Sediment Microbiology WS 2010/11 - Uni Oldenburg file1 (c) Heribert Cypionka, Sediment Microbiology WS 2010/11 Sand Residues of algae and mussels Diatoms (brown) Sulfur FeS Microcolonies

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(c) Heribert Cypionka, www.pmbio.icbm.de

Sediment MicrobiologyWS 2010/11

Sand

Residues of algae andmussels

Diatoms (brown)

FeSSulfur

Microcolonies on a sediment flake from the Black Sea


Dates and topics

Practical course

Feb 28 – Mar 25

VL08 by Tim Engelhardt on IODP Leg 329 to the South Pacific Gyre(during practical course)

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Literature

Recommended books

- Brock. Biology of Microorganisms

- Ehrlich H. L. (1996) Geomicrobiology, Marcel Dekker, New York- Richard Y. Morita (1997) Bacteria in Oligotrophic Environments, Chapman & Hall- L.A. Meyer-Reil, M. Köster (1993) Mikrobiologie des Meeresbodens. Fischer- Daniel M. Alongi (1998) Coastal Ecosystem Processes. CRC Press- Susan M. Libes (1992) An Introduction to marine biogeochemistry, John Wiley- Tom Fenchel and Bland J. Finlay (1995) Ecology and Evolution in Anoxic Worlds,Oxford University Press

- Jame K. Fredrickson, Madilyn Fletcher (ed. 2001) Subsurface Microbiology andBiogeochemistry, Wiley

- Amy P.S., Haldeman D.L (ed., 1997) The Microbiology of the Terrestrial DeepSubsurface, Lewis Publ. New York

- Schulz HD, Zabel M (ed., 2000) Marine Geochemistry. Springer, Berlin


Literature online

Literature on the web

- www.pmbio.icbm.de/litlinks.htm (many journals!)

- isiknowledge.com (Web of Science - from University IP)

- scholar.google.com (Science at Google)

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Questions

Which types of Sediments are known?

What is the origin of sediment material?

How fast do sediments accumulate?

What are stromatolites and banded iron formations?

Which properties characterize sediments?

Which processes do occur within them?

How does the temperature change in the water column and in the sediment?

Which organisms form sediments?

How does new sediment form and old sediment vanish?


What are sediments

What are sediments?

latin: sedere = sit

sedimentum = what has settled down

• Particulate material accumulatedon the floor (cover 70 % of the earth'ssurface)

-- of lakes (lacustrine, limnic)

-- of rivers (riverine, fluvial)

-- of the sea (marine, tidal, coastal...)

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Origin of sediment material

What is the origin of sediment material?

-- aeolian = via the air

-- terrigenous = from the land

-- marine, autochthonous = from water column


Aeolian particles

Sahara sand coming across the alpes

Sahara sand above the Atlantic Ocean

Aeolian input to sediments

• Input of minerals, especially Fe as an important limiting factor

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Aeolian particles (2)

Ash eruptions from vulcanoes

Ash layer in Mediterranean sediment


Terrigenous sediments (2)

Lena river delta (Sibiria)

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Terrigenous sediments (3)

Peat in the backbarrier tidal flat of Spiekeroog, a former moor


Hang slip

Mediterranean sediment disturbed by hang slip

Disturbed sediment

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Marine primary production

Euphotic zone <= 200 m

Average production of the oceans:69 g C m -2 a-1

Note:1 chocolate bar per year and m 2

Marine primary production

marine: 146 109 t CO2 a-1

terrestrial:129 109 t CO2 a-1


Sedimentation

from Meyer-Reil

Only 0.1 to 1 % of the primary production reach the sediment. Often marine sediments grow only a few mm per 1000 years.

How fast do sediments accumulate?

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Microbial mats

Microbial mats

Farbstreifen-Sandwatt


Stromatolites

Stromatolite (pillow stone)

1.3 Ga

Ga = Giga years or billion years

Attention :

Engl. Billion = german Milliarde

Shark Bay, Australia

Undisturbed development in the absence of grazers

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Periodic changes between reducing and oxidizing conditions

Oxidation of Fe2+ to Fe3+ by (oxygenic?) photosynthesis,

Precipitation of oxidized iron salts

Banded Iron Formations (BIF's,gebänderte Eisensteine ) without microfossils, but showing isotope fractionation of 12C/13C as indicator for biological activity

Ditch, Oldenburg University

BIFs


Sediment properties

- TOC (total organic carbon): 0.2 - 2 %, sapropels up to 30 %- 50% carbonaceous Sediments (50 - 90 % TIC), less with silicates (Diatoms etc.)

- Water: porosity and permeability decreasing with depth and age- Varying particle size: mud, silt 63 - 200 µm, sand > 63 µm,- Varying density: ~1.5 to ~2.5 g/cm3

- Oxygen: upper mm to meters- Nitrate: slightly below oxygen- Ammonia as a product of degradation- Fe3+, Mn4+ -> Fe2+, Mn2+ with increasing depth- Sulfides- Methane hydrates

By which properties are sediments characterized?

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Tidal flat sediment


Carbon in Pacific sedimentCarbon in Pacific sediment

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Mediterranean sapropels

2407-2410

Meteor Leg M40-4 (1998)

Sapropel layers with up to 30 % organic carbon and increased microbial activity


Porosity

Porosity

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Tidal flat sediment (2)


Sediments at ODP Site 1231

Sediment slurries at ODP Site 1231

Oxidized iron and manganese as important electron accptors in low-carbon sediments

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Tidal Flats

Janssand

Neuharlingersieler Nacken

Gradients!

How can we detect processes inside the sediment column?


Sand-korn

Seawater

Diffusive boundary layer

Oxygen

Sediment

Oxygen profile Gradients

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Sulfate-methane interfacesSulfate-methane interfaces

ODP Site 1229

- Methanogenesis and sulfate reduction as dominant terminal processes

- Anaerobic methane oxidation as important process


Shallow versus deep biosphere

Engelen & Cypionka 2009

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Methane hydrates

Methane hydrate

(ODP Site 1230)

The most important reservoir of reduced carbon on earth


Sediment under pressure

Methane-bearing deep-sea sediment

1 bar pressure increase per 10 m water depth

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Sand at 50x magnification (stacked with PICOLAY)

A: Borkum

B: Puerto Rico

C: Mallorca


Sediment-forming organisms

- Carbonates

- Silicates

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Coccolithophorids

CoccolithophoridsCell size: 2-20 m m

Cell wall: CaCO3 coccoliths or scales

Chloroplasts: none, single thylakoid membrane

Photo-pigments: chlorophyll a & c, carotenoids

Reproduction: simple cell division, rarely sexual reproduction

Ecological roles: biflagellated, produce chalk deposits

Common genus: Emiliania

Emiliania huxleyi

Botanical Bulletin of Academia Sinica, Vol. 42, 2001

lat. coccus = round, gr. lithos = stone, gr. pherein = carry


Sediment-forming organisms

English Channel 1999 Chalk cliffs of Rügen

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ForaminiferaForaminifera

Mallorca Sand


Foraminifera

"Sand" at the Bight of Alcudia, Mallorca

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Foraminifera

lat. foramen = hole, lat. ferre = carry

Deutsch: Foraminiferen, Kammerlinge, Klasse der Rhizopoda (Wurzelfüßer)

Foraminifera

www.picolay.de


DiatomsDiatoms (Kieselalgen)

Benthic diatoms(tidal flat): pennate

Pelagic diatoms (Pacific): centric

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Diatoms (Kieselalgen)

Sediment off Namibia

(For cross- or parallel viewing)

(For red-green glasses)

Pictures for stereo-viewing produced by means of PICOLAY


RadiolariansRadiolarians (Strahlentierchen)

From Haeckel: "Kunstformen der Natur"

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TemperatureSediment Temperature

-> Seafloor mostly around 0 - 2 °C

-> Temperature increase with depth,depending on geological parameters

-> Hydrothermal vents with temperatures above 300 °C


Oxygen isotopes

-> Natural 18O:16O ratio about 1:500, determined in microfossils, that use O for shell formation (benthic and planktonic foraminifers, coccolithophorids)

-> Variation of delta 18O values controlled by temperature: preferred evaporationof light H2

16O molecules compared to heavier H218O.

-> Cold air carries relatively less H218O, which remains enriched in the water.

-> 1% increase of delta 18O corresponds to about 1 °C temperature decrease.

Oxygen isotope fractionation as a proxy for the ocean water temperature

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How old are sediments? Pangaea

Only 200 Mio. years before present there was only one continent, Pangaea

Online Biology Book

Mike Farabee

www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html


Eemian sapropel, about 160 000 years old

8 m per 160 000 years = 5 cm per 1000 years

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Plate tectonics

Plate tectonics


Hydrothermal vents (1)

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• Mid-oceanic ridges (spreading centers) form the longest mountain chain on earth.Inorganic reduced compounds are released, e.g., 30 Mio t H2S per year(Ocean water moves through the earth crust on average in 8 Mio a)

• Hydrothermal vent production, 0.02 % of total primary production = 10 % of the sea-floor production

• Rich communities based of bacterial chemosynthesis, e.g. Riftia pachyptila: huge worm without mouth and after, living from symbiotic autotrophic H2S oxidizers

• Energy from the oxidation of H2S, H2, Fe2+ etc. with oxygen (from photosynthesis!)


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Spiekeroog Janssand NeuharlingersielSchillbalje

+5 m

0 m

-10 m

-20 m

+5 m

0 m

-10 m

-20 m

1 km

Geol. Karte von Niedersachsen 1:25.0002212 SpiekeroogHolocene

NNW SSE

Location of the 20 m-cores

North Sea tidal flats

Core JS-Afilled channeluniform sediment structure

Core JS-Breflects historical sedimentationalternating sediment layers


Sediment structure and paleo-environment

300,000 -128,000 yrs

128,000 -115,000 yrs

ca. 325,000 yrs

115,000 -10,700 yrs

10,700 yrs -present

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Engelen B and Cypionka H (2009) The subsurface of ti dal flats as a model for the deep biosphere. Ocean Dynamics 59:385–391

Reinhard Wilms et al. (2006) Deep biosphere-related bacteria within the subsurface of tidal flat sediments. Environ Microbi ol 8:709-719

Reinhard Wilms et al. (2006) Specific bacterial, arc haeal, and eukaryotic communities in tidal-flat sediment along a vertical profile of several meters. Appl Environ Microbiol 72:2756-2764

Jörg Fichtel et al. (2007) Spore dipicolinic acid co ntents used for estimating the number of endospores in sediments. F EMS Microbiol Ecol 61:522–532

Literature


• www. mikrobiologischer-garten.de

Documents

Sediment Microbiology WS 2010/11 - Uni Oldenburg file1 (c) Heribert Cypionka, Sediment Microbiology WS 2010/11 Sand Residues of algae and mussels Diatoms (brown) Sulfur FeS Microcolonies