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Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

Pernthaler, Annelie and Dekas, Anne E. and Brown, C. Titus and Goffredi, Shana K. and Embaye, Tsegereda and Orphan, Victoria J. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proceedings of the National Academy of Sciences of the United States of America, 105 (19). pp. 7052-7057. ISSN 0027-8424. PMCID PMC2383945. doi:10.1073/pnas.0711303105.

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Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of 15N2 incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.

Item Type:Article
Related URLs:
URLURL TypeDescription CentralArticle Information
Dekas, Anne E.0000-0001-9548-8413
Brown, C. Titus0000-0001-6001-2677
Goffredi, Shana K.0000-0002-9110-9591
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2008 by the National Academy of Sciences. Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved March 18, 2008 (received for review November 29, 2007). Published ahead of print May 8, 2008. This article is a PNAS Direct Submission. We thank C. House for assistance with the ion microprobe measurements; D. Newman, J. Grotzinger, M. Joye, C. Gammon, D. Fike, I. Head, and two anonymous reviewers for invaluable comments that improved this manuscript; and S. Johnson, F. Rohwer, R. Edwards, B. Orcutt, and the 2006 science party of cruise AT15–11 and pilots of the D.S.R.V. Alvin for their assistance with various aspects of this work. This work was supported by National Science Foundation Award Grant MCB-0348492, the Gordon and Betty Moore Foundation, a Davidow grant to Caltech’s GPS Division (to V.J.O.); National Institutes of Health Grant P50HG004071 (to C.T.B.), in part by a Caltech GPS Texaco fellowship (to A.P.), and a National Science Foundation graduate fellowship (to A.D.). Author contributions: A.P. and V.J.O. designed research; A.P., A.E.D., S.K.G., T.E., and V.J.O. performed research; A.P. and C.T.B. contributed new reagents/analytic tools; A.P., A.E.D., C.T.B., S.K.G., and V.J.O. analyzed data; and A.P., C.T.B., and V.J.O. wrote the paper. The authors declare no conflict of interest. Data deposition: The sequence reported in this paper has been deposited in the GenBank database [accession nos. EU622281–EU622312 (16S rRNA) and EU647340–EU647354 (nifH)]. This article contains supporting information online at
Group:Division of Geological and Planetary Sciences
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
Davidow Discovery FundUNSPECIFIED
Caltech GPS Texaco FellowshipUNSPECIFIED
NSF Graduate Research FellowshipUNSPECIFIED
Subject Keywords:beta proteobacteria; methanotrophy; nitrogen fixation; syntrophy
Issue or Number:19
PubMed Central ID:PMC2383945
Record Number:CaltechAUTHORS:PERpnas08
Persistent URL:
Official Citation:Annelie Pernthaler, Anne E. Dekas, C. Titus Brown, Shana K. Goffredi, Tsegereda Embaye, and Victoria J. Orphan Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics PNAS 2008 105 (19) 7052-7057; published ahead of print May 8, 2008, doi:10.1073/pnas.0711303105
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11123
Deposited By: Tony Diaz
Deposited On:16 Jul 2008 17:09
Last Modified:01 Jun 2023 23:06

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