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Fine-Scale Control of Microbial Communities in Methane-Rich Marine Sediments

This study explores the fine-scale variability in microbial communities in deep marine sediments containing hydrates and high concentrations of methane. The goal is to understand the factors that control the number, type, and distribution of microorganisms such as methanogens and heterotrophs. The research uses molecular ecology techniques, geology and chemistry analysis, and multivariate analysis to refine computational models with biological rate terms. The study aims to increase our understanding of the complex microbial processes in methane-rich sediments.

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Fine-Scale Control of Microbial Communities in Methane-Rich Marine Sediments

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  1. 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

  2. microbiology 0 mbsf geochemistry, sedimentology Hydrate microbiology geochemistry, sedimentology No hydrate M = Microbiology G/S = geochem, sedimentology, etc. 100 mbsf 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/chemistry Temperature, IR imagery (PNNL); grain size analysis (USGS WH); porewater chemistry (OSU; Scripps); hydrocarbons, C-isotope ratios, hydrogen (USGS) • Multivariate analysis Nonmetric multidimensional scaling

  3. 19A 17A 15A Cl- temperature IR images • 46 microbiology cores • 31 hydrate; 15 non-hydrate • Mostly KG Basin (passive margin) • 12 from Andaman Islands (deep hydrates, convergent margin)

  4. 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?

  5. Terminal restriction fragment length polymorphism (T-RFLP) from Gruntzig et al. 2002 PhyloChip • 500,000 probes300,000 target 16S genes2 domains --> 9000 taxa

  6. t-RFLP Depth (mbsf) Phylotypes Site relative fluorescence 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

  7. 200-800 taxa detected 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 14A-19X 10D-4H 10D-10X

  8. Bacteria • Key observations: • Sulfate reducers, sulfur oxidizers, ANAMMOX, acetogens, aerobic methanotrophs, metal reducers 3B-20X 10D-4H 10D-10X 14A-19X

  9. An unusual microbial community in methane-rich sediments? Offshore India • pink/orange slime • fractures; 0.5-20 mbsf • large coccoid cells, often as tetrads • above the SMI Hydrate Ridge Ca. 30 um Offshore Vancouver Island (Riedel et al. 2006)

  10. Summary Fine-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

  11. 4H2 + CO2 CH4 + 2H2O CH3COOH CH4 + CO2 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?

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