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Bibliography
Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P. H., Schloter, M.,
Roslev, P. & Wagner, M. (2003). The isotope array, a new tool that employs substrate-mediated
labeling of rRNA for determination of microbial community structure and function. Appl Environ
Microbio/69, 6875-6887.
Ahmed, 1., Yokota, A. & Fujiwara, T. (2007a). A novel highly boron tolerant bacterium,
Bacillus boroniphilus sp. nov., isolated from soil, that requires boron for its growth.
Extremophiles 11,217-224.
Ahmed, I., Yokota, A., Yamazoe, A. & Fujiwara, T. (2007b). Proposal of Lysinibacillus
boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiform is to Lysinibacillus fusiform is
comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov. Int J Syst Evol
Microbia/57, 1117-1125.
Albert, R. A., Archambault, J., Lempa, M. & other authors (2007). Proposal of Viridibacillus
gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as
Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus
neidei comb. nov. Int J Syst Evol Microbiol57, 2729-2737.
Allan, R.N., Lebbe, L., Heyrman, J., DeVos, P., Buchanan, C. J. & Logan, N. A. (2005).
Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov., two novel
thermoacidophiles isolated from geothermal soils of northern Victoria Land, Antarctica. Int J
Syst Evol Microbia/55, 1039-1050.
Amann, R. I., Ludwig, W. & Schleifer, K. H. (1995). Phylogenetic identification and in situ
detection of individual microbial cells without cultivation. Microbial Rev 59, 143-169.
An, S. Y., Asahara, M., Goto, K., Kasai, H. & Yokota, A. (2007). Terribacillus
saccharophilus gen. nov., sp. nov. and Terribacillus halophilus sp. nov., spore-forming
bacteria isolated from field soil in Japan. Int J Syst Evol Microbiol57, 51-55.
Anton, J., Oren, A., Benlloch, S., Rodriguez-Valera, F., Amann, R. & Rossello-Mora, R.
(2002). Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the
Bacteria from saltern crystallizer ponds. Int J Syst Evol Microbia/52, 485-491.
Archer, D. B., & Peck, M.W. (1989). The microbiology of methane production in landfills. In
Microbiology of extreme environments and its potential for biotechnology, pp. 187-204. Edited
by J. C. W. M.S. da Costa; Duarte, R.A.D. London and New York: Elsiever applied science.
261
Bibliography
Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M.D. (1991). Phylogenetic heterogeneity
of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA
sequences. Lett Appl Microbio/13, 202-206.
Ash, C., Priest, F. G. & Collins, M.D. (1993). Molecular identification ofrRNA group 3 bacilli
(Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new
genus Paenibacillus. Antonie Van Leeuwenhoek 64, 253-260.
Atlas, R. M. (1984). Diversity of microbial communities. In Advances in microbial ecology, pp.
1-47. Edited by M. K. C. New York: Plenum.
Attal, A., Akunna, J., Camacho, P., Salmon, P., & Paris, I. (1992). Anaerobic degradation of
municipal solid wastes in landfill. Wat Sci Techno/25, 243-253.
Baek, S. H., Im, W. T., Oh, H. W., Lee, J. S., Oh, H. M. & Lee, S. T. (2006). Brevibacillus
ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. Int J Syst Evol
Microbia/56, 2665-2669.
Balch, W. E., Fox, G. E., Magrum, L. J., Woese, C. R. & Wolfe, R. S. (1979). Methanogens:
reevaluation of a unique biological group. Microbial Rev 43, 260-296.
Barer, M. R. & Harwood, C. R. (1999). Bacterial viability and culturability. Adv Microb
Physio/41, 93-137.
Barlaz, M. A. (1997). Microbial studies of landfills and anaerobic refuse decomposition. In
Manual of environmental microbiology. Edited by C. J. K. Hurst, G. R; Mcinerney, M. I;
Stezenbach L. D. and Water, M. V. Washington, D.C.: American society for microbiology
Barlaz, M.A., Schaefer, D.M., & Ham, R.K. (1989a). Mass balance analysis of anaerobically
decomposed refuse. J Environ Eng Div 115, 1088-1102.
Barlaz, M.A., Schaefer, D.M., & Ham, R.K. (1989b). Bacterial population development and
chemical characteristics of refuse decomposition in a simulated sanitary landfill. Appl Environ
Microbia/55, 55-65.
Barlaz, M.A., Milke, M.W. and Ham, R.K. (1987). Gas production parameters in sanitary
landfill simulators. Waste. Manag. Res. 5, 27-39.
262
Bibliography
Barns, S. M., Delwiche, C. F., Palmer, J. D. & Pace, N. R. (1996). Perspectives on archaeal
diversity, thermophily and monophyly from environmental rRNA sequences. Proc Nat/ Acad Sci
USA 93, 9188-9193.
Barns, S. M., Takata, S. L. & Kuske, C. R. (1999). Wide distribution and diversity of members
of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbial 65, 1731-
1737.
Becker, P. M., Stottmeister, U. (1998). General (Biolog GN) versus site-relevant (pollutant
dependant) sole-carbon-source-utilization patterns as a means to approaching community
functioning .. Can J Microbio/44, 913-919.
Beeman, R. E. & Sulfita, J. M. (1987). Microbial ecology of a shallow unconfmed ground
water aquifer polluted by municipal landfill leachate. Microb Eco/14, 39-54.
Behrendt, U., Ulrich, A. & Schumann, P. (2001). Description of Microbacterium foliorum sp.
nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and
the surface litter after mulching the sward, and reclassification of Aureobacterium resistens
(Funke eta/. 1998) as Microbacterium resistens comb. nov. Int J Syst Evol Microbio/51, 1267-
1276.
Bej, A. K., Perlin, M., Atlas, R. M. (1991). Effect of introducing genetically engineered
microorganisms on soil microbial community diversity FEMS Microbial Eco/86, 169-176.
Bell, P. J., Sunna, A., Gibbs, M.D., Curach, N.C., Nevalainen, H. & Bergquist, P. L. (2002).
Prospecting for novel lipase genes using PCR. Microbiology 148, 2283-2291.
Bernander, R. (2000). Chromosome replication, nucleoid segregation and cell division m
archaea. Trends Microbio/8, 278-283.
Bingemer, H. G and Crutzen, P. J. (1987). The production of methane from solid wastes.
Journal of Geophysical Research, 92, 2182-2187.
Blake, D. R. & Rowland, F. S. (1988). Continuing Worldwide Increase in Tropospheric
Methane, 1978 to 1987. Science 239, 1129-1131.
Blanc, M., Marilley, L., Beja, T. and Aragno, M. (1999) Thermophilic bacterial communities
in hot composts as revealed by most probable number counts and molecular (16S rDNA)
methods. Microbial Eco/28, 141-149.
263
Bibliography
Boeckx, P. & Van Cleemput, 0. (1996). Flux estimates from soil methanogenesis and
methanotrophy: Landfills, rice paddies, natural wetlands and aerobic soils. Environ Mon Asses
42, 189-207.
Bookter, T. J., & Ham, R. K (1982). Stabilization of solid waste in landfills. J Environ Eng Div
Proc ASCE 108, 1089-1100.
Boone, D. R., & Whitman, W. B. (1988). Proposal of minimal standards for describing new
taxa ofmethanogenic bacteria. Int J Syst Bacterio/38, 212-219.
Boone, D. R., Whitman, W. B., & Rouviere, P (1993). Diversity and taxonomy of
methanogens. In Methanogenesis, pp. 35-80. Edited by J. G. Ferry. New York: Chapman & Hall
Co.
Borneman, J. & Triplett, E. W. (1997). Molecular microbial diversity in soils from eastern
Amazonia: evidence for unusual microorganisms and microbial population shifts associated with
deforestation. Appl Environ Microbio/63, 2647-2653.
Borneman, J., Skroch, P. W., O'Sullivan, K. M., Palus, J. A., Rumjanek, N. G., Jansen, J.
L., Nienhuis, J. & Triplett, E. W. (1996). Molecular microbial diversity of an agricultural soil
in Wisconsin. Appl Environ Microbio/62, 1935-1943.
Bossio, D. A., Scow, K. M., Gunapala, N. & Graham, K. J. (1998). Determinants of Soil
Microbial Communities: Effects of Agricultural Management, Season, and Soil Type on
Phospholipid Fatty Acid Profiles. Microb Eco/36, 1-12.
Brady, S. F. & Clardy, J. (2000). Long-chain N-acyl amino acid antibiotics isolated from
heterologously expressed environmental DNA. JAm Chern Soc 2000, 122: 12903-12904.
Brenner, D. J., Staley, J. T. & Kreig, N. R. (2001). Classification of prokaryotic organisms and
the concept of bacterial speciation, Vol 1, pp. 27-31. Edited by D. R. Boone & G. M. Garrity.
New York: Springer.
Breznak, J, A. (2004). Invertebrates-Insects. In Microbial diversity and Bioprospecting, pp. 191-
203. Edited by A. L. Bull. Washington, D.C: ASM press.
Britschgi, T. B. & Giovannoni, S. J. (1991). Phylogenetic analysis of a natural marine
bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbio/51,
1707-1713.
264
Bibliography
Brochier, C., Gribaldo, S., Zivanovic, Y., Confalonieri, F. & Forterre, P. (2005).
Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeallineage
related to Thermococcales? Genome Biol6, R42.
Brown, B. A., Springer, B., Steingrube, V. A. & other authors (1999). Mycobacterium
wolinskyi sp. nov. and Mycobacterium goodii sp. nov., two new rapidly growing species related
to Mycobacterium smegmatis and associated with human wound infections: a cooperative study
from the International Working Group on Mycobacterial Taxonomy. Int 1 Syst Bacterial 49,
1493-1511.
Bruce, K. D., Osborn, A. M., Pearson, A. J., Strike, P. & Ritchie, D. A. (1995). Genetic
diversity within mer genes directly amplified from communities of non-cultivated soil and
sediment bacteria. Mol Ecol4, 605-612.
Bruns, A., Nubel, U., Cypionka, H. & Overmann, J. (2003). Effect of signal compounds and
incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbial
69, 1980-1989.
Bryant, M.P., Wolin, E. A., Wolin, M. J. & Wolfe, R. S. (1967). Methanobacillus omelianskii,
a symbiotic association of two species ofbacteria. Arch Mikrobiol59, 20-31.
Buckley, D. H., & Schmidt, T. M. (2002). Exploring the diversity of soil- a microbial rain
forest. In Biodiversity of microbial life: Foundations of Earth's Biosphere. Edited by J. T. Staley,
Reysenbach A-L. New York: Wiley-Liss.
Bult, C. J., White, 0., Olsen, G. J. & other authors (1996). Complete genome sequence of the
methanogenic archaeon, Methanococcusjannaschii. Science 273, 1058-1073.
Busse, G. S., & Auling, G. (1988). Polyamine pattern as a chemotaxonomic marker within the
Proteobacteria. Syst Appl Microbiolll, 1-8.
Button, D. K., Schut, F., Quang, P., Martin, R. & Robertson, B. R. (1993). Viability and
Isolation of Marine Bacteria by Dilution Culture: Theory, Procedures, and Initial Results. Appl
Environ Microbia/59, 881-891.
Caetano-Anolles, G., Bassam, B. J. & Gresshoff, P. M. (1991). DNA amplification
fmgerprinting using very short arbitrary oligonucleotide primers. Biotechnology (N }j 9, 553-
557.
265
Bibliography
Campbell, C. D., Grayston, S. J., Hirst, D. J. (1997). Use of rhizosphere carbon sources in sole
carbon source tests to discriminate soil microbial communities J Microbial Methods 30, 33-41.
Campbell, D. J. V., Fielding, E.R. & Archer, D.B. (1985). Understanding refuse
decomposition process to improve landfill gas energy potential. In Proc Energy Biomass, Third
international conference, pp. 1151-1155. Edited by W. Palz. London: Elsiever science publishing.
Carra, J. S. and Cossu, R. (1990). International perspectives on municipal solid wastes and
sanitary landfilling. London: Academic Press Ltd.
Case, R. J., Boucher, Y., Dahllof, I., Holmstrom, C., Doolittle, W. F. & Kjelleberg, S. (2007).
Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl
Environ Microbiol13, 278-288.
Chaudhuri, S. R. & Thakur, A. R. 2006. Microbial genetic resource mapping of East Calcutta
wetlands. Curr Sci 91, 212-217
Chen, A. C., Imachi, H., Sekiguchi, Y., Ohashi, A. & Harada, H. (2003a). Archaeal
community compositions at different depths (up to 30 m) of a municipal solid waste landfill in
Taiwan as revealed by 16S rDNA cloning analyses. Biotechnol Lett 25, 719-724.
Chen, A. C., Ueda, K., Sekiguchi, Y., Ohashi, A. & Harada, H. (2003b). Molecular detection
and direct enumeration of methanogenic Archaea and methanotrophic Bacteria in domestic solid
waste landfill soils. Biotechnol Lett 25, 1563-1569.
Chin, K. J., Hahn, D., Hengstmann, U., Liesack, W. & Janssen, P. H. (1999).
Characterization and identification of numerically abundant culturable bacteria from the anoxic
bulk soil of rice paddy microcosms. Appl Environ Microbio/65, 5042-5049.
Choi, K. H. & Dobbs, F. C. (1999). Comparison of two kinds of Biolog microplates (GN and
ECO) in their ability to distinguish among aquatic microbial communities. J Microbial Methods
36, 203-213.
Chynoweth, D.P. (1996). Environmental impact ofbiomethanogenesis. Environ Mon Asses 42,
3-18.
Claus, D. & Fahmy, F. (1986). Genus Sporosarcina Kluyver & van Niel 1936, 401AL. In
Bergey's Manual of Systematic Bacteriology, Vol2, pp. 1202-1206. Edited by P. H. A. Sneath,
N. S. Mair, M. E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
266
Bibliography
Claus, D., & Berkeley, R. D. W. (1986). Genus Bacillus Cohn 1872, 174Au. In Bergey's
Manual of Systematic Bacteriology, Vol2, pp. 1105-1139. Edited by P. H. A. Sneath, N. S. Mair,
M. E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
Clegg, C. D., Ritz, K., Griffiths, B. S. (2000). % G+C profiling and cross hybridization of
microbial DNA reveals great variation in below-ground community structure in UK upland
grasslands. Appl Soil Ecol14, 125-134.
Cohan, F. M., Roberts, M. S. & King, E. C. (1991). The potential for genetic exchange by
transformation within a natural population of Bacillus subtilis. Evolution 45, 1393-1421.
Collins, M. D. & Jones, D. (1981). Distribution of isoprenoid quinone structural types in
bacteria and their taxonomic implication. Microbial Rev 45, 316-354.
Colwell, R. R. (1970). Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio
cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacterio/104, 410-433.
Combet-Blanc, Y., Ollivier, B., Streicher, C., Patel, B. K., Dwivedi, P. P., Pot, B., Prensier,
G. & Garcia, J. L. (1995). Bacillus thermoamylovorans sp. nov., a moderately thermophilic and
amylolytic bacterium. Int J Syst Bacteriol45, 9-16.
Cook, H. A., Cromwell, D.L., & Wilson, H.A. (1967). Microorganisms in household refuse and
seepage water from sanitary landfills. Proc West Vir Acad Sci 39, 107-114.
Cooksey, R. C., de Waard, J. H., Yakrus, M. A., Rivera, I., Chopite, M., Toney, S. R.,
Morlock, G. P. & Butler, W. R. (2004). Mycobacterium cosmeticum sp. nov., a novel rapidly
growing species isolated from a cosmetic infection and from a nail salon. Int J Syst Evol
Microbia/54, 2385-2391.
Cossu, R. (1989). Role of landfilling in solid waste management. In Sanitary Landjilling:
Process, Technology and Environmental Impact, pp. 3-9. Edited by T. H. Christensen, R. Cossu
and R. Stegmann. U.K.: Academic Press.
Costas, M. (1992). Classification, identification, and typing of bacteria by the analysis of their
one-dimensional polyacrylamide gel electrophoretic protein patterns Advances in electrophoresis
5, 351-408.
267
Bibliography
Courtois, S., Cappellano, C. M., Ball, M. & other authors (2003). Recombinant
environmental libraries provide access to microbial diversity for drug discovery from natural
products. Appl Environ Microbiol69, 49-55.
Cowan, S.T. (1965). Principles and practice of bacterial taxonomy a forward look. J Gen
Microbio/39, 148-159.
Daims, H., Nielsen, J. L., Nielsen, P. H., Schleifer, K. H. & Wagner, M. (2001). In situ
characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment
plants. Appl Environ Microbio/67, 5273-5284.
Daly, K., Sharp, R. J. & McCarthy, A. J. (2000). Development of oligonucleotide probes and
PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology
146, 1693-1705.
Daniel, R. (2005). The metagenomics of soil. Nat Rev Microbiol3, 470-478.
DeLong, E. F., Wickham, G. S. & Pace, N. R. (1989). Phylogenetic stains: ribosomal RNA
based probes for the identification of single cells. Science 243, 1360-1363.
Derakshani, M., Lukow, T. & Liesack, W. (2001). Novel bacterial lineages at the (sub)
division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from
bulk soil and rice roots of flooded rice microcosms. Appl Environ Microbial 67, 623-631.
Derry, A. M., Staddon, W. J., Kevan, P. G., Trevors, J. T. (1998). Functional diversity and
community structure of micro-organisms in three arctic soils as determined by sole-carbon
source-utilization. Biodivers Conserv 8, 205-221.
Derry, A. M., Staddon, W. J., Trevors, J. T. (1999). Functional diversity and community
structure of micro-organisms in uncontaminated and creosote-contaminated soils as determined
by sole-carbon-source-utilization World J Microbial Biotechnol14, 571-578.
Dojka, M. A., Hugenholtz, P., Haack, S. K. & Pace, N. R. (1998). Microbial diversity in a
hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation.
Appl Environ Microbiol64, 3869-3877.
Domenech, P., Jimenez, M. S., Menendez, M. C., Bull, T. J., Samper, S., Manrique, A. &
Garcia, M. J. (1997). Mycobacterium mageritense sp. nov. Int J Syst Bacteriol47, 535-540.
268
Bibliography
Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J.P. & Raoult, D. (2000). 16S
ribosomal DNA sequence analysis of a large collection of environmental and clinical
unidentifiable bacterial isolates. J Clin Microbio/38, 3623-3630.
Dunbar, J., Barns, S. M., Ticknor, L. 0. & Kuske, C. R. (2002). Empirical and theoretical
bacterial diversity in four Arizona soils. Appl Environ Microbio/68, 3035-3045.
Dunbar, J., Takala, S., Barns, S. M., Davis, J. A. & Kuske, C. R. (1999). Levels of bacterial
community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl
Environ Microbio/65, 1662-1669.
Edwards, T. & McBride, B. C. (1975). New method for the isolation and identification of
methanogenic bacteria. App/ Microbio/29, 540-545.
Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of
bacteria, comparison of trees ofRecA's and 16S rRNA's from the same species. J Mol Evo/41,
1105-1123.
el Fantroussi, S., Verschuere, L., Verstraete, W. & Top, E. M. (1999). Effect of phenylurea
herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints
and community-level physiological profiles. Appl Environ Microbio/65, 982-988.
Ellis, R. J., Thompson, I. P., Bailey, M. J. (1995). Metabolic profiling as a means of
characterizing plant-associated microbial communities. FEMS Microbial Eco/16, 9-18.
Entcheva, P., Liebl, W., Johann, A., Hartsch, T. & Streit, W. R. (2001). Direct cloning from
enrichment cultures, a reliable strategy for isolation of complete operons and genes from
microbial consortia. Appl Environ Microbio/61, 89-99.
Eschenfeldt, W. H., Stols, L., Rosenbachum, H., Khambatta, Z. S., Quaite-Randall, E., Wu,
S., Kilgore, D. C., Trent, J.D., Donnelly, M. I. (2001). DNA from uncultured organisms as a
source of2, 5-diketo-D-gluconic acid reductases. Appl Environ Microbio/67, 4206-4214.
Evans, J. B. (1986). Genus Aerococcus Williams, Hirch & Cowan 1953, 475AL. In Bergey's
Manual of Systematic Bacteriology, Vol 2, pp. 1080. Edited by P. H. A. Sneath, N. S. Mair, M.
E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
269
Bibliography
Farrow, J. A. & Collins, M. D. (1984). DNA base composition, DNA-DNA homology and
long-chain fatty acid studies on Streptococcus thermophilus and Streptococcus salivarius. J Gen
Microbio/130, 357-362.
Farrow, J. A., Ash, C., Wallbanks, S. & Collins, M.D. (1992). Phylogenetic analysis of the
genera Planococcus, Marinococcus and Sporosarcina and their relationships to members of the
genus Bacillus. FEMS Microbial Lett 72, 167-172.
Farrow, J. A., Wallbanks, S. & Collins, M. D. (1994). Phylogenetic interrelationships of
round-spore-forming bacilli containing cell walls based on lysine and the non-spore-forming
genera Caryophanon, Exiguobacterium, Kurthia, and Planococcus. Int J Syst Bacterial 44, 74-
82.
Felsenstein, J. (1993). PHYLIP (Phylogeny inference package), version 3.5c. distributed by the
author. Department of Genome Sciences, University of Washington, Seattle, USA.
Felske, A. & Akkermans, A. D. L. (1998a). Spatial Homogeneity of Abundant Bacterial 16S
rRNA Molecules in Grassland Soils. Microb Eco/36, 31-36.
Felske, A., Wolterink, A., Van Lis, R. & Akkermans, A. D. (1998b). Phylogeny of the main
bacterial 16S rRNA sequences in Drentse A grassland soils (The Netherlands). Appl Environ
Microbio/64, 871-879.
Ferry, J. G. (1993). Fermentation of acetate. In Methanogenesis, pp. 305-334. Edited by J. G.
Ferry. New York: Chapman and Hall, Inc.
Fisher, M. M. & Triplett, E. W. (1999). Automated approach for ribosomal intergenic spacer
analysis of microbial diversity and its application to freshwater bacterial communities. Appl
Environ Microbio/65, 4630-4636.
Fjellbirkeland, A., Torsvik, V. & Ovreas, L. (2001). Methanotrophic diversity in an
agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF
and 16S rDNA sequences. Antonie Van Leeuwenhoek 79, 209-217.
Forterre, P., Brochier, C. & Philippe, H. (2002). Evolution of the Archaea. Theor. Popul. Bioi.
61, 409-422.
Fortina, M. G., Pukall, R., Schumann, P., Mora, D., Parini, C., Manachini, P. L. &
Stackebrandt, E. (2001). Ureibacillus gen. nov., a new genus to accommodate Bacillus
270
Bibliography
thermosphaericus (Andersson et al. 1995), emendation of Ureibacillus thermosphaericus and
description of Ureibacillus terrenus sp. nov. Int J Syst Evol Microbia/51, 447-455.
Fox, G. E., E. Stackebrandt, R. B. Hespell, J. Gibson, J. Maniloff, T. A. Dyer, R. S. Wolfe,
W. E. Balch, R. Tanner, L. Magrum, L. B. Zablen, R. Blakemore, R. Gupta, L. Bonen, B. J.
Lewis, D. A. Stahl, K. R. Luehrsen, K. N. Chen, and C. R. Woese. 1980. The phylogeny of
prokaryotes. Science 209, 457-463.
Fox, G. E., Wisotzkey, J. D., & Jurtshuk, P, Jr. (1992). How close is close: 16S rRNA
sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacterio/42, 166-
170.
Franzmann, P. D., Liu, Y., Balkwill, D. L., Aldrich, H. C., Conway de Macario, E., &
Boone, D. R. (1997). Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen
from Ace Lake, Antarctica. Int J Syst Bacterio/47, 1068-1072.
Fry, J. C. (1990a). Direct methods and biomass estimation. In Methods in microbiology, pp. 41-
85. Edited by R.N. Grigorova, J. R. London, United Kingdom: Academic Press.
Fry, J. C. (1990b). Oligotrophs. In Microbiology of Extreme Environments, pp. 93-116. Edited
by I. C. Edwards. Milton Keynes, United Kingdom: Open University Press.
Fuhrman, J. A., McCallum, K., & Davis, A. A. (1993). Phylogenetic diversity of subsurface
marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbia/59,
1294-1302.
Funke, G., Hutson, R. A., Bernard, K. A., Pfyffer, G. E., Wauters, G. & Collins, M. D.
(1996). Isolation of Arthrobacter sp. from clinical specimens and description of Arthrobacter
cumminsii sp. nov. and Arthrobacter woluwiensis sp. nov, J Clin Microbio/34, 2356-2363.
Funke, G., Hutson, R. A., Hilleringmann, M., Heizmann, W. R. & Collins, M. D. (1997).
Corynebacterium lipophilojlavum sp. nov. isolated from a patient with bacterial vaginosis. FEMS
Microbial Lett 150, 219-224.
Funke, G., Lawson, P. A., Nolte, F. S., Weiss, N. & Collins, M.D. (1998). Aureobacterium
resistens sp. nov., exhibiting vancomycin resistance and teicoplanin susceptibility. FEMS
Microbial Lett 158, 89-93.
271
Bibliography
Gallego, V., Sanchez-Porro, C., Garcia, M. T. & Ventosa, A. (2006). Roseomonas aquatica
sp. nov., isolated from drinking water. Int J Syst Evol Microbia/56, 2291-2295.
Garcia, J. L., Patel, B. K., & Ollivier, B. (2000). Taxonomic, phylogenetic, and ecological
diversity of methanogenic Archaea. Anaerobe 6, 205-226.
Garcia, M. T., Gallego, V., Ventosa, A. & Mellado, E. (2005). Thalassobacillus devorans gen.
nov., sp. nov., a moderately halophilic, phenol-degrading, Gram-positive bacterium. Int J Syst
Eva! Microbia/55, 1789-1795.
Garland, J. L. (1996). Patterns of potential C source utilization by rhizosphere communities.
Soil Bioi Biochem 28, 223-230.
Garland, J. L., & Mills, A. L. (1991). Classification and Characterization of Heterotrophic
Microbial Communities on the Basis of Patterns of Community-Level Sole-Carbon-Source
Utilization. Appl Environ Microbia/57, 2351-2359.
Gendebien, A., Pauwels, M., Constant, M., Ledrut-Damanet, M. J., Willumsen, H. C.,
Butson, J., Fabry, R., Ferrero, G. L. and Nyns, E. J. (1992). Landfill gas: from environment to
energy. Luxemburg: Office for Official Publications of the European Community.
Ghosh, A., Bhardwaj, M., Satyanarayana, T., Khurana, M., Mayilraj, S. & Jain, R. K.
(2007a). Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. Int J Syst Evol
Microbia/57, 238-242.
Ghosh, A., Maity, B., Chakrabarti, K. & Chattopadhyay, D. (2007b). Bacterial diversity of
East Calcutta Wet land area: possible identification of potential bacterial population for different
biotechnological uses. Microb Eco/54, 452-459.
Ginolhac, A., Jarrin, C., Gillet, B. & other authors (2004). Phylogenetic analysis of
polyketide synthase I domains from soil metagenomic libraries allows selection of promising
clones. Appl Environ Microbio/70, 5522-5527.
Giovannoni, S. J., & Rappe, M. S. (2000). Evolution, diversity, and molecular ecology of
marine prokaryotes. In Microbial Ecology of the Oceans, pp. 47-84. Edited by D. L. Kirchmann.
New York: Wiley.
Glazunova, 0. 0., Raoult, D. & Roux, V. (2006). Bacillus massiliensis sp. nov., isolated from
cerebrospinal fluid. Int J Syst Evol Microbia/56, 1485-1488.
272
Bibliography
Gonzalez, J. M., & Moran, M. A. (1997). Numerical dominance of a group of marine bacteria
in the alpha-subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbial 63,
4237-4242.
Goodfellow, M & Lechevalier, M.P. (1986). Genus Nocardia Trevisan 1889, 9AL. In Bergey's
Manual of Systematic Bacteriology, Vol2, pp. 1459-1471. Edited by P. H. A. Sneath, N. S. Mair,
M. E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
Goodfellow, M., & O'Donnell, A. G. (1993). Roots of bacterial systematics. In Handbook of
New Bacterial Systematics, pp. 3-56. Edited by M. Goodfellow, & 0' Donnell, A. G. San Diego:
Academic Press Inc.
Goodfellow, M., Jones, A. L., Maldonado, L. A. & Salanitro, J. (2004). Rhodococcus
aetherivorans sp. nov., a new species that contains methyl t-butyl ether-degrading actinomycetes.
Syst Appl Microbiol27, 61-65.
Goodfellow, M., Manfio, G. P., & Chun, J. (1997). Towards a practical species concept for
cultivable bacteria. In Species: the units of biodiversity, pp. 25-59. Edited by M. F. Claridge, &
Dawah, H. A. London: Chapman & Hall.
Gordon, D. A., & Giovannoni, S. J. (1996). Detection of stratified microbial populations related
to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl Environ
Microbiol62, 1171-1177.
Goto, K., Fujita, R., Kato, Y., Asahara, M. & Yokota, A. (2004). Reclassification of
Brevibacillus brevis strains NCIMB 13288 and DSM 6472 (=NRRL NRS-887) as
Aneurinibacillus danicus sp. nov. and Brevibacillus limnophilus sp. nov. Int J Syst Evol
Microbia/54, 419-427.
Goto, K., Omura, T., Hara, Y., Sadiae, Y (2000). Application of the partial 16S rDNA
sequence as an index for rapid identification of species in the genus Bacillus. J Gen. Appl.
Microbiol46, 1-8.
Grayston, S. J., & Campbell, C. D. (1996). Functional biodiversity of microbial communities in
the rhizospheres of hybrid larch (Larix eurilepsis) and Sitka spruce (Picea sitchensis). Tree
physio/16, 1031-1038.
Grayston, S. J., Wang, S., Campbell, C. D., Edwards, A. C. ·(1998). Selective influence of
plant species on microbial diversity in the rhizosphere. Soil Bioi Biochem 30, 369-378.
273
Bibliography
Greene, E. A. & Voordouw, G. (2003). Analysis of environmental microbial communities by
reverse sample genome probing. J Microbial Methods 53, 211-219.
Greene, E. A., Kay, J. G., Jaber, K., Stehmeier, L. G. & Voordouw, G. (2000). Composition
of soil microbial communities enriched on a mixture of aromatic hydrocarbons. Appl Environ
Microbio/66, 5282-5289.
Griffiths, B. S., Ritz, K, Ebblewhite, N., Dobson, G. (1999). Soil microbial community
structure: effects of substrate loading rates. Soil Bioi Biochem 31, 145-153.
Grosskopf, R., Janssen, P. H. & Liesack, W. (1998). Diversity and structure of the
methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and
direct 16S rRNA gene sequence retrieval. Appl Environ Microbio/64, 960-969.
Guo, C., Sun, W., Harsh, J. B. & Ogram, A. (1997). Hybridization Analysis of Microbial DNA
from Fuel Oil-Contaminated and Non-contaminated Soil. Microb Eco/34, 178-187.
Gupta, R.S. (1998). What are archaebacteria: life's third domain or monoderm prokaryotes
related to Gram-positive bacteria? A new proposal for the classification of prokaryotic
organisms. Mol Microbio/29, 695-707.
Gurijala, K. R. & Sulfita, J. M. (1993). Environmental factors influencing methanogenesis
from refuse in landfill samples. Env Sci Techn 27, 1176-1181.
Gurijala, K R., Ping, S.A., & Robinson, J.A. (1997). Statistical modeling of methane
production from landfill samples. Appl Environ Microbio/63, 3797-3803.
Hagenauer, A., Hippe, H. & Rainey, F. A. (1997). Desulfotomaculum aeronauticum sp. nov., a
spore forming, thiosulfate-reducing bacterium from corroded aluminium alloy in an aircraft. Syst
Appl Microbiol20, 65-71.
Ham, R. K., Fritschel, P.R., & Robbins Norman, M. (1993). Refuse decomposition at a large
landfill. In Proc of the fourth International landfill symposium, pp. 1045-1054. Edited by R.
Cossu. Cagliari.
Hamana, k., & Matsuzaki, S. (1990). Five types of polyamine distribution patterns in
thiobacilli. FEMS Microbial Lett 40, 347-352.
Harper, J. L., & Haksworth, D. L. (1995). Preface. In Biodiversity, Measurement and
Estimation, pp. 5-12. Edited by D. L. Hakswoth. London, United kingdom: Chapman & Hall.
274
Bibliography
Head, I. M., Saunders, J. R., Pickup, R. W. (1998). Microbial evolution, diversity, and
ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35,
1-21.
Henne, A., Daniel, R., Schmitz, R. A. & Gottschalk, G. (1999). Construction of environmental
DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization
of 4-hydroxybutyrate. Appl Environ Microbio/65, 3901-3907.
Henne, A., Schmitz, R. A., Bomeke, M., Gottschalk, G. & Daniel, R. (2000). Screening of
environmental DNA libraries for the presence of genes conferring lipolytic activity on
Escherichia coli. Appl Environ Microbio/66, 3113-3116.
Hentschel, U., Hopke, J., Horn, M., Friedrich, A. B., Wagner, M., Hacker, J. & Moore, B.
S. (2002). Molecular evidence for a uniform microbial community in sponges from different
oceans. Appl Environ Microbio/68, 4431-4440.
Heyndrickx, M., Lebbe, L., Kersters, K., DeVos, P., Forsyth, C & Logan, N. A. (1998).
Virgibacillus: a new genus to accomodate Bacillus pantothenticus (Proom and Knight 1950).
Emended description of Virgibacillus pantothenticus. Int J Syst Bacterio/48, 99-106.
Heyndrickx, M., Lebbe, L., Vancanneyt, M. & 7 other authors (1997). A polyphasic
reassessment of the genus Aneurinibacillus, reclassification of Bacillus thermoaerophilus
(Meier-Stauffer et al. 1996) as Aneurinibacillus thermoaerophilus comb. nov., and emended
descriptions of A. aneurinilyticus corrig., A. migulanus, and A. thermoaerophilus. Int J Syst
Bacterial 47, 808-817.
Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P. & other authors (1995).
Paenibacillus (formerly Bacillus) gordonae (Pichinoty et al. 1986) Ash eta/. 1994 is a later
subjective synonym of Paenibacillus (formerly Bacillus) validus (Nakamura 1984) Ash et a/.
1994: emended description of P. validus. Int J Syst Bacterio/45, 661-669.
Heyrman, J. & Swings, J. (2001). 16S rDNA sequence analysis of bacterial isolates from
biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain). Syst
Appl Microbio/24, 417-422.
Heyrman, J., Logan, N. A., Rodriguez-Diaz, M., Scheldeman, P., Lebbe, L., Swings, J.,
Heyndrickx, M. & DeVos, P. (2005a). Study of mural painting isolates, leading to the transfer
of 'Bacillus maroccanus' and 'Bacillus carotarum' to Bacillus simplex, emended description of
275
Bibliography
Bacillus simplex, re-examination of the strains previously attributed to 'Bacillus macroides' and
description of Bacillus muralis sp. nov. Int J Syst Evol Microbial 55, 119-131.
Heyrman, J., Rodriguez-Diaz, M., Devos, J., Felske, A., Logan, N. A. & DeVos, P. (2005b).
Bacillus arenosi sp. nov., Bacillus arvi sp. nov. and Bacillus humi sp. nov., isolated from soil. Int
J Syst Evol Microbial 55, 111-117.
Heyrman, J., Vanparys, B., Logan, N. A., Balcaen, A., Rodriguez-Diaz, M., Felske, A. & De
Vos, P. (2004). Bacillus nova/is sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus
bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst
Evol Microbia/54, 47-57.
Holben, W. E., Feris, K. P., Kettunen, A. & Apajalahti, J. H. (2004). GC fractionation
enhances microbial community diversity assessment and detection of minority populations of
bacteria by denaturing gradient gel electrophoresis. Appl Environ Microbio/70, 2263-2270.
Holmes, A. J., Tujula, N. A., Holley, M., Contos, A., James, J. M., Rogers, P. & Gillings, M.
R. (2001). Phylogenetic structure of unusual aquatic microbial formations in Nullarbor caves,
Australia. Environ Microbio/3, 256-264.
Huang, L. N., Zhou, H., Chen, Y.Q., Luo, S., Lan, C.Y., & Qu, L. H. (2002). Diversity and
structure of the archaeal community in the leachate of a full scale recirculating landfills as
examined by direct 16S rRNA gene sequence retrieval. FEMS Microbial Lett 214, 235-240.
Huang, L. N., Zhou, H., Chen, Y.Q., Luo, S., Lan, C.Y., & Qu, L. H. (2003). Characterization
of methanogenic archaea in the leachate of a closed municipal solid waste landfill. FEMS
Microbial Ecol 46, 171-177.
Huang, L. N., Zhou, H., Zhu, S., & Qu, L. H. (2004). Phylogenetic diversity ofbacteria in the
leachate of a full-scale recirculating landfill. FEMS Microbial Eco/50, 175-183.
Huang, L. N., Zhou, H., Zhu, S., & Qu, L. H .. (2005). Molecular phylogenetic diversity of
bacteria associated wit the leachate of a closed municipal solid waste landfill. FEMS Microbial
Lett 242, 297-303.
Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C. & Stetter, K. 0. (2002). A
new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417,
63-67.
276
Bibliography
Huber, R., Burggraf, S., Mayer, T., Barns, S. M., Rossnagel, P. & Stetter, K. 0. (1995).
Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis. Nature 376, 57-58.
Huber, R., Huber, H. & Stetter, K. 0. (2000). Towards the ecology of hyperthermophiles:
biotopes, new isolation strategies and novel metabolic properties. FEMS Microbial Rev 24, 615-
623.
Hubert, C., Shen, Y. & Voordouw, G. (1999). Composition of toluene-degrading microbial
communities from soil at different concentrations of toluene. Appl Environ Microbial 65, 3064-
3070.
Hugenholtz, P. (2002). Exploring prokaryotic diversity in the genomic era. Genome Bioi 3,
REVIEWS0003.
Hugenholtz, P., Goebel, B. M. & Pace, N. R. (1998b). Impact of culture-independent studies on
the emerging phylogenetic view of bacterial diversity. J Bacterio/180, 4765-4774.
Hugenholtz, P., Pitulle, C., Hershberger, K. L. & Pace, N. R. (1998a). Novel division level
bacterial diversity in a Yellowstone hot spring. J Bacterio/180, 366-376.
Hugenholtz, P., Tyson, G. W., Webb, R. I., Wagner, A. M. & Blackall, L. L. (2001).
Investigation of candidate division TM7, a recently recognized major lineage of the domain
Bacteria with no known pure-culture representatives. Appl Environ Microbial 67, 411-419.
Hungate, R. E. (1947). Studies on Cellulose Fermentation: III. The Culture and Isolation for
Cellulose-decomposing Bacteria from the Rumen of Cattle. J Bacteria/53, 631-645.
Hunter-Cevera, J. C. (1998). The value of microbial diversity. Curr Opin Microbio/1, 278-285.
lbekwe, A.M., & Kennedy, A. C. (1998). Phospholipid fatty acid profiles and carbon utilization
patterns for analysis of microbial community structure under field and greenhouse conditions.
FEMS Microbial Eco/26, 151-163.
Ishikawa, M., Ishizaki, S., Yamamoto, Y. & Yamasato, K. (2002). Paraliobacillus
ryukyuensis gen. nov., sp. nov., a new Gram-positive, slightly halophilic, extremely halotolerant,
facultative anaerobe isolated from a decomposing marine alga. J Gen Appl Microbial 48, 269-
279.
Ishikawa, M., Nakajima, K., Itamiya, Y., Furukawa, S., Yamamoto, Y. & Yamasato, K.
(2005). Halolactibacillus halophilus gen. nov., sp. nov. and Halolactibacillus miurensis sp. nov.,
277
Bibliography
halophilic and alkaliphilic marine lactic acid bacteria constituting a phylogenetic lineage in
Bacillus rRNA group 1. Int J Syst Eva! Microbia/55, 2427-2439.
Janssen, P. H., Schuhmann, A., Morschel, E. & Rainey, F. A. (1997). Novel anaerobic
ultramicrobacteria belonging to the Verrncomicrobiales lineage of bacterial descent isolated by
dilution culture from anoxic rice paddy soil. Appl Environ Microbio/63, 1382-1388.
Janssen, P. H., Yates, P. S., Grinton, B. E., Taylor, P. M. & Sait, M. (2002). Improved
culturability of soil bacteria and isolation in pure culture of novel members of the divisions
Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbial
68, 2391-2396.
Jetten, M.S., Wagner, M., Fuerst, J., van Loosdrecht, M., Kuenen, G. & Strous, M. (2001).
Microbiology and application of the anaerobic ammonium oxidation ('anammox') process. Curr
Opin Biotechno/12, 283-288.
Jiang, C. Y., Dai, X., Wang, B. J., Zhou, Y. G. & Liu, S. J. (2006). Roseomonas lacus sp. nov.,
isolated from freshwater lake sediment. Int J Syst Evol Microbia/56, 25-28.
Jones, A. L., Brown, J. M., Mishra, V., Perry, J.D., Steigerwalt, A. G. & Goodfellow, M.
(2004). Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and
phenol-contaminated soil. lnt J Syst Eva! Microbial 54, 407-411.
Jones, W. J., Nagle, D.P., Jr. & Whitman, W. B. (1987). Methanogens and the diversity of
archae bacteria. Microbial Rev 51, 135-177.
Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein
Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
Jurgens, G., Lindstrom, K. & Saano, A. (1997). Novel group within the kingdom
Crenarchaeota from boreal forest soil. Appl Environ Microbio/63, 803-805.
Kageyama, A., Morisaki, K., Omura, S. & Takahashi, Y. (2008). Arthrobacter oryzae sp. nov.
and Arthrobacter humicola sp. nov. Int J Syst Eva! Microbia/58, 53-56.
Kageyama, A., Takahashi, Y. & Omura, S. (2006). Microbacterium deminutum sp. nov.,
Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov. Int J Syst Evol
Microbial 56, 2113-2117.
278
Bibliography
Kageyama, A., Yazawa, K., Mukai, A., Kohara, T., Nishimura, K., Kroppenstedt, R. M. &
Mikami, Y. (2004). Nocardia araoensis sp. nov. and Nocardia pneumoniae sp. nov., isolated
from patients in Japan. Int J Syst Evol Microbia/54, 2025-2029.
Kageyama, A., Yazawa, K., Taniguchi, H., Chibana, H., Nishimura, K., Kroppenstedt, R.
M. & Mikami, Y. (2005). Nocardia concava sp. nov., isolated from Japanese patients. Int J Syst
Evol Microbia/55, 2081-2083.
Kampfer, P. (1994). Limits and possibilities of total fatty acid analysis for classification and
identification of Bacillus species. Syst Appl Microbio/11, 86-98.
Kampfer, P., Rossello-Mora, R., Falsen, E., Busse, H. J. & Tindall, B. J. (2006). Cohnella
thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as
Cohnella hongkongensis sp. nov. lnt J Syst Evol Microbial 56, 781-786.
Kane, M. D., Poulsen, L. K. & Stahl, D. A. (1993). Monitoring the enrichment and isolation of
sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from
environmentally derived 16S rRNA sequences. Appl Environ Microbia/59, 682-686.
Kanso, S. & Patel, B. K. (2003). Microvirga subterranea gen. nov., sp. nov., a moderate
thermophile from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbial 53,
401-406.
Kanso, S., Greene, A. C. & Patel, B. K. (2002). Bacillus subterraneus sp. nov., an iron- and
manganese-reducing bacterium from a deep subsurface Australian thermal aquifer. Int J Syst Evol
Microbia/52, 869-874.
Karl, D. M., Bird, D. F., Bjorkman, K., Houlihan, T., Shackelford, R. & Tupas, L. (1999).
Microorganisms in the accreted ice ofLake Vostok, Antarctica. Science 286, 2144-2147.
Karner, M. & Fuhrman, J. A. (1997). Determination of Active Marine Bacterioplankton: a
Comparison of Universal 16S rRNA Probes, Autoradiography, and Nucleoid Staining. Appl
Environ Microbio/63, 1208-1213.
Karner, M. B., DeLong, E. F. & Karl, D. M. (2001). Archaeal dominance in the mesopelagic
zone of the Pacific Ocean. Nature 409, 507-510.
Kashefi, K. & Lovley, D. R. (2003). Extending the upper temperature limit for life. Science 301,
934.
279
Bibliography
Keddie, R. M., Collins, M.D. & Jones, D. (1986). Genus Arthrobacter Conn & Dimmick 1947,
300AL. In Bergey's Manual of Systematic Bacteriology, Vol2, pp. 1288-1301. Edited by P. H. A.
Sneath, N. S. Mair, M. E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
Kelly, J. J., Haggblom, M., Tate III, R. L. (1999). Changes in soil microbial communities over
time resulting from one time application of zinc: a laboratory microcosm study. Soil Bioi
Biochem 31, 1455-1465.
Kim, H., Honda, D., Hanada, S., Kanamori, N., Shibata, S., Miyaki, T., Nakamura, K. &
Oyaizu, H. (2000). A deeply branched novel phylotype found in Japanese paddy soils.
Microbiology 146 ( Pt 9), 2309-2315.
Kim, S. B., Nedashkovskaya, 0. I., Mikhailov, V. V., Han, S. K., Kim, K. 0., Rhee, M.S. &
Bae, K. S. (2004). Kocuria marina sp. nov., a novel actinobacterium isolated from marine
sediment. Int J Syst Evol Microbia/54, 1617-1620.
Kim, Y. G., Choi, D. H., Hyun, S. & Cho, B. C. (2001a). Oceanobacillus profondus sp. nov.,
isolated from a deep-sea sediment core. Int J Syst Evol Microbia/51, 409-413.
Kim, Y. G., Hwang, C. Y., Yoo, K. W., Moon, H. T., Yoon, J. H. & Cho, B. C. (2001b).
Pelagibacillus goriensis gen. nov., sp. nov., a moderately halotolerant bacterium isolated from
coastal water off the east coast ofKorea. Int J Syst Evol Microbia/51, 1554-1560.
Kloos, W. E. & Schleifer, K. H. (1986). Genus Staphylococcus Rosenbach 1884, 18AL. In
Bergey's Manual of Systematic Bacteriology, Vol2, pp. 1105-1139. Edited by P. H. A. Sneath,
N. S. Mair, M. E. Sharpe., & J. G. Holt. Baltimore: Williams & Wilkins.
Knief, C., Lipski, A. & Dunfield, P. F. (2003). Diversity and activity of methanotrophic
bacteria in different upland soils. Appl Environ Microbio/69, 6703-6714.
Knietsch, A., Waschkowitz, T ., Bowien, S., Henne, A. & Daniel, R. (2003). Metagenomes of
complex microbial consortia derived from different soils as sources for novel genes conferring
formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbial Biotechnol
5, 46-56.
Ko, K. S., Oh, W. S., Lee, M. Y., Lee, J. H., Lee, H., Peck, K. R., Lee, N.Y. & Song, J. H.
(2006). Bacillus in/antis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with
neonatal sepsis. Int J Syst Evol Microbia/56, 2541-2544.
280
Bibliography
Kogure, K., Simidu, U. & Taga, N. (1979). A tentative direct microscopic method for counting
living marine bacteria. Can J Microbio/25, 415-420.
Konopka, A., Oliver, L. & Turco, R. F., Jr. (1998). The Use of Carbon Substrate Utilization
Patterns in Environmental and Ecological Microbiology. Microb Eco/35, 103-115.
Kotouckova, L., Schumann, P., Durnova, E., Sproer, C., Sedlacek, I., Neca, J., Zdrahal, Z.
& Nemec, M. (2004). Arthrobacter nitroguajacolicus sp. nov., a novel4-nitroguaiacol-degrading
actinobacterium. Int J Syst Evol Microbia/54, 773-777.
Krishnamurthi, S. & Chakrabarti, T. (2008). Proposal for transfer of Pelagibacillus goriensis
Kim et a/. 2007 to the genus Terribacillus as Terribacillus goriensis comb. nov. Int J Syst Evol
Microbial (in press).
Kroppenstedt, R. M., Mayilraj, S., Wink, J. M., Kallow, W., Schumann, P., Secondini, C. &
Stackebrandt, E. (2005). Eight new species of the genus Micromonospora, Micromonospora
citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp.
nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov.,
Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora
viridifaciens sp. nov. Syst Appl Microbio/28, 328-339.
Kruger, C. & Orr, F. M., Jr. (2003). No strings attached to 225m dollars sponsorship. Nature
422, 15.
Kruger, M., Meyerdierks, A., Glockner, F. 0. & other authors (2003). A conspicuous nickel
protein in microbial mats that oxidize methane anaerobically. Nature 426, 878-881.
Kuske, C. R., Barns, S. M. & Busch, J.D. (1997). Diverse uncultivated bacterial groups from
soils of the arid southwestern United States that are present in many geographic regions. Appl
Environ Microbio/63, 3614-3621.
Kwon, S. W., Kim, B. Y., Song, J., Weon, H. Y., Schumann, P., Tindall, B. J., Stackebrandt,
E. & Fritze, D. (2007). Sporosarcina lwreensis sp. nov. and Sporosarcina soli sp. nov., isolated
from soil in Korea. Int J Syst Evol Microbia/57, 1694-1698.
La Due, M. T., Satomi, M. & Venkateswaran, K. (2004). Bacillus odysseyi sp. nov., a round
spore-forming bacillus isolated from the Mars Odyssey spacecraft. Int J Syst Evol Microbia/54,
195-201.
281
Bibliography
Ladapo, J. A., & Barlaz, M.A (1997). Isolation and characterization of refuse methanogens. J
Appl Microbio/82, 751-758.
Laloui-Carpentier, W., Li, T., Vigneron, V., Mazeas, L. & Bouchez, T. (2006). Methanogenic
diversity and activity in municipal solid waste landfillleachates. Antonie Van Leeuwenhoek 89,
423-434.
Layton, A. C., Karanth, P. N., Lajoie, C. A., Meyers, A. J., Gregory, I. R., Stapleton, R. D.,
Taylor, D. E. & Sayler, G. S. (2000). Quantification of Hyphomicrobium populations in
activated sludge from an industrial wastewater treatment system as determined by 16S rRNA
analysis. Appl Environ Microbio/66, 1167-1174.
Le Roes, M. & Meyers, P.R. (2007). Actinomadura rudentiformis sp. nov., isolated from soil.
Int J Syst Evol Microbia/51, 45-50.
Lechner, S., Mayr, R., Francis, K. P., Pruss, B. M., Kaplan, T., Wiessner-Gunkel, E.,
Stewart, G. S. & Scherer, S. (1998). Bacillus weihenstephanensis sp. nov. is a new
psychrotolerant species of the Bacillus cereus group. Int J Syst Bacterio/48, 1373-1382.
Lee, D. H., Zo, Y. G. & Kim, S. J. (1996). Non-radioactive method to study genetic profiles of
natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ
Microbio/62, 3112-3120.
Lee, J. S., Lee, K. C. & Park, Y. H. (2006). Microbacterium koreense sp. nov., from sea water
in the South Sea ofKorea. Int J Syst Evol Microbia/56, 423-427.
Lee, S. W., Won, K., Lim, H. K., Kim, J. C., Choi, G. J. & Cho, K. Y. (2004). Screening for
novel lipolytic enzymes from uncultured soil microorganisms. Appl Microbial Biotechnol 65,
720-726.
Leedle, Z. A., & Hespell, B. R. 1980. Differential carbohydrate media and anaerobic replica
plating techniques in delineating carbohydrate-utilizing subgroups in rumen bacterial
populations. Appl Environ Microbio/39, 709-719.
Levy-Frebault, V. V. & Portaels, F. (1992). Proposed minimal standards for the genus
Mycobacterium and for description of new slowly growing Mycobacterium species. Int J Syst
Bacterial 42, 315-323.
282
Bibliography
Li, L., Kato, C., Horikoshi, K. (1999). Microbial diversity in sediments collected from the
deepest cold-sea area, the Japan Trench. Mar Biotechnol1, 391-400.
Liesack, W. & Stackebrandt, E. (1992). Occurrence of novel groups of the domain Bacteria as
revealed by analysis of genetic material isolated from an Australian terrestrial environment. J
Bacterio/174, 5072-5078.
Liles, M. R., Manske, B. F., Bintrim, S. B., Handelsman, J. & Goodman, R. M. (2003). A
census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl
Environ Microbiol69, 2684-2691.
Lim, J. M., Jeon, C. 0., Park, D. J., Xu, L. H., Jiang, C. L. & Kim, C. J. (2006).
Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China. Int J Syst Evol
Microbial 56, 2579-2582.
Lim, J. M., Jeon, C. 0., Song, S.M. & Kim, C. J. (2005). Pontibacillus chungwhensis gen.
nov., sp. nov., a moderately halophilic Gram-positive bacterium from a solar saltern m
Korea. Int J Syst Evol Microbio/55, 165-170.
Liu, W. T., Marsh, T. L., Cheng, H. & Forney, L. J. (1997). Characterization of microbial
diversity by determining terminal restriction fragment length polymorphisms of genes encoding
168 rRNA. Appl Environ Microbio/63, 4516-4522.
Lloyd-Jones, G. & Lau, P. C. (1998). A molecular view of microbial diversity in a dynamic
landfill in Quebec. FEMS Microbial Lett 162, 219-226.
Logan, A. N. (2005). International Committee on Systematics of Prokaryotes; Subcommittee on
the taxonomy of the genus Bacillus and related organisms: Minutes of the meeting, 30 July 2002,
Paris, France. Int J Syst Evol Microbial, 55, 977-979.
Logan, N. A., Forsyth, G., Lebbe, L. & other authors (2002). Polyphasic identification of
Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of
Brevibacillus invocatus sp. nov. Int J Syst Evol Microbia/52, 953-966.
Lu, J., Nogi, Y. & Takami, H. (2001). Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea
extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the lheya
Ridge. FEMS Microbial Lett 205, 291-297.
283
Bibliography
Ludwig, W., Bauer, S. H., Bauer, M., Held, I., Kirchhof, G., Schulze, R., Huber, I., Spring,
S., Hartmann, A. & Schleifer, K. H. (1997). Detection and in situ identification of
representatives of a widely distributed new bacterial phylum. FEMS Microbial Lett 153, 181-190.
Ludwig, W., Strunk, 0., Klugbauer, S., Klugbauer, N., Weizenegger, M., Neumaier, J.,
Bachleitner, M. & Schleifer, K. H. (1998). Bacterial phylogeny based on comparative sequence
analysis. Electrophoresis 19, 554-568.
MacKenzie, S. L. (1987). Gas chromatographic analysis of ammo acids as the N
heptafluorobutyryl isobutyl esters. J Assoc of Anal Chern 70, 151-160.
Madrid, V. M., Aller, J. Y., Aller, R. C., Christoserdov, A. Y. (2001). High prokaryote
diversity and analysis of community structure in mobile and mud deposits off French Guiana:
identification of two candidate bacterial divisions. FEMS Microbial Eco/31, 197-209.
Magee, J. (1993). Whole-organism fmgerprinting. In Handbook of new bacterial systematics, pp.
383-427. Edited by M.A. G. 0. D. Goodfellow. London: Academic Press Ltd.
Magli, A., Rainey, F. A. & Leisinger, T. (1995). Acetogenesis from Dichloromethane by a
Two-Component Mixed Culture Comprising a Novel Bacterium. Appl Environ Microbial 61,
2943-2949.
Maiden, M. C., Bygraves, J. A., Feil, E. & other authors (1998). Multilocus sequence typing:
a portable approach to the identification of clones within populations of pathogenic
microorganisms. Proc Nat/ Acad Sci USA 95, 3140-3145.
Majernik, A., Gottschalk, G. & Daniel, R. (2001). Screening of environmental DNA libraries
for the presence of genes conferring Na(+) Li(+)/H(+) antiporter activity on Escherichia coli:
characterization of the recovered genes and the corresponding gene products. J Bacterial 183,
6645-6653.
Marilley, L., Hartwig, U. A. & Aragno, M. (1999). Influence of an Elevated Atmospheric C02
Content on Soil and Rhizosphere Bacterial Communities beneath Lolium perenne and Trifolium
repens under Field Conditions. Microb Eco/38, 39-49.
Marsh, T. L. (1999). Terminal restriction fragment length polymorphism (T-RFLP): an
emerging method for characterizing diversity among homologous populations of amplification
products. Curr Opin Microbio/2, 323-327.
284
Bibliography
Martinez-Murcia, A. J., Benlloch, S. & Collins, M.D. (1992). Phylogenetic interrelationships
of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA
sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacterial 42,
412-421.
Massol-Deya, A. A., Odelson, D. A., Hickey, R. F., Tiedje, J. M. (1995). Bacterial community
fingerprinting of amplified 16S and 16S-23S ribosomal DNA gene sequences and restriction
endonuclease analysis (ARDRA). In Molecular Microbial Ecology Manual, pp. 3.3.2.1-3.3.2.8.
Edited by A. D. L. Akkermans, van Elsas, J. D., de-Bruijn, F. J. Boston: Kluwer Academic
publishing.
Mathrani, I. M., Boone, D. R., Mah, R. A., Fox, G. E. & Lau, P. P. (1988).
Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen. lnt
J Syst Bacterio/38, 139-142.
Mayilraj, S., Suresh, K., Kroppenstedt, R. M. & Saini, H. S. (2006). Dietzia kunjamensis sp.
nov., isolated from the Indian Himalayas. Int J Syst Evol Microbia/56, 1667-1671.
Mayr, R., Busse, H. J., Worliczek, H. L., Ehling-Schulz, M. & Scherer, S. (2006).
Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and
Ornithinibacillus californiensis sp. nov. Int J Syst Evol Microbia/56, 1383-1389.
McCaig, A. E., Glover, L. A. & Prosser, J. I. (1999). Molecular analysis of bacterial
community structure and diversity in unimproved and improved upland grass pastures. Appl
Environ Microbio/65, 1721-1730.
McCliment, E. A., Voglesonger, K. M., 0' Day, P. A., Dunn, E. E., Holloway, J. R. & Cary,
S. C. (2006). Colonization of nascent, deep-sea hydrothermal vents by a novel Archaeal and
Nanoarchaeal assemblage. Environ Microbio/8, 114-125.
Mcinerney, M. J., Bryant, M. P., Respell, R. B., & Costerton, J. W. (1979). Anaerobic
bacterium that degrades fatty acids in syntrophic association with methanogens. Arch Microbial
122, 129-135.
McMinn, E. J., Alderson, G., Dodson, H. I., Goodfellow, M. & Ward, A. C. (2000). Genomic
and phenomic differentiation of Rhodococcus equi and related strains. Antonie van Leeuwenhoek
78,31-340.
285
Bibliography
Mori, K., Sparling, R., Hatsu, M. & Takamizawa, K. (2003). Quantification and diversity of
the archaeal community in a landfill site. Can J Microbio/49, 28-36.
Moturi, M. C. Z., Rawat, M., & Subramanian, V. (2004a). Distribution and sequential
extraction of heavy metals in solid waste from the industrial belt of Delhi, India. Environ Manit
Assess 95, 185-199.
Moturi, M. C. Z., Rawat, M., & Subramanian, V. (2004b). Distribution and partitioning of
phosphorus in solid waste and sediments from drainage canals in the industrial belt of Delhi,
India. Chemosphere 60,237-244.
Miiyzer, G. & Smalla, K. (1998). Application of denaturing gradient gel electrophoresis
(DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van
Leeuwenhoek 73, 127-141.
Miiyzer, G. (1999). DGGE/TGGE a method for identifying genes from natural ecosystems. Curr
Opin Microbio/2, 317-322.
Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. (1993). Profiling of complex microbial
populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction
amplified genes coding for 16S rRNA. Appl Environ Microbia/59, 695-700.
Myllykallio, H., Lopez, P., Lopez-Garcia, P., Heilig, R., Saurin, W., Zivanovic, Y., Philippe,
H. & Forterre, P. (2000). Bacterial mode of replication with eukaryotic-like machinery in a
hyperthermophilic archaean. Science 288, 2212-2215.
Nagel, M. & Andreesen, J. R. (1991). Bacillus niacini sp. nov., a nicotinate-metabolizing
mesophile isolated from soil. Int J Syst Bacterio/41, 134-139.
Nakamura, L. K. (1987). Deoxyribonucleic acid relatedness of lactose-positive Bacillus subtilis
strains and Bacillus amyloliquefaciens. Int J Syst Evol Microbio/37, 444-445.
Nakamura, L. K. (1989). Taxonomic relationship of black-pigmented Bacillus subtilis strains
and a proposal for Bacillus atrophaeus sp. nov. Int J Syst Evol Microbio/39, 295-300.
Nakamura, L. K. (1998). Bacillus pseudomycoides sp. nov. Int J Syst Bacterio/48, 1031-1035.
Nakamura, L. K., Roberts, M. S. & Cohan, F. M. (1999). Relationship of Bacillus subtilis
clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp.
nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacterio/49, 1211-1215.
286
Bibliography
Nakamura, L. K., Shida, 0., Takagi, H. & Komagata, K. (2002). Bacillus pycnus sp. nov. and
Bacillus neidei sp. nov., round-spored bacteria from soil. Int J Syst Evol Microbia/52, 501-505.
Nesterenko, 0. A., Nogina, T. M., Kasumova, S. A., Kvasnikov, E. I. & Batrakov, S. G.
(1982). Rhodococcus luteus nom. nov. and Rhodococcus maris nom. nov. Int J Syst Bacterio/32,
1-14.
Niu, L., Song, L. & Dong, X. (2008). Proteiniborus ethanoligenes gen. nov., sp. nov., an
anaerobic protein-utilizing bacterium. Int J Syst Evol Microbia/58, 12-16.
Noguchi, H., Uchino, M., Shida, 0., Takano, K., Nakamura, L. K. & Komagata, K. (2004).
Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium
isolated from Vietnamese fish sauce. lnt J Syst Evol Microbia/54, 2117-2120.
Nold, S. C., Kopczynski, E. D. & Ward, D. M. (1996). Cultivation of aerobic
chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat.
Appl Environ Microbio/62, 3917-3921.
Nozhevnikova, A. N., Lebedev, V. S. and Lifshitz, A. b. (1992). Microbiological processes
occurring in landfills. Proceedings of International Symposium on Anaerobic Digestion of Solid
Waste pp. 303-312. Venice, Italy.
Nunes, I., Tiago, I., Pires, A. L., da Costa, M. S. & Verissimo, A. (2006). Paucisalibacillus
globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil. Int J Syst Evol
Microbia/56, 1841-1845.
Nusslein, K. & Tiedje, J. M. (1999). Soil bacterial community shift correlated with change from
forest to pasture vegetation in a tropical soil. Appl Environ Microbial 65, 3622-3626.
Ohkuma, M. & Kudo, T. (1996). Phylogenetic diversity of the intestinal bacterial community in
the termite Reticulitermes speratus. Appl Environ Microbio/62, 461-468.
Ollivier, B., Fardeau, M. L., Cayol, J. L., Magot, M., Patel, B. K., Prensier, G. & Garcia, J.
L. (1998). Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well.
Int J Syst Bacterial 48 Pt 3, 821-828.
Olsen, G. J., Woese, C. R. & Overbeek, R. (1994). The winds of (evolutionary) change:
breathing new life into microbiology. J Bacterio/116, 1-6.
287
Bibliography
Oremland, R. S. & Polcin, S. (1982). Methanogenesis and Sulfate Reduction: Competitive and
Noncompetitive Substrates in Estuarine Sediments. Appl Environ Microbio/44, 1270-1276.
Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. (2001).
Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis.
Science 293, 484-487.
Osborn, A.M., Moore, E. R. & Timmis, K. N. (2000). An evaluation of terminal-restriction
fragment length polymorphism (T -RFLP) analysis for the study of microbial community
structure and dynamics. Environ Microbio/2, 39-50.
Osman, S., Satomi, M. & Venkateswaran, K. (2006). Paenibacillus pasadenensis sp. nov. and
Paenibacillus barengoltzii sp. nov., isolated from a spacecraft assembly facility. Int J Syst Evol
Microbia/56, 1509-1514.
Pace, N. R. (1996). New perspective on the natural microbial world: molecular microbial
ecology. ASM News, 463-470.
Pace, N. R. (1997). A molecular view of microbial diversity and the biosphere. Science 276, 734-
740.
Pace, N. R. (1999). Microbial ecology and diversity. ASM News, 328-333.
Pace, N. R., Stahl, D. A., Lane D. J. & Olsen G. J. (1986). The analysis of natural microbial
populations by ribosomal RNA sequences. Advances in microbial ecology 9, 1-55.
Palmisano, A. C., Maruscik, D.A., & Schwab. (1993). Analysis of Microbial DNA from fuel
oil-contaminated and non-contaminated Soil. J Gen Microbio/139, 387-391.
Palmisano, A.C., Maruscik, D.A. and Schwab, B.S. (1993). Enumeration of fermentative and
hydrolytic microorganisms from three sanitary landfills. J Gen Microbio/139, 387-391.
Palmisano, M. M., Nakamura, L. K., Duncan, K. E., !stock, C. A. & Cohan, F. M. (2001).
Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the
Sonoran Desert, Arizona. Int J Syst Evol Microbia/51, 1671-1679.
Park, H. Y., Kim, K. K., Jin, L. & Lee, S. T. (2006). Microbacterium paludicola sp. nov., a
novel xylanolytic bacterium isolated from swamp forest. Int J Syst Evol Microbia/56, 535-539.
288
Bibliography
Park, M. J., Kim, H. B., An, D. S., Yang, H. C., Oh, S. T., Chung, H. J. & Yang, D. C.
(2007). Paenibacillus soli sp. nov., a xylanolytic bacterium isolated from soil. Int J Syst Evol
Microbia/51, 146-150.
Parkes, A. J., & Senior, E. (1988). Multistage chemostats and other models for studying anoxic
ecosystems. In Handbook of laboratory model systems for microbial ecosystems, pp. 51-71.
Edited by J. W. T. Wimpenny. Boca Raton: CRC Press.
Parshina, S. N., Sipma, J., Nakashimada, Y., Henstra, A. M., Smidt, H., Lysenko, A. M.,
Lens, P. N., Lettinga, G. & Starns, A. J. (2005). Desulfotomaculum carboxydivorans sp. nov., a
novel sulfate-reducing bacterium capable of growth at 100% CO. Int J Syst Evol Microbia/55,
2159-2165.
Peters, S., Koschinsky, S., Schwieger, F. & Tebbe, C. C. (2000). Succession of microbial
communities during hot composting as detected by PeR-single-strand-conformation
polymorphism-based genetic profiles of small-subunit rRNA genes. Appl Environ Microbial 66,
930-936.
Pettersson, B., de Silva, S. K., Uhlen, M. & Priest, F. G. (2000). Bacillus siralis sp. nov., a
novel species from silage with a higher order structural attribute in the 16S rRNA genes. Int J
Syst Evol Microbia/50, 2181-2187.
Pettersson, B., Lembke, F., Hammer, P., Stackebrandt, E. & Priest, F. G. (1996). Bacillus
sporothermodurans, a new species producing highly heat-resistant endospores. Int J Syst
Bacterio/46, 759-764.
Pohland, F. G., Harper, S.R, Chang, K-C., Pertien, J.T., & Chiao, E.S.K. (1985). Leachate
generation and control at landfill disposal sites. Wat poll res} Can 20, 10-24.
Poschner, J., Kroppenstedt, R. M., Fischer, A., Stackebrandt, E (1985). DNA-DNA
reassociation and chemotaxonomic studies on Actinomadura, Microbispora, Microtetraspora,
Micropolyspora and Nocardiopsis. Syst Appl Microbio/6, 264-270.
Pourcher, A. M., Sutra, L., Hebe, I., Moguedet, G., Bollet, C., Smoneau, P., & Gardan, L.
(2001). Enumeration and characterization of cellulolytic bacteria from refuse of a landfill. FEMS
Microbial Eco/34, 229-241.
289
Bibliography
Precigou, S., Goulas, P. & Duran, R. (2001). Rapid and specific identification of nitrile
hydratases (NHase )-encoding genes in soil samples by polymerase chain reaction. FEMS
Microbial Lett 204, 155-161.
Qian, X., & Barlaz, M.A. (1996). Enumeration of anaerobic refuse decomposing
microorganisms on refuse constituents. Waste Manag Res 14, 151-161.
Quaiser, A., Ochsenreiter, T., Klenk, H. P., Kletzin, A., Treusch, A. H., Meurer, G., Eck, J.,
Sensen, C. W. & Schleper, C. (2002). First insight into the genome of an uncultivated
crenarchaeote from soil. Environ Microbial 4, 603-611.
Quaiser, A., Ochsenreiter, T., Lanz, C., Schuster, S.C., Treusch, A. H., Eck, J. & Schleper,
C. (2003). Acidobacteria form a coherent but highly diverse group within the bacterial domain:
evidence from environmental genomics. Mol Microbia/50, 563-575.
Quintana, E. T., Trujillo, M. E. & Goodfellow, M. (2003). Actinomadura mexicana sp. nov.
and Actinomadura meyerii sp. nov., two novel soil sporoactinomycetes. Syst Appl Microbio/26,
511-517.
Radajewski, S., lneson, P., Parekh, N. R. & Murrell, J. C. (2000). Stable-isotope probing as a
tool in microbial ecology. Nature 403, 646-649.
Rainey, F. A., Burghardt, J., Kroppenstedt, R. M., Klatte, S. &Stackebrandt, E. (1995).
Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the
evolutionary origins of the genus Nocardia from within the radiation of Rhodococcus species.
Microbiology 141, 523-528.
Rainey, F. A., Klatte, S., Kroppenstedt, R. M. & Stackebrandt, E. (1995). Dietzia, a new
genus including Dietzia maris comb. nov., formerly Rhodococcus maris. Int J Syst Bacterial 45,
32-36.
Ranjard, L., Poly, F. & Nazaret, S. (2000). Monitoring complex bacterial communities using
culture-independent molecular techniques: application to soil environment. Res Microbial 151,
167-177.
Rappe, M. S. & Giovannoni, S. J. (2003). The uncultured microbial majority. Annu Rev
Microbia/57, 369-394.
290
Bibliography
Rappe, M. S., Connon, S. A., V ergin, K. L. & Giovannoni, S. J. (2002). Cultivation of the
ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630-633.
Raskin, L., Rittmann, B. E. & Stahl, D. A. (1996). Competition and Coexistence of Sulfate
Reducing and Methanogenic Populations in Anaerobic Biofilms. Appl Environ Microbial 62,
3847-3857.
Rawat, M., Singh, U. K., Mishra, A. K., Subramanian, V. (2008). Methane emission and
heavy metals quantification from selected landfill areas in India. Environ Manit Assess 137, 67-
74.
Reddy, G. S., Matsumoto, G. I. & Shivaji, S. (2003a). Sporosarcina macmurdoensis sp. nov.,
from a cyanobacterial mat sample from a pond in the McMurdo Dry Valleys, Antarctica. Int J
Syst Eva/ Microbia/53, 1363-1367.
Reddy, G. S., Prakash, J. S., Prabahar, V., Matsumoto, G. I., Stackebrandt, E. & Shivaji, S.
(2003b). Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from
an Antarctic cyanobacterial mat sample. Int J Syst Eva/ Microbial 53, 183-187.
Ren, P. G. & Zhou, P. J. (2005a). Tenuibacillus multivorans gen. nov., sp. nov., a moderately
halophilic bacterium isolated from saline soil in Xin-Jiang, China. Jnt J Syst Evol Microbial 55,
95-99.
Ren, P. G. & Zhou, P. J. (2005b). Salinibacillus aidingensis gen. nov., sp. nov. and
Salinibacillus kushneri sp. nov., moderately halophilic bacteria isolated from a neutral saline lake
in Xin-Jiang, China. Int J Syst Evol Microbia/55, 949-953.
Rheims, H., Fruhling, A., Schumann, P., Rohde, M. & Stackebrandt, E. (1999). Bacillus
silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall. Int J
Syst Bacterio/49, 795-802.
Rheims, H., Rainey F. A., Stackebrandt, E. (1996). A molecular approach to search for
diversity among bacteria in the environment. J Ind Microbio/11, 159-169.
Riegel, P., Creti, R., Mattei, R., Nieri, A. & von Hunolstein, C. (2006). Isolation of
Corynebacterium tuscaniae sp. nov. from blood cultures of a patient with endocarditis. J Clin
Microbio/44, 307-312.
291
Bibliography
Riesenfeld, C. S., Goodman, R. M. & Handelsman, J. (2004). Uncultured soil bacteria are a
reservoir of new antibiotic resistance genes. Environ Microbio/6, 981-989.
Ribs, J. D., Brenner, D. J., Weaver, R. E., Steigerwalt, A. G., Hollis, D. G. & Yu, V. L.
(1993). Roseomonas, a new genus associated with bacteraemia and other human infections. J
Clin Microbio/31, 3275-3283.
Rivas, R., Trujillo, M. E., Sanchez, M., Mateos, P. F., Martinez-Molina, E. & Velazquez, E.
(2004). Microbacterium ulmi sp. nov., a xylanolytic, phosphate-solubilizing bacterium isolated
from sawdust of Ulmus nigra. Int J Syst Evol Microbia/54, 513-517.
Roberts, M. S. & Cohan, F. M. (1995). Recombination and migration rates in natural
populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49, 1081-1094.
Roberts, M. S., Nakamura, L. K. & Cohan, F. M. (1994). Bacillus mojavensis sp. nov.,
distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and
differences in fatty acid composition. Int J Syst Bacterio/44, 256-264.
Roberts, M. S., Nakamura, L. K. & Cohan, F. M. (1996). Bacillus vallismortis sp. nov., a
close relative of Bacillus subtilis, isolated from soil in Death Valley, California. Int J Syst
Bacterio/46, 470-475.
Robertson, C. E., Harris, J. K., Spear, J. R. & Pace, N. R. (2005). Phylogenetic diversity and
ecology of environmental archaea. Curr Opin Microbio/8, 638-642.
Rodhe, H. (1990). A Comparison ofthe Contribution ofVarious Gases to the Greenhouse Effect.
Science 248, 1217-1219.
Rondon, M. R., August, P.R., Bettermann, A. D. & other authors (2000). Cloning the soil
metagenome: a strategy for accessing the genetic and functional diversity of uncultured
microorganisms. Appl Environ Microbial 66, 2541-254 7.
Rondon, M. R., Goodman, R. M. & Handelsman, J. (1999). The Earth's bounty: assessing and
accessing soil microbial diversity. Trends Biotechno/11, 403-409.
Rossello-Mora, R. & Amann, R. (2001). The species concept for prokaryotes. FEMS Microbial
Rev 25, 39-67.
292
Bibliography
Rossello-Mora, R. A., Lalucat, J., Dott, W. & Kampfer, P. (1994). Biochemical and
chemotaxonomic characterization of Pseudomonas stutzeri genomovars. J Appl Bacterial 76,
226-233.
Roux, V. & Raoult, D. (2004). Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp.
nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Eva/
Microbial 54, 1049-1054.
Ruimy, R., Riegel, P., Boiron, P., Monteil, H. & Christen, R. (1995). Phylogeny of the genus
Corynebacterium deduced from analyses of small-subunit ribosomal DNA sequences. Int J Syst
Bacterio/45, 740-746.
Rusch, D. B., Halpern, A. L., Sutton, G. & other authors (2007). The Sorcerer II Global
Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLOS Bioi 5,
e77.
Rushbrook, P. E. (1983). Estimating waste management costs for pre-design and preliminary
design purposes AERE R11406, HSMO, London, UK.
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing
phylogenetic trees. Mol Bio Evo/4, 406-425.
Satomi, M., La Due, M. T. & Venkateswaran, K. (2006). Bacillus safensis sp. nov., isolated
from spacecraft and assembly-facility surfaces. Int J Syst Eva/ Microbia/56, 1735-1740.
Scheldeman, P., Goossens, K., Rodriguez-Diaz, M., Pil, A., Goris, J., Herman, L., De Vos,
P., Logan, N. A. & Heyndrickx, M. (2004). Paenibacillus lactis sp. nov., isolated from raw and
heat-treated milk. Int J Syst Eva/ Microbia/54, 885-891.
Scheldeman, P., Pil, A., Herman, L., De Vos, P. & Heyndrickx, M. (2005). Incidence and
diversity of potentially highly heat-resistant spores isolated at dairy farms. Appl Environ
Microbio/71, 1480-1494.
Schlegel, H. G. (1999). Halle: Deutsche Akademie der Naturforscher Leopoldina.
Schlegel, H. G., & Kohler, W. (1999). Bacteriology paved the way to cell biology: a historical
account. In Biology of the prokaryotes. Edited by J. W. Lengeler, Drews, G., & Schlegel, H. G.
Stuttgart: Thieme.
293
Bibliography
Schlegel, L., Grimont, F., Ageron, E., Grimont, P. A. & Bouvet, A. (2003). Reappraisal of the
taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species:
description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp.
macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov. Int J Syst Evol
Microbia/53, 631-645.
Schlegel, L., Grimont, F., Collins, M.D., Regnault, B., Grimont, P. A. & Bouvet, A. (2000).
Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and
Streptococcus infantarius subsp. coli subsp. nov., isolated from humans and food. Int J Syst Evol
Microbia/50, 1425-1434.
Schleifer, K. H. & Kandler, 0. (1972). Peptidoglycan types of bacterial cell walls and their
taxonomic implications. Bacterial Rev 36, 407-477.
Schleifer, K. H. (1985). Analysis of the chemical composition and primary structure of murein.
Methods Microbio/18, 123-156.
Schleifer, K. H. (2004). Microbial diversity: facts, problems and prospects. Syst Appl Microbial
27, 3-9.
Schlesner, H., Lawson, P. A., Collins, M. D., Weiss, N., Wehmeyer, U., Volker, H. &
Thomm, M. (2001). Filobacillus milensis gen. nov., sp. nov., a new halophilic spore-forming
bacterium with Om-D-Glu-type peptidoglycan. Int J Syst Evol Microbia/51, 425-431.
Schmalenberger, A., Schwieger, F. & Tebbe, C. C. (2001). Effect of primers hybridizing to
different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based
microbial community analyses and genetic profiling. Appl Environ Microbio/61, 3557-3563.
Schmeisser, C., Stockigt, C., Raasch, C. & other authors (2003). Metagenome survey of
biofilms in drinking-water networks. Appl Environ Microbiol69, 7298-7309.
Scholten, J. C., Joye, S. B., Hollibaugh, J. T. & Murrell, J. C. (2005). Molecular analysis of
the sulfate reducing and archaeal community in a meromictic soda lake (Mono Lake, California)
by targeting 16S rRNA, mcrA, apsA, and dsrAB genes. Microb Eco/50, 29-39.
Schramm, A., Larsen, L. H., Revsbech, N. P., Ramsing, N. B., Amann, R. & Schleifer, K. H.
(1996). Structure and function of a nitrifying biofilm as determined by in situ hybridization and
the use of microelectrodes. Appl Environ Microbial 62, 4641-464 7.
294
Bibliography
Schumann, P., Rainey, F. A., Burghardt, J., Stackebrandt, E. & Weiss, N. (1999).
Reclassification of Brevibacterium oxydans (Chatelain and Second 1966) as Microbacterium
oxydans comb. nov. Int J Syst Bacterio/49, 175-177.
Schut, F., de Vries, E. J., Gottschal, J. C., Robertson, B. R., Harder, W., Prins, R. A. &
Button, D. K. (1993). Isolation of Typical Marine Bacteria by Dilution Culture: Growth,
Maintenance, and Characteristics of Isolates under Laboratory Conditions. Appl Environ
Microbia/59, 2150-2160.
Schwieger, F. & Tebbe, C. C. (1998). A new approach to utilize PCR-single-strand
conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl
Environ Microbio/64, 4870-4876.
Segers, P., Vancanneyt, M., Pot, B., Torck, U., Hoste, B., Dewettinck, D., Falsen, E.,
Kersters, K. & De Vos, P. (1994). Classification of Pseudomonas diminuta Leifson and Hugh
1954 and Pseudomonas vesicularis Busing, Doll, and Freytag 1953 in Brevundimonas gen. nov.
as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively.
Int J Syst Bacterio/44, 499-510.
Seow, K. T., Meurer, G., Gerlitz, M., Wendt-Pienkowski, E., Hutchinson, C. R. & Davies, J.
(1997). A study of iterative type II polyketide synthases, using bacterial genes cloned from soil
DNA: a means to access and use genes from uncultured microorganisms. J Bacterio/119, 7360-
7368.
Shen, Y., Stehmeier, L. G. & Voordouw, G. (1998). Identification of Hydrocarbon-Degrading
Bacteria in Soil by Reverse Sample Genome Probing. Appl Environ Microbio/64, 637-645.
Shen, Y., Stehmeier, L. G. & Voordouw, G. (1998). Identification of Hydrocarbon-Degrading
Bacteria in Soil by Reverse Sample Genome Probing. Appl Environ Microbio/64, 637-645.
Shida, 0., Takagi, H., Kadowaki, K. & Komagata, K. (1996). Proposal for two new genera,
Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int J Syst Bacterio/46, 939-946.
Shida, 0., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Transfer of
Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus,
Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibaci/lus and emended
description of the genus Paenibacillus. Int J Syst Bacterio/41, 289-298.
295
Bibliography
Shivaji, S., Chaturvedi, P., Suresh, K., Reddy, G. S., Dutt, C. B., Wainwright, M., Narlikar,
J. V. & Bhargava, P.M. (2006). Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus
stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for
collecting air samples from high altitudes. Int J Syst Evol Microbial 56, 1465-14 73.
Siciliano, S. D., Germida, J. J. (1998). Biolog analysis and fatty acid methyl ester profiles
indicate that Pseudomonad inoculants that promote phytoremediation alter the root-associated
microbial community of Bromus biebbersteinii. Soil Bioi Biochem 30, 1717-1723.
Sikorski, J., Rossello-Mora, R. A, & Lorenz, M. G (1999). Analysis of genotypic diversity and
relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and
multilocus enzyme electrophoresis. Syst Appl Microbio/22, 393-402.
Smit, E., Leeflang, P., Wernars, K. (1997). Detection of shifts in microbial community
structure and diversity in soil caused by copper contamination using amplified ribosomal DNA
restriction analysis. FEMS Microbial Eco/23, 249-261.
Spring, S., Ludwig, W., Marquez, M. C., Ventosa, A. & Schleifer, K. H. (1996). Halobacillus
gen. nov., with descriptions of Ha/obacillus litoralis sp. nov. and Halobacillus trueperi sp. nov.,
and transfer of Sporosarcina halophila to Ha/obacillus halophilus comb. nov. Int J Syst Bacterial
46, 492-496.
Stach, J. E. M., Bathe, S., Clapp, J. P., Bruns, R. G. (2001). PCR-SSCP comparison of 16S
rONA sequence diversity in soil DNA obtained using different isolation and purification
methods. FEMS Microbial Eco/36, 139-151.
Stackebrandt, E. & Ebers, J. (2005). Taxonomic parameters revisited: tarnished gold standards.
Microbial Today 33, 152-155.
Stackebrandt, E. W. & Woese, C. R. (1984). The phylogeny of prokaryotes. Microbial Sci 1,
117-122.
Stackebrandt, E., & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA
reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
Int J Syst Bacterio/44, 846-849.
Stackebrandt, E., & Liesack, W. (1993). Nucleic acids and classification. In Handbook of new
bacterial systematics, pp. 151-194. Edited by M. Goodfellow, & A. G. O'Donnell. London:
Academic Press Ltd.
296
Bibliography
Stackebrandt, E., Frederiksen, W., Garrity, G. M. & other authors (2002). Report of the ad
hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol
Microbio/52, 1043-1047.
Stackebrandt, E., Koch, C., Gvozdiak, 0. & Schumann, P. (1995). Taxonomic dissection of
the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov.,
Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacterio/45, 682-
692.
Stackebrandt, E., Liesack, W. & Goebel, B. M. (1993). Bacterial diversity in a soil sample
from a subtropical Australian environment as determined by 16S rONA analysis. F ASEB J 7,
232-236.
Staley, J. T. & Konopka, A. (1985). Measurement of in situ activities of non-photosynthetic
microorganisms in aquatic and terrestrial habitats. Annu Rev Microbio/39, 321-346.
Steele, L. P., Dlugokencky, E. J., Lang, P.M., Tans, P. P., Martin, R. C. & Masarie, K. A.
(1992). Slowing down of the global accumulation of atmospheric methane during the 1980's.
Nature 238,313-316.
Stephen, J. R., Chang, Y. J., Macnaughton, S. J., Kowalchuk, G. A., Leung, K. T.,
Flemming, C. A. & White, D. C. (1999). Effect of toxic metals on indigenous soil beta
subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity
by inoculated metal-resistant bacteria. Appl Environ Microbio/65, 95-101.
Stolz, A., Busse, H. J. & Kampfer, P. (2007). Pseudomonas knackmussii sp. nov. Int J Syst
Evol Microbio/51, 572-576.
Sulfita, M. J., Gerba, C.P., Ham, R.K., Palmisano, A.C., Rathje, W.L., & Robinson, J.A
(1992). The world's largest landfill-a multidisciplinary investigation. Environ Sc Techno/ 26,
1486-1495.
Suresh, K., Prabhagaran, S. R., Sengupta, S. & Shivaji, S. (2004). Bacillus indicus sp. nov.,
an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India. Int J Syst Evol
Microbio/54, 1369-1375.
Suzuki, M. T., Rappe, M. S., Haimberger, Z. W., Winfield, H., Adair, N., Strobel, J. &
Giovannoni, S. J. (1997). Bacterial diversity among small-subunit rRNA gene clones and
cellular isolates from the same seawater sample. Appl Environ Microbio/63, 983-989.
297
Bibliography
Takahashi, T., Satoh, I. & Kikuchi, N. (1999). Phylogenetic relationships of 38 taxa of the
genus Staphylococcus based on 168 rRNA gene sequence analysis. Int J Syst Bacterial 49, 725-
728.
Takai, K., Hirayama, H., Sakihama, Y., lnagaki, F., Yamato, Y. & Horikoshi, K. (2002).
Isolation and metabolic characteristics of previously uncultured members of the order Aquificales
in a subsurface gold mine. Appl Environ Microbio/68, 3046-3054.
Takai, K., Komatsu, T., Inagaki, F. & Horikoshi, K. (2001a). Distribution of archaea in a
black smoker chimney structure. Appl Environ Microbio/61, 3618-3629.
Takai, K., Moser, D.P., DeFlaun, M., Onstott, T. C. & Fredrickson, J. K. (2001b). Archaeal
diversity in waters from deep South African gold mines. Appl Environ ltficrobio/61, 5750-5760.
Takeda, M., Suzuki, I. & Koizumi, J. (2004). Ba/neomonas jlocculans gen. nov., sp. nov., a
hew cellulose-producing member of the alpha-2 subclass of Proteobacteria. Syst Appl Microbial
27, 139-145.
Takeuchi, M., & Hatano, K. (1998). Union of the genera Microbacterium Orla-Jensen and
Aureobacterium Collins et a/. in a redefined genus Microbacterium. Int J Syst Bacterial 48, 739-
747.
Taiibel, M., Kampfer, P., Buczolits, S., Lubitz, W. & Busse, H. J. (2003). Bacillus barbaricus
sp. nov., isolated from an experimental wall painting. Int J Syst Eva/ Microbia/53, 725-730.
Tchnobanoglous, G., Hilary, T. and Vigil, S. 1993. Integrated solid waste management:
Engineering principles and management issues. McGraw-Hill, New York.
Teather, R. M. (1982). Maintenance of Laboratory strains of obligately anaerobic rumen
bacteria. Appl Environ Microbio/44, 499-501.
Ten, L. N., Baek, S. H., Im, W. T., Larina, L. L., Lee, J. S., Oh, H. M. & Lee, S. T. (2007).
Bacillus pocheonensis sp. nov., a moderately halotolerant, aerobic bacterium isolated from soil of
a ginseng field. Int J Syst Eva/ Microbia/51, 2532-2537.
Ten, L. N., Baek, S. H., Im, W. T., Lee, M., Oh, H. W. & Lee, S. T. (2006). Paenibacillus
panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea.
Int J Syst Eva/ Microbia/56, 2677-2681.
298
Bibliography
Teske, A., Hinrichs, K. U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S. P., Sogin,
M. L. & Jannasch, H. W. (2002). Microbial diversity of hydrothermal sediments in the
Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbial
68, 1994-2007.
Theron, J. & Cloete, T. E. (2000). Molecular techniques for determining microbial diversity and
community structure in natural environments. Crit Rev Microbio/26, 37-57.
Thompson, B. and Zandi, I. (1975). Future of sanitary landfill. Journal of the Environmental
Engineering Division 101, 41-54.
Tiedje, J. M., Asuming-Brempong, S., Nusslein, K., Marsh, T. L. (1999). Opening the black
box of soil microbial diversity. Appl Soil Eco/13, 109-122.
Todorov, J. R., Chistoserdov, A. Y. & Aller, J. Y. (2000). Molecular analysis of microbial
communities in mobile deltaic muds of Southeastern Papua New Guinea. FEMS Microbial Ecol
33, 147-155.
Torsvik, V., Daae, F. L., Sandaa, R. A. & Ovreas, L. (1998). Novel techniques for analysing
microbial diversity in natural and perturbed environments. J Biotechno/64, 53-62.
Torsvik, V., Goksoyr, J. & Daae, F. L. (1990). High diversity in DNA of soil bacteria. Appl
Environ Microbia/56, 782-787.
Torsvik, V., Sorheim, R., Goksoyr, J. (1996). Total bacterial diversity in soil and sediment
communities- a review. J Ind Microbiol11, 170-178.
Tourova, T. P. & Antonov A. S. (1987). Identification of microorganisms by rapid DNA-DNA
hybridization. Methods Microbiol19, 333-335.
Triiper, H. G. (1999). How to name a prokaryote? Etymological considerations, proposals and
practical advice in prokaryote nomenclature. FEMS Microbial Rev 23, 231-249.
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M.,
Solovyev, V. V., Rubin, E. M., Rokhsar, D. S. & Banfield, J. F. (2004). Community structure
and metabolism through reconstruction of microbial genomes from the environment. Nature 428,
37-43.
Ueda, T., Suga, Y., Matsugushi T. (1995). Molecular phylogenetic analysis of a soil microbial
community in a soybean field. Eur J Soil Sci 46, 415-421.
299
Bibliography
Urbach, E., Vergin, K. L., Young, L., Morse, A., Giovannonni, S. J. (2001). Unusual
bacterioplankton community structure in ultra-oligotrophic Crater Lake. Limnology and
Oceanography 46, 557-572.
Uz, I., Rasche, M. E., Townsend, T., Ogram, A. V. & Lindner, A. S. (2003). Characterization
of methanogenic and methanotrophic assemblages in landfill samples. Proc Bioi Sci 270 Suppl
2, S202-205.
van Amstel, A. R., Swart, R. J., Kroll, M.S., Beck, J. E, Bouwman, A. E and van der Hoek,
K. W. (1993). Methane, the Other Greenhouse Gas', RIVMReport No 481507001, pp 108, The
Netherlands.
Van de Peer, Y. & De Wachter, R. (1997). Construction of evolutionary distance trees with
TREECON for Windows: accounting for variation in nucleotide substitution rate among sites.
Comput Appl Biosc 13,227-230.
Van Dyke, M. I. & McCarthy, A. J. (2002). Molecular biological detection and characterization
of Clostridium populations in municipal landfill sites. Appl Environ Microbiol68, 2049-2053.
Van Rossum, D., Schuurmans, F. P., Gillis, M., Muyotcha, A., Van Verseveld, H. W.,
Stouthamer, A. H. & Boogerd, F. C. (1995). Genetic and phenetic analyses of Bradyrhizobium
strains nodulating peanut (Arachis hypogaea L.) roots. Appl Environ Microbio/61, 1599-1609.
Vandamme, P., Pot, B., Gillis, M., de Vos, P., Kersters, K. & Swings, J. (1996). Polyphasic
taxonomy, a consensus approach to bacterial systematics. Microbial Rev 60,407-438.
Venter, J. C., Remington, K., Heidelberg, J. F. & other authors (2004). Environmental
genome shotgun sequencing ofthe Sargasso Sea. Science 304, 66-74.
Voget, S., Leggewie, C., Uesbeck, A., Raasch, C., Jaeger, K. E. & Streit, W. R. (2003).
Prospecting for novel biocatalysts in a soil metagenome. App/ Environ Microbio/69, 6235-6242.
von Wintzingerode, F., Goebel, U. B. & Stackebrandt, E. (1997). Determination of microbial
diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbial Rev
21, 213-229.
Voordouw, G., Shen, Y., Harrington, C. S., Telang, A. J., Jack, T. R. & Westlake, D. W.
(1993). Quantitative Reverse Sample Genome Probing of Microbial Communities and Its
Application to Oil Field Production Waters. Appl Environ Microbia/59, 4101-4114.
300
Bibliography
Voordouw, G., Voordouw, J. K., Jack, T. R., Foght, J., Fedorak, P.M. & Westlake, D. W.
(1992). Identification of Distinct Communities of Sulfate-Reducing Bacteria in Oil Fields by
Reverse Sample Genome Probing. Appl Environ Microbia/58, 3542-3552.
Voordouw, G., Voordouw, J. K., Karkhoff-Schweizer, R. R., Fedorak, P.M. & Westlake, D.
W. (1991). Reverse Sample Genome Probing, a New Technique for Identification of Bacteria in
Environmental Samples by DNA Hybridization, and Its Application to the Identification of
Sulfate-Reducing Bacteria in Oil Field Samples. Appl Environ Microbia/51, 3070-3078.
Waino, M., Tindall, B. J., Schumann, P. & Ingvorsen, K. (1999). Gracilibacillus gen. nov.,
with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus
dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus
Salibacillus gen. nov., as Salibacil/us sa/exigens comb. nov. Int J Syst Bacterio/49, 821-831.
Wang, G. Y., Graziani, E., Waters, B. & other authors (2000). Novel natural products from
soil DNA libraries in a streptomycete host. Org Lett 2, 2401-2404.
Wang, L. T., Lee, F. L., Tai, C. J. & Kuo, H. P. (2008). Bacillus velezensis is a later
heterotypic synonym of Bacillus amylo/iquefaciens. Int J Syst Evol Microbia/58, 671-675.
Wang, L. T., Lee, F. L., Tai, C. J., Yokota, A. & Kuo, H. P. (2007). Reclassification of
Bacillus axarquiensis Ruiz-Garcia et a/. 2005 and Bacillus malacitensis Ruiz-Garcia et a/. 2005
as later heterotypic synonyms of Bacillus mojavensis Roberts et a/. 1994. Int J Syst Evol
Microbia/51, 1663-1667.
Wang, L., Zhang, Y., Lu, Z., Shi, Y., Liu, Z., Maldonado, L. & Goodfellow, M. (2001).
Nocardia beijingensis sp. nov., a novel isolate from soil. Int J Syst Evol Microbial 51, 1783-
1788.
Wang, Y. S., Byrd, C.S., & Barlaz, M.A (1994). Anaerobic biodegradability of cellulose and
hemicellulose in excavated samples using a biochemical methane potential assay. J Ind Microbial
13, 147-153.
Ward, D. M., Bateson, M. M., Weller, R., RuftRoberts, A. L. (1992). Ribosomal RNA
analysis of microorganisms as they occur in nature. Advances in microbial ecology 12, 219-286.
Ward-Raynet N., Rainey F.A., Schlesner H., Stackebrandt E. (1995). Assignment of hitherto
unidentified 16S rDNA species to a main line of descent within the domain bacteria,
Microbiology 141, 3247-3250.
301
Bibliography
Wayne, L. G., Brenner, D. J., Colwell, R. R. & nine other authors (1987). International
Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of
approaches to bacterial systematics. Int J Syst Bacterio/31, 463-464.
Weller, R., Bateson, M. M., Heimbuch, B. K., Kopczynski, E. D. & Ward, D. M. (1992).
Uncultivated cyanobacteria, Chlorojlexus-like inhabitants, and spirochete-like inhabitants of a
hot spring microbial mat. Appl Environ Microbia/58, 3964-3969.
Welsh, J. & McClelland, M. (1990). Fingerprinting genomes using PCR with arbitrary primers.
Nucleic Acids Res 18,7213-7218.
Westlake, K., Archer, D.B. and Boone, D.R. (1995) Diversity of cellulolytic bacteria in
landfill. J Appl Bacterio/19, 73-78.
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. (1998). Prokaryotes: the unseen majority.
Proc Nat! Acad Sci US A 95, 6578-6583.
Widmer, F., Shaffer, B. T., Porteous, L. A. & Seidler, R. J. (1999). Analysis of nif H gene
pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain
range. Appl Environ Microbio/65, 374-380.
Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A. & Tingey, S. V. (1990). DNA
polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res
18,6531-6535.
Wilson E. 0. (1988). Biodiversity. Edited by Wilson E. 0. Washington, D.C: National Academy
Press.
Wise, M. G., McArthur, J. V. & Shimkets, L. J. (1997). Bacterial diversity of a Carolina bay
as determined by 16S rRNA gene analysis: confirmation of novel taxa. Appl Environ Microbial
63, 1505-1514.
Wise, M.G., McArthur, J.V., & Shimkets, L.J. (1999). Methanotroph diversity in landfill soil:
Isolation of Type I and Type II Methanotrophs whose presence was suggested by culture
independent 16S rRNA analysis. Appl Environ Microbio/65, 4887-4897.
Woese, C. R. & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: the
primary kingdoms. Proc Nat! Acad Sci US A 14, 5088-5090.
Woese, C. R. (1987). Bacterial evolution. Microbial Rev 51, 221-271.
302
Bibliography
Woese, C. R., Kandler, 0. & Wheelis, M. L. (1990). Towards a natural system of organisms:
proposal for the domains Archaea, Bacteria, and Eucarya. Proc Nat/ Acad Sci USA 81, 4576-
4579.
Yamamura, S., Yamashita, M., Fujimoto, N., Kuroda, M., Kashiwa, M., Sei, K., Fujita, M.
& Ike, M. (2007). Bacillus selenatarsenatis sp. nov., a selenate- and arsenate-reducing bacterium
isolated from the effluent drain of a glass-manufacturing plant. Int J Syst Evol Microbial 57,
1060-1064.
Yang, P., De Vos, P., Kersters, K., & Swings, J. (1993). Polyamine patterns as
chemotaxonomic markers for the genus Xanthomonas. Int J Syst Bacterial 43, 709-714.
Yassin, A. F. (2007). Corynebacterium ureicelerivorans sp. nov., a lipophilic bacterium isolated
from blood culture. Int J Syst Evol Microbia/51, 1200-1203.
Yassin, A. F., Rainey, F. A. & Steiner, U. (2001). Nocardia cyriacigeorgici sp. nov. Int J Syst
Eva/ Microbial 51, 1419-1423.
Yokota, A., Takeuchi, M., Sakane, T. & Weiss, N. (1993). Proposal of six new species in the
genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus
Aureobacterium as Aureobacterium esteraromaticum comb. nov. Int J Syst Bacterial 43, 555-
564.
Yoon, J. H., Kang, K. H. & Park, Y. H. (2002). Lentibacillus salicampi gen. nov., sp. nov., a
moderately halophilic bacterium isolated from a salt field in Korea. Int J Syst Evol Microbial 52,
2043-2048.
Yoon, J. H., Kang, S. J., Oh, H. W. & Oh, T. K. (2007). Roseomonas terrae sp. nov. Int JSyst
Evol Microbia/51, 2485-2488.
Yoon, J. H., Kang, S. S., Lee, K. C., Kho, Y. H., Choi, S. H., Kang, K. H. & Park, Y. H.
(2001a). Bacillus jeotgali sp. nov., isolated from jeotgal, Korean traditional fermented seafood.
Int J Syst Evol Microbia/51, 1087-1092.
Yoon, J. H., Kim, I. G., Kang, K. H., Oh, T. K. & Park, Y. H. (2003). Bacillus marisjlavi sp.
nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in
Korea. Int J Syst Evol Microbia/53, 1297-1303.
303
Bibliography
Yoon, J. H., Lee, C. H. & Oh, T. K. (2005a). Bacillus cibi sp. nov., isolated from jeotgal, a
traditional Korean fermented seafood. Int J Syst Evol Microbia/55, 733-736.
Yoon, J. H., Lee, CH., Yeo, S. H. & Oh, T. K. (2005b). Psychrobacter aquimaris sp. nov. and
Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea. Int J Syst
Evol Microbia/55, 1007-1013.
Yoon, J. H., Lee, K. C., Weiss, N., Kho, Y. H., Kang, K. H. & Park, Y. H. (2001b).
Sporosarcina aquimarina sp. nov., a bacterium isolated from seawater in Korea, and transfer of
Bacillus globisporus (Larkin and Stokes 1967), Bacillus psychrophilus (Nakamura 1984) and
Bacillus pasteurii (Chester 1898) to the genus Sporosarcina as Sporosarcina globispora comb.
nov., Sporosarcina psychrophila comb. nov. and Sporosarcina pasteurii comb. nov., and
emended description ofthe genus Sporosarcina. Int J Syst Evol Microbia/51, 1079-1086.
Young, L.Y., and Frazer, A.C. 1987. The fate of lignin and lignin derived compounds in
anaerobic environments. Geomicrobiology J 5, 261-293.
Yu, Z. & Moho, W. W. (2001). Bioaugmentation with resin-acid-degrading bacteria enhances
resin acid removal in sequencing batch reactors treating pulp mill effluents. Water Res 35, 883-
890.
Yumoto, I., Hirota, K., Yamaga, S., Nodasaka, Y., Kawasaki, T., Matsuyama, H. &
Nakajima, K. (2004). Bacillus asahii sp. nov., a novel bacterium isolated from soil with the
ability to deodorize the bad smell generated from short-chain fatty acids. Int J Syst Evol
Microbia/54, 1997-2001.
Zelles, L. (1999). Fatty acid patterns of phospholipids and lipopolysaccharides m the
chracterization of microbial communities in soil: a review. Bio Fertil Soils 29, 111-129.
Zhang, L., Xu, Z. & Patel, B. K. (2007). Bacillus decisifrondis sp. nov., isolated from soil
underlying decaying leaffoliage. Int J Syst Evol Microbia/51, 974-978.
Zhou, J., Davey, M. E., Figueras, J. B., Rivkina, E., Gilichinsky, D. & Tiedje, J. M. (1997).
Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.
Microbiology 143, 3913-3919.
Zinder, S. H. (1993). Physiological ecology of methanogens. In Methanogenesis, pp. 128-296.
Edited by J. G. Ferry. New York: Chapman and Hall, Inc.
304
Bibliography
Zumstein, E., Moletta, R. & Godon, J. J. (2000). Examination of two years of community
dynamics in an anaerobic bioreactor using fluorescence polymerase chain reaction (PCR) single
strand conformation polymorphism analysis. Environ Microbiol2, 69-78.
Zwart, G., Crump, B. C., Kamst-van Agterveld, M.P., Hagen, F., Han, S-K. (2002). Typical
freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes
and rivers. Aquatic microbial ecology 28, 141-155.
305