201
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Biddle JF, Lipp JS, Lever MA, Lloyd KG, Sørensen KB, Anderson R, Fredricks HF, Elvert M, Kelly TJ, Schrag DP, Sogin ML, Brenchley JE, Teske A, House CH, Hinrichs KU. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc Natl Acad Sci U S A 2006; 103:3846-51. [PMID: 16505362 PMCID: PMC1533785 DOI: 10.1073/pnas.0600035103] [Citation(s) in RCA: 342] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.
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Affiliation(s)
| | - Julius S. Lipp
- Organic Geochemistry Group, Deutsche Forschungsgemeinschaft Research Center for Ocean Margins and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Mark A. Lever
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Karen G. Lloyd
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Ketil B. Sørensen
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Rika Anderson
- Organic Geochemistry Group, Deutsche Forschungsgemeinschaft Research Center for Ocean Margins and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
- Carleton College, Northfield, MN 55057
| | - Helen F. Fredricks
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Marcus Elvert
- Organic Geochemistry Group, Deutsche Forschungsgemeinschaft Research Center for Ocean Margins and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
| | - Timothy J. Kelly
- Pennsylvania State Astrobiology Research Center and Departments of
- Geosciences and
| | - Daniel P. Schrag
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138; and
| | - Mitchell L. Sogin
- The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543
| | - Jean E. Brenchley
- Pennsylvania State Astrobiology Research Center and Departments of
- Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Christopher H. House
- Pennsylvania State Astrobiology Research Center and Departments of
- Geosciences and
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Deutsche Forschungsgemeinschaft Research Center for Ocean Margins and Department of Geosciences, University of Bremen, D-28334 Bremen, Germany
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
- To whom correspondence should be addressed at:
Organic Geochemistry Group, RCOM and Department of Geosciences, University of Bremen, PO Box 330 440, 28334 Bremen, Germany. E-mail:
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202
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Inagaki F, Nunoura T, Nakagawa S, Teske A, Lever M, Lauer A, Suzuki M, Takai K, Delwiche M, Colwell FS, Nealson KH, Horikoshi K, D'Hondt S, Jørgensen BB. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc Natl Acad Sci U S A 2006; 103:2815-20. [PMID: 16477011 PMCID: PMC1413818 DOI: 10.1073/pnas.0511033103] [Citation(s) in RCA: 338] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes and their phylogenetic diversities in deeply buried marine sediments of the Pacific Ocean Margins. During the Ocean Drilling Program Legs 201 and 204, we obtained sediment cores from the Peru and Cascadia Margins that varied with respect to the presence of dissolved methane and methane hydrate. To examine differences in prokaryotic distribution patterns in sediments with or without methane hydrates, we studied >2,800 clones possessing partial sequences (400-500 bp) of the 16S rRNA gene and 348 representative clone sequences (approximately 1 kbp) from the two geographically separated subseafloor environments. Archaea of the uncultivated Deep-Sea Archaeal Group were consistently the dominant phylotype in sediments associated with methane hydrate. Sediment cores lacking methane hydrates displayed few or no Deep-Sea Archaeal Group phylotypes. Bacterial communities in the methane hydrate-bearing sediments were dominated by members of the JS1 group, Planctomycetes, and Chloroflexi. Results from cluster and principal component analyses, which include previously reported data from the West and East Pacific Margins, suggest that, for these locations in the Pacific Ocean, prokaryotic communities from methane hydrate-bearing sediment cores are distinct from those in hydrate-free cores. The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth's essential biogeochemical processes.
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Affiliation(s)
- Fumio Inagaki
- Subground Animalcule Retrieval Project, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan.
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203
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Köpke B, Wilms R, Engelen B, Cypionka H, Sass H. Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients. Appl Environ Microbiol 2006; 71:7819-30. [PMID: 16332756 PMCID: PMC1317335 DOI: 10.1128/aem.71.12.7819-7830.2005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.
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Affiliation(s)
- Beate Köpke
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl-von-Ossietzky Strasse 9-11, D-26111 Oldenburg, Germany
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205
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Jones S. What lives beneath? Nat Rev Microbiol 2005. [DOI: 10.1038/nrmicro1255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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