched GDGTs on the central Loess Plateau during the past 130–5 ka. Quaternary International 503, 3-9.


This study investigated the glycerol dialkyl glycerol tetraethers (GDGTs) in a loess-paleosol sequence (LPS) to quantitatively reconstruct the mean annual air temperature (MAT) on the central Chinese Loess Plateau (CLP) during the past 130–5 ka. The results show that: (1) MAT variations reconstructed by global MBT (methylation index of branched tetraethers) and CBT (cyclisation ratio of branched tetraethers) transfer functions at Xifeng range from 7.3 °C to 28.4 °C. The MAT variation on the central CLP (Xifeng site) is between the previously reported MAT variations on the western (Yuanbao site) and eastern CLP (Mangshan site), in agreement with the pattern that temperature increases from the northwestern CLP to the southeastern CLP. (2) MAT variations estimated by transfer functions of global MBT-CBT, global MBT′-CBT and Chinese MBT-CBT for LPS are nearly all higher than the modern MAT at Xifeng, indicating that the reconstructed MAT values are probably overestimated. (3) The maximum value of magnetic susceptibility at Xifeng lagged that of the MAT derived by MBT-CBT proxy during the last interglacial (∼9 ka lag) and since the last deglacial (∼6 ka lag).

Zeng, K., Jiang, P., Lun, Z., Xu, R., 2019. Molecular simulation of carbon dioxide and methane adsorption in shale organic nanopores. Energy & Fuels 33, 1785-1796.


Using carbon dioxide as a displacing fluid to enhance shale gas recovery is a promising technique given its potential for significant contributions to both unconventional resource development and CO2

geological sequestration. The adsorption capacity of CO2 in nanoscale shale organic pores is the key issue to evaluate the feasibility of CO2-enhanced shale gas recovery technology. However, as a result of the complex organic component of the solid surface, the fluid–solid interaction between the confined fluid and the solid surface, and the intermolecular interaction between the confined fluids, the adsorption behavior of CO2 in the shale is not clear. In this work, shale organic nanopores with different geometries (slit pore and cylindrical pore) and different sizes (1, 2, and 4 nm) are constructed using molecular dynamics and Monte Carlo methods. Isothermal adsorption of CO2 and methane as single components and competitive adsorption of a CO2–methane binary mixture are simulated in a nanoscale methane/CO2/organic matter system. The density profile and distribution contour indicate that CO2 adsorption in shale organic mesopores does not occur via monolayer adsorption. Considering the inadaptability of the Langmuir model to analyze the CO2 adsorption curve, a modified Brunauer–Emmett–Teller (BET) model is applied to describe and fit the data for the CO2 and methane adsorption amount, with the parameters in the modified BET model used to characterize the adsorption capacity and affinity of the fluid. The maximum adsorption amount, characteristic pressure, and selectivity parameter of CO2, methane, and a binary mixture indicate that

the adsorption capacity and affinity of CO2 are stronger than those of methane under reservoir pressure, which provides useful support for enhancing shale gas recovery by injecting CO2.

Zhai, X., Li, J.-L., Zhang, H.-H., Tan, D.-D., Yang, G.-P., 2019. Spatial distribution and biogeochemical cycling of dimethylated sulfur compounds and methane in the East China Sea during spring. Journal of Geophysical Research: Oceans 124, 1074-1090.

https://doi.org/10.1029/2018JC014488

Abstract: The spatial distributions of dimethylsulfide (DMS), dimethylsulfoniopropionate (DMSP), dimethylsulfoxide (DMSO), and methane (CH4) were studied in the East China Sea during May 2017, and the possible controlling factors and biogeochemical cycling processes are discussed. The mean surface concentrations of DMS and CH4 were 10.66 and 9.93 nmol/L in the coastal area and 7.60 and 6.88 nmol/L in the open ocean, respectively. Horizontal and vertical profiles of the dimethylated sulfur compounds and CH4 were largely affected by different water masses, with enhancement observed in the coastal area. Significant correlations were found between CH4 and particulate DMSP (r = 0.609, p < 0.01, n = 42), and between CH4 and dissolved DMSO (r = 0.654, p < 0.01, n = 42). A dissolved DMSP (DMSPd) spike experiment revealed that the bacterial communities had potential to utilize DMSPd, meanwhile producing CH4 under oligotrophic conditions. The average mixing ratio of atmospheric DMS was 109 ± 49 pptv. Variations of marine DMS and wind speed explained 23 and 40% of the variation in the mixing ratios of atmospheric DMS, respectively. The sea‐to‐air fluxes of DMS and CH4 were estimated to be 18.64 ± 14.92 and 13.85 ± 15.03 μmol m−2 d−1, respectively.

Plain Language Summary: Some gases in the atmosphere can alter the environment and climate, such as dimethylsulfide (DMS) and methane (CH4). The oceans are an important source of DMS, and a nonnegligible source of CH4, especially the coastal and estuarine areas. DMS and CH4 emissions from the ocean to the atmosphere depend directly on their concentrations in the surface water. To know what factors control DMS and CH4 concentrations is therefore of great importance. In our study, the horizontal and vertical distributions of DMS, CH4, and related compounds were determined, and deck incubation experiments were carried out to assess the effects of biological activities on their cyclings. We also present the first analysis of the atmospheric DMS concentrations in the marine boundary layer above the East China Sea. We find that the DMS and CH4 concentrations were mainly influenced by the complex water masses, especially the freshwater input, and biological processes. Under some circumstances, dimethylsulfoniopropionate (DMSP), a ubiquitous compound in the seawater, is a precursor of both DMS and CH4.

Zhang, C., Cheng, S., Li, Y., Zhang, W., Xiao, S., 2019. Diel methane flux from a subtropical eutrophic pond in November based on continuous monitoring. Acta Geochimica 38, 232-240.

https://doi.org/10.1007/s11631-019-00317-1

A field campaign was carried out to investigate continuous diel methane (CH4) flux from a subtropical eutrophic pond in November 2016. The diffusive methane flux of a single measurement had a range from 2.68 × 10−5 to 0.028 mmol·m−2·h−1 with an average of 0.011 ± 0.005 mmol·m−2·h−1. The diffusive methane flux of measurements from 9:00 to 10:30 and from 21:00 to 22:30 were very close to the average diffusive flux of all measurements. The bubble methane flux at different time measurements had much more variability than the diffusive methane flux. The bubble methane flux of a single measurement had a range from 0 to 0.312 mmol·m−2·h−1 with an average of 0.024 ± 0.054 mmol·m−2·h−1. For the eutrophic pond, the average bubble and diffusive CH4 flux were 0.56 ± 0.18 and 0.26 ± 0.04 mmol·m−2·day−1, respectively, and the CH4 ebullition flux accounted for 68.23%

of the total flux. The maximum of the bubble CH4 flux was about 4.6 times of the minimum CH4 ebullition. The maximum of diffusive CH4 flux was ~ 1.7 times of the corresponding minimum. The diffusive methane fluxes in daytime and nighttime were almost equal. However, the bubble methane flux in daytime was 0.029 mmol·m−2·h−1, which was 1.6 times of that at night. Wind speed, the surface water temperature, and DO dominate methane effluxes from the pond, and the latter is in nature subjected to the metabolism of algae in the pond. However, key environmental factors which dominate gas flux processes vary with different weather conditions. Wind speed is unimportant when it is extremely low.

Zhang, C., Zhao, L., Yu, D., Liu, G., Pei, Y., Huang, F., Liu, B., 2019. The evaluation on physical property and fracture conductivity of a new self-generating solid proppant. Journal of Petroleum Science and Engineering 177, 841-848.


Most fracturing treatments today require injecting solid proppants to keep hydraulic fractures open. However, traditional proppants have disadvantages such as causing the reduced propped-fracture volume and abrasion to the pumping equipments and tubulars. To solve these problems, a new self-generating solid proppant has been developed through liquid-solid transition of self-propping fracturing fluid under reservoir conditions. To select the best self-generating solid proppant and compare it with conventional ones, physical property and fracture conductivity tests were done. Experimental results show that two self-generating solid proppants, including S101 and S505, are firstly selected because of their low density, high strength and excellent fracture conductivity. The apparent density is 1.09 g/cm3 for S101 and 1.10 g/cm3 for S505. The crushing rate of S101 is 1.47% while that of S505 is 1.29%. These data illustrate physical properties of self-generating solid proppant are obviously better than those of conventional proppants. Under the same conditions, the larger the spherical particle size of S101 and S505, the higher the fracture conductivity. Non-uniform distribution of proppant pack can increase fracture conductivity. Fracture conductivities of S101 and S505 are higher than that of quartz sand, and even higher than that of ceramsite at low closure stresses. Based on the experimental results, the pumping rate and injecting proportion of self-propping fracturing fluid can be optimized during the fracturing process.


https://doi.org/10.1080/01490451.2018.1512688

The impact of indigenous microorganisms on the mineral corrosion and mineral trapping in the SO2 co-injected CO2-saline-sandstone interaction was investigated in this study by lab experiments under 55 °C, 15 M pa. The results verified that co-injection of SO2 resulted in a decrease in biomass and shifts in microbial communities within 90 days, but some microorganisms still could adapt to acidic, high-temperature, high-pressure, and high-salinity environments. Firmicutes and Proteobacteria remained dominant phylum, but phylum Proteobacteria showed better tolerance to the co-injection of SO2 in the initial period. In the SO2 co-injected CO2-saline-sandstone interaction under microbial mediation, acid-producing bacteria further promoted the corrosion of K-feldspar, albite, and clay minerals, meanwhile mobilizing more K+, Na+, Ca2+, Mg2+ into solution. The acidogenic effect may be linked to the dominant genus of Bacillus, Paenibacillus, Acinetobacter, Pseudomonas and Exiguobacterium. Co-injection of SO2 inhibited the carbonates capture, while microbial acid production further reduced the pH, further inhibiting carbonates capture. As a result, no secondary

carbonate (e.g., calcite) was observed on a short time scale within 90 days. So, microbial acidogenic effect was not conducive to carbonates capture in short term.



The characterization of the pore structure and shale gas content provides useful information for shale gas reservoir assessment and evaluation and guides the exploration and development of shale gas. Fresh core samples obtained from three different basin formations in China were analyzed by field-emission scanning electron microscopy, low-pressure CO2 and N2 gas adsorption–desorption, high-pressure mercury intrusion, and methane adsorption experiments to clarify the pore structure characteristics of coal-bearing shales and their effects on shale gas content. The inter- and intraparticle pores, organic matter pores, and microfractures were well developed in coal-bearing shales. These pores had different geneses, morphologies, and sizes with main diameters of <6.5 and 80–200 nm and the main shape of slit, taper, and ink bottle. Pores with diameters <10 nm dominated the shale pore networks. Shale gas content was directly influenced by shale pores, and small pores had a large surface area, which resulted in the high adsorption capacity of shale gas. Clay mineral and total organic carbon contents positively controlled the pore structures and shale gas adsorption, whereas brittle minerals were counterproductive. Coal-bearing shale gas content was lower than marine shale gas content, with an adsorption gas content percentage of 50–85%. The proportion of adsorbed gas decreased with the increase of pore size diameters, whereas the proportion of free gas increased. When the pore size diameter reached approximately 3.5 nm, the free and adsorption gases reached dynamic balance. The adsorption gas content would be slightly low with pore size ranges of >6.5 nm, whereas the free gas content would be stable and merely increase in the range of 100–300 nm.



It is well known that CO2 is one of the most effective enhanced hydrocarbon recovery agents due to its thermodynamic characteristics, and extensive research and pilot studies have been conducted in recent years on how to utilize CO2 for enhanced gas recovery in shales. The common delivery method involves injecting CO2 in its liquid or supercritial form into a shale formation. In this paper, we propose a novel approach to shale gas recovery that uses zeolite as a multi-functional proppant and carrier of adsorbed CO2 to enhance shale gas recovery as well as CO2 sequestration and storage. This process involves complex thermodynamic and transport processes, among which the competitive adsorption behaviors of CO2 and CH4 into organic matter and zeolite is the most critical to the success of the proposed approach. In this paper, we carry out a systematic molecular simulation study to investigate the adsorption behaviors of methane and CO2 into organic matter (kerogen) and silica zeolite (silicalite-1). We use grand canonical Monte Carlo simulations to measure single-component adsorption isotherms and calculate the isosteric heat of adsorption at surface temperature and at elevated temperatures of up to 425 K. Moreover, we simulate the competitive adsorption of binary mixtures of CH4 and CO2 with various compositions and investigate the competition between the two gas components in kerogen and silicalite-1. Both silicalite and kerogen show a stronger affinity for

CO2 than for CH4. While the adsorption capacity of kerogen is about two times that of silicalite, the isosteric heat of adsorption demonstrates that the kerogen/CO2 interaction is the strongest among all four single-component adsorption systems. These findings demonstrate the great potential of using zeolite as a proppant and CO2 carrier to displace CH4 in shale organic matter under subsurface conditions. This observation is also validated via a competitive adsorption study, in which kerogen preferentially adsorbs CO2 over CH4 under all conditions and silicalite exhibits weaker CO2/CH4 selectivity, especially when the CO2 fraction is very low in the bulk phase. These results suggest the potential applicability of using zeolite as a proppant and CO2 carrier to enhance shale gas recovery. In reservoir conditions, the CO2 desorbed from zeolite can be favorably adsorbed by kerogen due to the increase in temperature and decrease in pressure; in the meantime, it can displace the adsorbed CH4 to enhance gas production.


http://msystems.asm.org/content/4/1/e00225-18.abstract

Abstract: Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem.

Importance: Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.

Zhang, K., Song, Y., Jiang, S., Jiang, Z., Jia, C., Huang, Y., Wen, M., Liu, W., Wang, P., Li, X., Liu, T., Xie, X., Shan, C., #x, an, Liu, X., Wang, X., 2019. Accumulation mechanism of marine shale gas

reservoir in anticlines: A case study of the southern Sichuan Basin and Xiuwu Basin in the Yangtze region. Geofluids 2019, Article 5142712.

https://doi.org/10.1155/2019/5274327

The study of tectonics is one of the important aspects of shale gas preservation. It is vital for understanding how to determine the enrichment regularity of marine shale gas in anticlines. This paper focuses on typical shale blocks in the southern Sichuan Basin and shale in the Upper Ordovician and the Lower Silurian. In this study, triaxial unloading tests, permeability tests perpendicular and parallel to the stratification plane, FIB-HIM tests, and inclusion analyses are carried out with real drilling data. The enrichment regularity of marine shale gas in anticlines is studied by considering 2 aspects: the angle of the limbs and the burial depth. For anticlines with adjacent synclines, the migration regularity of shale gas is considered by 3 aspects: the dynamics, channels, and processes of migration. This study reveals that a limb angle greater than 120° reflects relatively good conditions for shale gas preservation, while limb angles lesser than 70° indicate relatively poor conditions. This study also suggests that during the process of uplift, large-scale concentrated fractures will form at a certain depth range and horizontal stress field, resulting in the large loss of shale gas. The regression equation of the fractured depth (H) and the horizontal stress (S) is presented as H=15.40S -754.41 (with a correlation coefficient R2=0.6834). The stratification plane and the organic pores form the migration channel of natural gas that is horizontal to the stratification plane in shale. Under the condition of both anticlines and contiguous synclines, shale gas escapes through fractures resulting from extrusion along the anticline and the uplift effect. In addition, driven by differences in the formation pressure coefficients, shale gas is capable of migrating in a short-distance stair-type style from synclines to the adjacent anticlines. Thus, if the drilling costs allow, the well locations should be placed in the more deeply buried synclines.

Zhang, L., Wu, S., Zhao, L., Lu, X., Pierce, E.M., Gu, B., 2019. Mercury sorption and desorption on organo-mineral particulates as a source for microbial methylation. Environmental Science & Technology 53, 2426–2433.


In natural freshwater and sediments, mercuric mercury (Hg(II)) is largely associated with particulate minerals and organics, but it remains unclear under what conditions particulates may become a sink or a source for Hg(II) and whether the particulate-bound Hg(II) is bioavailable for microbial uptake and methylation. In this study, we investigated Hg(II) sorption–desorption characteristics on three organo-coated hematite particulates and a Hg-contaminated natural sediment and evaluated the potential of particulate-bound Hg(II) for microbial methylation. Mercury rapidly sorbed onto particulates, especially the cysteine-coated hematite and sediment, with little desorption observed (0.1–4%). However, the presence of Hg-binding ligands, such as low-molecular-weight thiols and humic acids, resulted in up to 60% of Hg(II) desorption from the Hg-laden hematite particulates but <6% from the sediment. Importantly, the particulate-bound Hg(II) was bioavailable for uptake and methylation by a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under anaerobic incubations, and the methylation rate was 4–10 times higher than the desorption rate of Hg(II). These observations suggest direct contacts and interactions between bacterial cells and the particulate-bound Hg(II), resulting in rapid exchange or uptake of Hg(II) by the bacteria. The results highlight the importance of Hg(II) partitioning at particulate–water interfaces and the role of particulates as a significant source of Hg(II) for methylation in the environment.

Zhang, Q., Xu, H., Liu, R., Gao, P., Yang, X., Jin, W., Zhang, Y., Bi, K., Li, Q., 2019. A novel strategy for targeted lipidomics based on LC-tandem-MS parameters prediction, quantification, and multiple statistical data mining: Evaluation of lysophosphatidylcholines as potential cancer biomarkers. Analytical Chemistry 91, 3389–3396.


Lipid quantification is the ultimate goal in lipidomics studies challenged by the availability of standard compounds. A novel strategy for targeted lipidomics based on LC-MS/MS parameters prediction and multivariate statistical analysis was developed for the quantitation of lysophosphatidylcholines (LPCs) in this study. Multiple linear regression models were established with the acyl chain length and number of double bonds after the prediction correlation coefficients (R2pred) were evaluated. Then related analytical parameters including collision energy, declustering potential, retention time, and response factor were successfully predicted for any given LPC. With this “model-prediction” strategy, sensitivity, accuracy, and coverage of targeted lipidomics were improved significantly, and 60 LPCs were determined simultaneously in plasma for the first time. An integrated evaluation method for multi-indexes, logistic regression-ROC analysis was also proposed after biomarkers were identified by Student’s t test, univariate ROC curve, and PLS-DA. Then the developed workflow was successfully used to discover and evaluate multi-LPCs indexes (a set of LPCs biomarkers with the best discriminating ability) for differentiating lung, breast, colorectal, and gastric cancer from controls, and among different types of cancer. Finally, the multi-LPCs index for lung cancer was compared with the plasma before and after treatment to test its utility. The novel targeted lipidomics methodology for LPCs was expected to provide a new insight into quantitative lipidomics and further clinical application.

Zhang, Y., Di, Y., Yu, W., Sepehrnoori, K., 2019. A comprehensive model for investigation of carbon dioxide enhanced oil recovery with nanopore confinement in the Bakken tight oil reservoir. SPE Reservoir Evaluation & Engineering 22, 122-136.

https://doi.org/10.2118/187211-PA

Carbon dioxide (CO2) injection is an effective enhanced-oil-recovery (EOR) method in unconventional oil reservoirs. However, investigation of the CO2 huff ’n’ puff process in tight oil reservoirs with nanopore confinement is lacking in the petroleum industry. The conventional models need to be modified to consider nanopore confinement in both phase equilibrium and fluid transport.

Hence, we develop an efficient model to fill this gap and apply to the field production of the Bakken tight oil reservoir. Complexfracture geometries are also handled in this model. First, we revised the phase equilibrium calculation and evaluated the fluid properties with nanopore confinement. An excellent agreement between this proposed model and the experimental data is obtained considering nanopore confinement. Afterward, we verified the calculated minimum miscibility pressure (MMP) using this model against the experimental data from a rising-bubble apparatus (RBA). We analyzed the MMP and well performance of CO2 EOR in the Bakken tight oil reservoir. On the basis of the prediction of the field data, the MMP is 450 psi lower than the MMP with bulk fluid when the pore size reduces to 10 nm. Subsequently, we examined the effects of key parameters such as matrix permeability and CO2 molecular diffusion on the CO2 huff ’n’ puff process. Results show that both CO2-diffusion and capillary pressure effects improve the oil recovery factor from tight oil reservoirs, which should be correctly implemented in the simulation model. Finally, we analyzed well performance of a field-scale horizontal well from the Bakken Formation with nonplanar fractures and natural fractures. Contributions of CO2-diffusion and capillary pressure effects are also examined in depth in field scale with complex-fracture geometries. The oil recovery factor of the CO2 huff ’n’

puff process with both CO2-diffusion and capillary pressure effects increases by as much as 5.1% in the 20-year period compared with the case without these factors.

This work efficiently analyzes the CO2 huff ’n’ puff process with complex-fracture geometries considering CO2 diffusion and nanopore confinement in the field production from the Bakken tight oil reservoir. This model can provide a strong basis for accurately predicting the long-term production with complex-fracture geometries in tight oil reservoirs.


https://doi.org/10.1080/01490451.2018.1492047

Fe(II) in geothermal fluids was among the most important electron and energy sources for extremophiles and early life, and microbial oxidation of Fe(II) in turn contributed to the global Fe deposits such as banded iron formation (BIF). However, information was rare on Fe(II) bio-oxidation and consequent mineral formation in geothermal systems. In the present study, we investigated the anaerobic nitrate-depending Fe(II) oxidation (ANDFO) in the Tibetan hot springs with temperature ranging 52–86°C. ANDFO cultivation was established by inoculating sediments from the studied hot springs. Positive ANDFO reaction was observed in the cultures from three high-temperature hot springs (>80°C). Phylogenetic analysis showed that bacteria in the three obtained ANDFO cultures were mainly affiliated with phyla of Betaproteobacteria, Alphaproteobacteria, and Firmicutes. In the obtained ANDFO cultures, ferrous iron oxidation occurred with nitrate reduction, accompanied with the formation of magnetite and/or siderite, which could be finished within one week. The resulting euhedral magnetite was at the micrometer scale, which was larger in size and showed better crystallinity than its counterparts (usually <1 µm) formed by chemical reactions. Thus, it can be concluded that ANDFO bacteria and denitrifiers played important roles in the magnetite and siderite precipitation in the studied Tibetan hot springs. The coupling between Fe(II) oxidation and nitrate reduction mediated by thermophiles might provide a new mechanism for euhedral magnetite and siderite deposition in BIFs during the Precambrian period.


https://doi.org/10.1155/2019/2573937

Gas hydrates, acting as a dynamic methane reservoir, store methane in the form of a solid phase under high-pressure and low-temperature conditions and release methane through the sediment column into seawater when they are decomposed. The seepage of methane-rich fluid (i.e., cold hydrocarbon seeps) fuels the chemosynthetic biota-inhabited surface sediments and represents the major pathway to transfer carbon from sediments to the water column. Generally, the major biogeochemical reactions related to carbon cycling in the anoxic marine sediments include organic matter degradation via sulfate reduction (OSR), anaerobic oxidation of methane (AOM), methanogenesis (ME), and carbonate precipitation (CP). In order to better understand the carbon turnover in the cold seeps and gas hydrate-bearing areas of the northern South China Sea (SCS), we collected geochemical data of 358 cores from published literatures and retrieved 37 cores and corresponding pore water samples from three areas of interest (i.e., Xisha, Dongsha, and Shenhu areas). Reaction-transport simulations indicate that the rates of organic matter degradation and carbonate precipitation are comparable in the

three areas, while the rates of AOM vary over several orders of magnitude (AOM: 8.3-37.5 mmol·m -

2·yr-1 in Dongsha, AOM: 12.4-170.6 mmol·m-2·yr-1 in Xisha, and AOM: 9.4-30.5 mmol·m-2·yr-1 in Shenhu). Both the arithmetical mean and interpolation mean of the biogeochemical processes were calculated in each area. Averaging these two mean values suggested that the rates of organic matter degradation in Dongsha (25.7 mmol·m-2·yr-1) and Xisha (25.1 mmol··m-2·yr-1) are higher than that in Shenhu (12 mmol··m-2·yr-1) and the AOM rate in Xisha (135.2 mmol··m-2·yr-1) is greater than those in Dongsha (27.8 mmol··m-2·yr-1) and Shenhu (17.5 mmol··m-2·yr-1). In addition, the rate of carbonate precipitation (32.3 mmol··m-2·yr-1) in Xisha is far higher than those of the other two regions (5.3 mmol··m-2·yr-1 in Dongsha, 5.8 mmol··m-2·yr-1 in Shenhu) due to intense AOM sustained by gas dissolution. In comparison with other cold seeps around the world, the biogeochemical rates in the northern SCS are generally lower than those in active continental margins and special environments (e.g., the Black sea) but are comparable with those in passive continental margins. Collectively, ~2.8 Gmol organic matter was buried and at least ~0.82 Gmol dissolved organic and inorganic carbon was diffused out of sediments annually. This may, to some extent, have an impact on the long-term deep ocean carbon cycle in the northern SCS.

Zhang, Z., Zhao, L., Zhuang, L., Li, Y., Zhang, H., 2019. The effect of acid treatment on pyrolysis of Longkou oil shale. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 1605-1614.

https://doi.org/10.1080/15567036.2018.1549135

The effect of acid treatment on mineral removal and pyrolysis of Longkou oil shale were investigated. X-ray diffraction (XRD) and X-ray fluorescence (XRF) indicated that the HCl treatment can remove the calcite, the H2SO4 treatment can convert the calcite to CaSO4, and the HF treatment can remove the quartz and convert the calcite to CaF2; moreover, all three treatments cannot remove the pyrite in the oil shale. Oil shale was individually treated with HCl, H2SO4, and HF before conducted the pyrolysis experiment. The pyrolysis results showed that oil shale treated with H2SO4 or HF almost equally enhanced the oil yield, while HCl treatment had a negative effect on the oil yield. Thermogravimetry (TG) analysis indicated that the carbonates had a catalytic effect, sulfates may also had a catalytic effect and the silicates had an inhibitive effect on the decomposition of kerogen. Combining the TG analysis, oil yield and the price of every acid, the H2SO4 treatment was considered to be the best method to treat oil shale.Moreover, the carbonate minerals can be removed after H2SO4 treatment, so it would reduce the amount of pyrolysis feed to increase production efficiency.

Zhao, C., Wang, Y., Chan, K.X., Marchant, D.B., Franks, P.J., Randall, D., Tee, E.E., Chen, G., Ramesh, S., Phua, S.Y., Zhang, B., Hills, A., Dai, F., Xue, D., Gilliham, M., Tyerman, S., Nevo, E., Wu, F., Zhang, G., Wong, G.K.S., Leebens-Mack, J.H., Melkonian, M., Blatt, M.R., Soltis, P.S., Soltis, D.E., Pogson, B.J., Chen, Z.-H., 2019. Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land. Proceedings of the National Academy of Sciences 116, 5015-5020.


Significance: The projected increase in drought severity and duration worldwide poses a significant threat to the health of terrestrial ecosystems. We reveal that unique genetic features of desiccation sensing and protection in streptophyte algae not only distinguish them from chlorophyte algae, but also represent a crucial evolutionary step that may have facilitated colonization and subsequent diversification of terrestrial habitats. We demonstrate the evolutionary significance of a molecular mechanism underlying how plants sense drought stress via the coordination of chloroplast retrograde signaling to trigger the closure of stomata, protecting vital photosynthetic tissue. Our findings

constitute a significant step forward in understanding the evolution of plant drought tolerance, contributing to the diversification of terrestrial plant communities through past global climate transitions.

Abstract: Chloroplast retrograde signaling networks are vital for chloroplast biogenesis, operation, and signaling, including excess light and drought stress signaling. To date, retrograde signaling has been considered in the context of land plant adaptation, but not regarding the origin and evolution of signaling cascades linking chloroplast function to stomatal regulation. We show that key elements of the chloroplast retrograde signaling process, the nucleotide phosphatase (SAL1) and 3′-phosphoadenosine-5′-phosphate (PAP) metabolism, evolved in streptophyte algae—the algal ancestors of land plants. We discover an early evolution of SAL1-PAP chloroplast retrograde signaling in stomatal regulation based on conserved gene and protein structure, function, and enzyme activity and transit peptides of SAL1s in species including flowering plants, the fern Ceratopteris richardii, and the moss Physcomitrella patens. Moreover, we demonstrate that PAP regulates stomatal closure via secondary messengers and ion transport in guard cells of these diverse lineages. The origin of stomata facilitated gas exchange in the earliest land plants. Our findings suggest that the conquest of land by plants was enabled by rapid response to drought stress through the deployment of an ancestral SAL1-PAP signaling pathway, intersecting with the core abscisic acid signaling in stomatal guard cells.

Zheng, S., Yao, Y., Liu, D., Cai, Y., Liu, Y., 2019. Nuclear magnetic resonance surface relaxivity of coals. International Journal of Coal Geology 205, 1-13.


Nuclear magnetic resonance (NMR) transverse relaxation time (T2) measurements of fully water-saturated rock samples can provide a reference for pore size distribution (PSD). Commonly, surface relaxivity of the rock must be known before obtaining an absolute PSD sample using NMR data. There are many reports concerning the surface relaxivity of sandstones, shales, and carbonate rocks, however, little research has been performed on the surface relaxivity of coals, which limit the application of the NMR in PSD evaluation of coals. To obtain a standard surface relaxivity for PSD measurements of coals, we performed NMR, low-temperature N2 adsorption (LTNA), and mercury intrusion porosimetry (MIP) measurements for 15 bituminous and anthracite coals, whose Ro range from 0.52% to 3.07%. The results show that the values of surface relaxivity from LTNA (ρ2-SVR) are inconsistent with those from MIP (ρ2-MIP) for all samples. Moreover, the applications of ρ2-SVR and ρ2-

MIP for PSD conversions are valid only for the smaller pores and larger pores, respectively. Evidently, both these two surface relaxivities cannot be used individually to calculate full-scale PSD. To obtain the actual surface relaxivity (ρ2) for full-scale PSD, we rebuilt a full-scale PSD by combining the pores smaller than 25 nm from LTNA and the pores larger than 25 nm from MIP. The results indicate that the calculated ρ2 provides excellent function for PSD transformation for all coal samples. Finally, the references of ρ2 for different coals are provided, i.e., values of 2.1 μm/s for sub-bituminous coal (low-rank coal), 3.0 μm/s for bituminous coal (medium-rank coal) and 1.6 μm/s for anthracite coal (high-rank coal). Using these referential surface relaxivities, a T2 distribution from NMR measurement can be converted to a PSD, which is applicable not only in the laboratory but also in field applications such as well logging.

Zhou, C., Lang, X., Huyskens, M.H., Yin, Q.-Z., Xiao, S., 2019. Calibrating the terminations of Cryogenian global glaciations. Geology 47, 251-254.


Cryogenian Sturtian and Marinoan glacial and associated strata record the most severe paleoclimatic events in Earth history and are the main test ground of the snowball Earth hypothesis (SEH). The SEH predicts that both Sturtian and Marinoan deglaciations were globally synchronous, rapid, and catastrophic. The sharp transition from glacial diamictite to the overlying cap dolostone represents a key event during these deglaciations. Thus, a positive test for globally synchronous deglaciation requires high-precision radiometric dates to tightly bracket this transition on each paleocontinent and within every substantial sedimentary basin; however, such high-resolution dates are scarce and have limited stratigraphic and paleogeographic coverage. Here, we report two high-precision U-Pb zircon chemical abrasion–isotope dilution–thermal ionization mass spectrometry ages of 658.80 ± 0.50 Ma and 634.57 ± 0.88 Ma from tuffaceous layers that occur, respectively, within the cap dolostone atop the Tiesi’ao diamictite (Sturtian age) and at the topmost Nantuo diamictite (Marinoan age) in South China. The 658.80 ± 0.50 Ma age represents a high-precision minimum age constraint on the termination of the Sturtian-age glaciation. The 634.57 ± 0.88 Ma age and a previously published age of 635.23 ± 0.57 Ma from the topmost cap dolostone are indistinguishable within uncertainty, and together they provide tight constraints on the termination of the Marinoan glaciation in South China at ca. 635 Ma and directly bracket the duration of the cap dolostone to be < 106 yr. The new data support the rapid termination of the Marinoan glaciation in South China and are consistent with global synchroneity of Cryogenian deglaciation events.

Zhou, X., Gao, G., Lü, X., Zhao, L., Dong, Y., Xu, X., Gan, J., 2019. Petroleum source and accumulation of WZ12 oils in the Weixi'nan sag, south China sea, China. Journal of Petroleum Science and Engineering 177, 681-698.


Source rocks are found in the Eocene Liushagang Formation (El1: bottom, El2 and El3:top members), in the Weixi'nan sag, Beibuwan Basin. The source rocks are mainly mudrocks, except El2, which consists of organic-rich shales at the bottom and mudrocks in the middle-upper part. Total organic carbon (TOC) and Rock-Eval analyses of 146 samples indicate that El2 rocks have the best hydrocarbon generating potential, especially for organic-rich shales that contain up to 10% TOC with HI > 800 mg/g. The vitrinite reflectance analysis suggests that El source rocks are marginally mature to mature. Geochemical analyses were conducted on 18 El rock extracts and 18 oil samples from the WZ12 field. El2 and El3 source rock have similar organic facies and are distinct from El1. El2 and El3 have higher C27 βα (20R + 20S) diasteranes/C27 αββ (20R + 20S) steranes (C27DiaS/C27S), Gammacerane/Hopane (G/H) and (C28 + C29) tricyclic terpane/((C28 + C29) tricyclic terpane + Ts) (ETR), and low C23 tricyclic terpane/hopane (C23/H) and C24 tetracyclic terpanes/C26 tricyclic terpane (C24/C26). These biomarker distributions indicate that El2 and El3 rocks were deposited under more alkaline-saline environment and had less import of terrestrial organic matter relative to El1. El2 can be distinguished from El3 as having higher 4-methylsteranes/C29 ααα steranes (4MSI) and G/H. WZ12 oils all exhibit similar compositions and display biomarker characteristics that correlate with the El2 and El3 rock extracts.

1D thermal and burial history model shows that El2 and El3 began to generate a great deal of hydrocarbon at ∼11.5 Ma and 23 Ma, respectively. At this stage, traps formed and faults actively extended downwards into the El2 and likely into El3. Oils expelled from El2 and El3 migrated upward into shallow intervals along faults then laterally along the structural slopes and accumulated in areas with good fault sealing primarily in the Miocene age Nx and Nj strata. Meanwhile, under the effect of overpressure in the middle of organic-rich shales, oils from El2 may have migrated downward into reservoirs in the upper part of El3. Lithologic traps in El1 reservoir may be charged with relatively immature oil derived from El1.



Microorganisms in petroleum reservoirs mediate hydrocarbon degradation coupling with methanogenesis process as the terminal step, they also contribute to microbial enhanced oil recovery (MEOR) worldwide with great economic and environmental benefits. Here, a molecular investigation, using the 16S rRNA and mcrA gene profiles based on MiSeq sequencing and clone library construction method, was conducted on oil and water (aqueous) phases of samples with high, moderate and low temperatures from seven petroleum reservoirs in China. A core bacterial microbiome with a small proportion of shared OUT, but a high proportion of sequences among all reservoirs was discovered, including aerobic degraders, sulfate/nitrate reducing bacteria, fermentative bacteria and sulfur cycling bacteria distributed mainly in Proteobacteria, Bacteroidetes, Deferribacteres, Deinococcus-Thermus, Firmicutes, Spirochaetae and Thermotogae. Their prevalence in the reported petroleum reservoirs and successive enrichment cultures suggest their common roles and functions involved in aliphatic and aromatic hydrocarbon degradation. Dominant methanogenesis process generally shifts from hydrogenotrophic pathway in water phase to acetoclastic pathway in oil phase in high temperature reservoirs, but the opposite is true for low temperature reservoirs. No differences were detected between two phases in moderate temperature reservoirs. Physiochemical factors, including pH, temperature, phase conditions, and nitrate, Mn2+, and Mg2+ concentrations are the main ones correlating to the microbial compositional and functional profiles significantly. LEfSe analysis shows distribution differences of microbial groups towards pH, temperature, and oil/water. Tax4Fun functional profiling indicates major functional metabolism differences between the two phases, including amino acids, hydrocarbons in the oil phase, and carbohydrates in the water phase.

Zhu, G., Wang, S., Wang, C., Zhou, L., Zhao, S., Li, Y., Li, F., Jetten, M.S.M., Lu, Y., Schwark, L., 2019. Resuscitation of anammox bacteria after >10,000 years of dormancy. The ISME Journal 13, 1098-1109.

https://doi.org/10.1038/s41396-018-0316-5

Water is essential for life on Earth, and an important medium for microbial energy and metabolism. Dormancy is a state of low metabolic activity upon unfavorable conditions. Many microorganisms can switch to a metabolically inactive state after water shortage, and recover once the environmental conditions become favorable again. Here, we resuscitated dormant anammox bacteria from dry terrestrial ecosystems after a resting period of >10 ka by addition of water without any other substrates. Isotopic-tracer analysis showed that water induced nitrate reduction yielding sufficient nitrite as substrate and energy for activating anammox bacteria. Subsequently, dissimilatory nitrate reduction to ammonium (DNRA) provided the substrate ammonium for anammox bacteria. The ammonium and nitrite formed were used to produce dinitrogen gas. High throughput sequencing and network analysis identified Brocadia as the dominant anammox species and a Jettenia species seemed to connect the other community members. Under global climate change, increasing precipitation and soil moisture may revive dormant anammox bacteria in arid soils and thereby impact global nitrogen and carbon cycles.

Zhuang, G.-C., Montgomery, A., Samarkin, V.A., Song, M., Liu, J., Schubotz, F., Teske, A., Hinrichs, K.-U., Joye, S.B., 2019. Generation and utilization of volatile fatty acids and alcohols in hydrothermally altered sediments in the Guaymas Basin, Gulf of California. Geophysical Research Letters 46, 2637-2646.

https://doi.org/10.1029/2018GL081284

Abstract: Volatile fatty acids (VFAs) and alcohols are key intermediates of anaerobic carbon metabolism, yet their biogeochemical cycling remains poorly constrained in hydrothermal systems. We investigated the abundance, stable carbon isotopic composition, and metabolic cycling of VFAs and alcohols to elucidate their generation and utilization pathways in hydrothermally influenced sediments (4 °C to 90 °C) from the Guaymas Basin. Acetate (up to 229 μM) and methanol (up to 37 μM) were abundant in porewaters. The δ13C values of acetate varied between −35.6‰ and −18.1‰. Carbon isotopic signatures, thermodynamic predictions, and experimental incubations suggested biological sources such as fermentation and acetogenesis for acetate. Acetate and methanol were predominantly consumed by nonmethanogenic processes (e.g., sulfate reduction), as reflected in high oxidation rates versus low methanogenesis rates, and further evidenced through inhibition experiments with molybdate. These results reveal an important role for VFAs and alcohols as energy sources for diverse chemoheterotrophs in organic‐rich hydrothermally influenced sediments.

Plain Language Summary: Hydrothermal systems are unique seafloor habitats that host abundant and diverse microbial communities, but questions remain regarding their energy strategy and metabolic activity. We found that low molecular weight organic compounds such as acetate and methanol were abundant in the hydrothermal sediments of Guaymas Basin. Multiple lines of evidence suggested that these substrates were produced largely via biological pathways. We further investigated the microbial metabolism of acetate and methanol and found that both compounds could be used as an energy source to support various microbial processes in the hydrothermal systems.


https://doi.org/10.1029/2018GB006129

Acetate is a key intermediate of organic matter mineralization, but its metabolism remains largely unconstrained in the pelagic ocean. We conducted an integrated biogeochemical study to investigate microbial acetate cycling in the northern Gulf of Mexico with the goal of elucidating the importance of acetate as a carbon and energy source. Acetate was used primarily as an energy source, as evidenced by observed oxidation rates (rate constant k: 0.06–0.22 day−1) that varied between 42% and 96% of total biological acetate uptake (i.e., assimilation + oxidation; k: 0.06–0.34 day−1). The assimilation of acetate into biomass (k: 0.01–0.20 day−1) illustrated the potential significance of acetate as a biomass carbon source, particularly in nutrient‐rich coastal waters. No relationship between acetate assimilation or oxidation and environmental factors, such as chlorophyll and nutrients, was observed. However, elevated acetate uptake in reduced oxygen waters characterized by particulate organic carbon mineralization suggests that acetate metabolism may be a good proxy for particulate organic carbon breakdown. Molecular genetic analysis revealed that SAR11 Alphaproteobacteria were the most abundant heterotrophic bacteria and suggest that they may utilize acetate. At some sites, acetate carbon may have accounted for up to 50.4% of the bacterial carbon production. These results suggest that acetate may serve as an important carbon and energy source for heterotrophic bacteria thus revealing a potentially significant role of acetate for dissolved organic carbon cycling in the ocean.

Zhuang, L., Tang, Z., Ma, J., Yu, Z., Wang, Y., Tang, J., 2019. Enhanced anaerobic biodegradation of benzoate under sulfate-reducing conditions with conductive iron-oxides in sediment of Pearl River Estuary. Frontiers in Microbiology 10, 374. doi: 310.3389/fmicb.2019.00374.


Anaerobic biodegradation of aromatic compounds under sulfate-reducing conditions is important to marine sediments. Sulfate respiration by a single bacterial strain and syntrophic metabolism a syntrophic bacterial consortium are primary strategies for sulfate-dependent biodegradation of aromatic compounds. The objective of this study was to investigate the potential of conductive iron oxides to facilitate the degradation of aromatic compounds under sulfate-reducing conditions in marine sediments, using benzoate as a model aromatic compound. Here, in anaerobic incubations of sediments from the Pearl River Estuary, the addition of hematite or magnetite (20 mM as Fe atom) enhanced the rates of sulfate-dependent benzoate degradation by 81.8% and 91.5%, respectively, compared with control incubations without iron oxides. Further experiments demonstrated that the rate of sulfate-dependent benzoate degradation accelerated with increased magnetite concentration (5, 10 and 20 mM). The detection of acetate as an intermediate product implied syntrophic benzoate degradation pathway, which was also supported by the abundance of putative acetate- or/and H2-utilizing sulfate reducers from microbial community analysis. Microbial reduction of iron oxides under sulfate-reducing conditions only accounted for 2-11% of electrons produced by benzoate oxidation, thus the stimulatory effect of conductive iron oxides on sulfate-dependent benzoate degradation was not mainly due to an increased pool of terminal electron acceptors. The enhanced rates of syntrophic benzoate degradation by the presence of conductive iron oxides probably resulted from the establishment of a direct interspecies electron transfer (DIET) between syntrophic partners. In the presence of magnetite, Bacteroidetes and Desulfobulbaceae with potential function of extracellular electron transfer might be involved in syntrophic benzoate degradation. Results from this study will contribute to the development of new strategies for in situ bioremediation of anaerobic sediments contaminated with aromatic compounds, and provide a new perspective for the natural attenuation of aromatic compounds in iron-rich marine sediments.

Zitnik, M., Sosič, R., Feldman, M.W., Leskovec, J., 2019. Evolution of resilience in protein interactomes across the tree of life. Proceedings of the National Academy of Sciences 116, 4426-4433.


Significance: The interactome network of protein–protein interactions captures the structure of molecular machinery that underlies organismal complexity. The resilience to network failures is a critical property of the interactome as the breakdown of interactions may lead to cell death or disease. By studying interactomes from 1,840 species across the tree of life, we find that evolution leads to more resilient interactomes, providing evidence for a longstanding hypothesis that interactomes evolve favoring robustness against network failures. We find that a highly resilient interactome has a beneficial impact on the organism’s survival in complex, variable, and competitive habitats. Our findings reveal how interactomes change through evolution and how these changes affect their response to environmental unpredictability.

Abstract: Phenotype robustness to environmental fluctuations is a common biological phenomenon. Although most phenotypes involve multiple proteins that interact with each other, the basic principles of how such interactome networks respond to environmental unpredictability and change during evolution are largely unknown. Here we study interactomes of 1,840 species across the tree of life involving a total of 8,762,166 protein–protein interactions. Our study focuses on the resilience of

interactomes to network failures and finds that interactomes become more resilient during evolution, meaning that interactomes become more robust to network failures over time. In bacteria, we find that a more resilient interactome is in turn associated with the greater ability of the organism to survive in a more complex, variable, and competitive environment. We find that at the protein family level proteins exhibit a coordinated rewiring of interactions over time and that a resilient interactome arises through gradual change of the network topology. Our findings have implications for understanding molecular network structure in the context of both evolution and environment.

Zou, C., Zhu, R., Chen, Z.-Q., Ogg, J.G., Wu, S., Dong, D., Qiu, Z., Wang, Y., Wang, L., Lin, S., Cui, J., Su, L., Yang, Z., 2019. Organic-matter-rich shales of China. Earth-Science Reviews 189, 51-78.


Organic-matter-rich shales are the main target rocks for unconventional oil and gas exploration and development across the world. In China, shale-gas geological resources are estimated as approximately 110 × 1012 m3, with recoverable gas reserves of ca. 20 × 1012 m3. Recoverable shale-oil reserves are estimated as ca. 5 × 109 t. A total 35 important organic-matter-rich shale units have been recognized from Mesoproterozoic to Cenozoic strata across the entire China. These shales are categorized according to their origin under marine, marine–nonmarine transitional and lacustrine conditions. Shales of marine origin, with ca. 9 × 1012 m3 recoverable resources, dominate China's potential in terms of total volume of organic-carbon. Currently, the most favorable marine shales for oil and gas exploration are found in the Sichuan Basin within the lower Cambrian Qiongzhusi Formation and in the Wufeng-Longmaxi formations of uppermost Ordovician through lower Silurian. A fortuitous combination of of sea-level variations, of paleo-productivity, of tectonic activity causing development and migration of partially closed deep basin depocenters, and of sediment accumulation rates controlled the extensive deposition and distribution of organic-matter-rich shales in these Wufeng and Longmaxi formations. Organic-matter-rich shales in marine-nonmarine transitional facies associated with coal measures occur in North China within the Carboniferous and Permian, and in South China within the Permian. These Carboniferous-Permian organic-matter-rich shales are important source rocks for the gas fields in the Ordos and Sichuan Basins. Abundant organic-rich shales are also widely distributed within coal-bearing clastics and coal-measure shales of fluvial, lacustrine, and swamp facies in Upper Triassic to Middle Jurassic successions of many basins. Lacustrine organic-rich shales were deposited during the Permian through Neogene in various freshwater to saline lake settings. Lacustrine organic-matter-rich shales are the main oil source rocks in the Songliao, Bohai Bay, Ordos and Junggar basins. Lacustrine algae contributed to the rain of organic matter; and the preservation of organic matter and distribution of organic-rich shale was controlled by lake currents, water depth and oxygen-poor conditions, with enhanced preservation when buried by turbidity currents. Algal blooms were partly induced by trace nutrients from volcanic ash falls in all of these lacustrine basins. Seawater intrusion into the freshwater lake of the Songliao Basin promoted some episodes of black shales. Saline lacustrine basins, such as middle Permian Junggar Basin, contain organic-rich dolomite mudstone that mainly formed during hot climate conditions when the lakes had high salinity and stratified water columns that deprived the bottom waters of oxygen, thereby preserving massive amounts of organic matter. Laminated calcite-rich mudstone in the saline lacustrine settings formed in more brackish waters under stable warm conditions and weak biological activity. The modeling of the factors controlling the distribution of organic-matter-rich shales within China's basins is important for the exploration and development of unconventional oil and gas resources.

Zuo, Z., 2019. Why algae release volatile organic compounds—the emission and roles. Frontiers in Microbiology 10, 491. doi: 410.3389/fmicb.2019.00491.


A wide spectrum of volatile organic compounds (VOCs) are released from algae in aquatic ecosystems. Environmental factors such as light, temperature, nutrition conditions and abiotic stresses affect their emission. These VOCs can enhance the resistance to abiotic stresses, transfer information between algae, play allelopathic roles, and protect against predators. For homogeneous algae, the VOCs released from algal cells under stress conditions transfer stress information to other cells, and induce the acceptors to make a preparation for the upcoming stresses. For heterogeneous algae and aquatic macrophytes, the VOCs show allelopathic effects on the heterogeneous neighbors, which benefit to the emitter growth and competing for nutrients. In cyanobacterial VOCs, some compounds such as limonene, eucalyptol, β-cyclocitral, α-ionone, β-ionone and geranylacetone have been detected as the allelopathic agents. In addition, VOCs can protect the emitters from predation by predators. It can be speculated that the emission of VOCs is critical for algae coping with the complicated and changeable aquatic ecosystems.



A method was developed to estimate the properties and assess the potential environmental risk of analytes in a complex mixture by comprehensive two-dimensional gas chromatography (GC × GC). A GC × GC-based estimation model was calibrated for 12 physicochemical properties that were relevant to the environment or to biological organisms, including human beings. Vehicle engine oil that had been contaminated by numerous compounds during its use was investigated as a case study to which the GC × GC model could be applied. Engine-oil samples were collected from a vehicle at intervals over a distance of 11407 km. The carbon and nitrogen contents in the oil remained unchanged at 83%–84% and 2%–5%, respectively, during the run; however, in excess of 100 compounds were present in the oil upon completion of the run. Post analyses of the studied mixture samples were performed with the developed GC × GC model, which links mass spectral information for structural identification. The GC × GC model allows us to classify the detected analytes in complex mixtures in terms of their properties, such as their aquatic bioaccumulation potential. The application of the model showed that the analyzed engine oil contained in excess of 100 compounds that could accumulate in aquatic biota and reach the arctic via long-range transport, which suggests that the components in the complex mixture of engine oil could pose a risk. The newly developed model that was derived in this study shows great potential for use in the mixture assessment.

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eaogorg.files.wordpress.com · Web viewGEOCHEMISTRY ARTICLES – March 2018. Analytical Chemistry. Atapattu, S.N., Rosenfeld, J.M., 2019. Micro scale analytical derivatizations on