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

@article{citeulike:2786454, abstract = {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. 10.1073/pnas.0711303105}, author = {Pernthaler, Annelie and Dekas, Anne E. and Brown, Titus C. and Goffredi, Shana K. and Embaye, Tsegereda and Orphan, Victoria J. }, citeulike-article-id = {2786454}, doi = {http://dx.doi.org/10.1073/pnas.0711303105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {16s, bacteria, fish, metagenomics, methods, probes}, month = {May}, pages = {0711303105+}, posted-at = {2008-05-25 07:33:33}, priority = {2}, title = {Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics}, url = {http://dx.doi.org/10.1073/pnas.0711303105}, year = {2008} }

TY - JOUR ID - citeulike:2786454 L3 - citeulike-article-id:2786454 TI - Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics JF - Proceedings of the National Academy of Sciences SP - 0711303105 N2 - 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. 10.1073/pnas.0711303105 KW - 16s KW - bacteria KW - fish KW - metagenomics KW - methods KW - probes AU - Pernthaler, Annelie AU - Dekas, Anne AU - Brown, Titus AU - Goffredi, Shana AU - Embaye, Tsegereda AU - Orphan, Victoria PY - 2008/05/08/ UR - http://dx.doi.org/10.1073/pnas.0711303105 ER -