Fine scale control of microbial communities in deep marine sediments

that contain hydrates and high concentrations of methane

F.S. Colwell, B. Briggs, P. Carini, M. Torres (Oregon State Univ)

M.E. Delwiche (Idaho National Laboratory)E. Brodie (Lawrence Berkeley National Laboratory)R. Daly (UC Berkeley)A. Hangsterfer, M. Kastner (Scripps)M. Holland (Geotek Ltd.)P. Long, H.T. Schaef (Pacific Northwest National

Laboratory)W. Winters (USGS Woods Hole)M. Riedel (McGill Univ)

Acknowledgements: U.S. Department of Energy, Office of Fossil Energy, National Energy Technology Lab; Integrated Ocean Drilling Program, Science Parties from Leg 204 & NGHP Offshore India

How does fine-scale variability in marine sediments control the number, type and distribution of microbial communities (methanogens, heterotrophs)?

--> Refine computational models with biological rate terms that are consistent with sediment conditions.

Approach:• Microbiology

Methanogen enumeration (OSU); molecular ecology by PhyloChip, t-RFLP, and clone library (LBNL/UCB, OSU, Scripps)

• Geology/chemistryTemperature, IR imagery (PNNL); grain

size analysis (USGS WH); porewater chemistry (OSU; Scripps); hydrocarbons, C-isotope ratios, hydrogen (USGS)

• Multivariate analysisNonmetric multidimensional scaling

Hydrate

No hydrate

M = MicrobiologyG/S = geochem, sedimentology, etc.

0mbsf

100mbsf

geochemistry, sedimentology

microbiology

geochemistry, sedimentology

microbiology

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

17A

19A

• 46 microbiology cores• 31 hydrate; 15 non-hydrate• Mostly KG Basin (passive margin)• 12 from Andaman Islands (deep hydrates, convergent margin)

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

15ACl- temperature IR images

DNA extractions (Scripps, OSU)

PCR on DNA extracted from India samples

• Diluted DNA is more likely to amplify:– correct concentration?– dilution of inhibitors?

• Bacterial vs. archaeal DNA is: – more prevalent?– more easily extracted?– more easily amplified?

Terminal restriction fragment length polymorphism (T-RFLP)

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

from Gruntzig et al. 2002

PhyloChip

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

-500,000 probes300,000 target 16S genes2 domains --> 9000 taxa

t-RFLP

rela

tive

flu

ore

sce

nce

21A 78.1 22

14A 103 16

20A

115.3 12

20A

120.7 21

Sit

e

Dep

th (

mb

sf)

Ph

ylo

typ

es

t-RFLP perfomed on DNA amplified using archaeal primers and HaeIII as the restriction enzyme No matches with t-RFs entered in the MSU RDPII database

Archaea- Key observations:

-methanogens, ANME-1 present-High temperature archaea most abundant in 10D-4H-Low temperature methanogen most abundant in 10D-10X -non-hydrate samples are more similar to each other than to hydrate samples; however, not very similar-ANME-1 has highest intensity in 10D-4h (shallowest sample)

3B-20X

10D-4H

10D-10X

14A-19X

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

200-800 taxa detected

Bacteria

- Key observations:-Sulfate reducers, sulfur oxidizers, ANAMMOX, acetogens, aerobic methanotrophs, metal reducers

3B-20X

10D-4H

10D-10X

14A-19X

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

An unusual microbial community in methane-rich sediments?• pink/orange

slime• fractures; 0.5-20

mbsf• large coccoid

cells, often as tetrads

• above the SMI

Offshore India

Hydrate Ridge

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Offshore Vancouver Island (Riedel et al. 2006)

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

Ca. 30 um

SummaryFine-scale control of microbial communities:• Preliminary molecular data suggests numerous

taxa detected including:– Archaea: methanogens, anaerobic methanotrophs,

thermophiles– Bacteria: sulfate reducers, sulfur oxidizers, metal

reducers, ANAMMOX, acetogens, aerobic methanotrophs

• C, S, N, and metal biogeochemical cycles possible

Next…• Multivariate analysis of communities; reconcile

with geochemistry, geology; determine controlling factors

• Determine identity and biogeochemistry of intriguing shallow biofilms

• Relationship of methanogenic rates to molecular biology data

Steady-state view of the global carbon cycle (Dickens, 2003)

• Accurate estimates to come from temporal modeling of CH4 inputs and outputs in appropriate hydrate environments

• CH4 inputs are poorly understood

• Realistic rates of methanogenesis?

• Methanogen locations and controlling factors?

• Other biogeochemical processes to sustain the system?

4H2 + CO2 CH4 + 2H2OCH3COOH CH4 + CO2