The genomic basis of trophic strategy in marine bacteria Export

@article{citeulike:5792317, abstract = {10.1073/pnas.0903507106 Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, S14 and RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.}, author = {Lauro, Federico M. and McDougald, Diane and Thomas, Torsten and Williams, Timothy J. and Egan, Suhelen and Rice, Scott and DeMaere, Matthew Z. and Ting, Lily and Ertan, Haluk and Johnson, Justin and Ferriera, Steven and Lapidus, Alla and Anderson, Iain and Kyrpides, Nikos and Munk, A. Christine and Detter, Chris and Han, Cliff S. and Brown, Mark V. and Robb, Frank T. and Kjelleberg, Staffan and Cavicchioli, Ricardo}, citeulike-article-id = {5792317}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0903507106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/37/15527.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/37/15527.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19805210}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19805210}, day = {15}, doi = {10.1073/pnas.0903507106}, journal = {Proceedings of the National Academy of Sciences}, keywords = {genome, metagenomics, niche}, month = {September}, number = {37}, pages = {15527--15533}, posted-at = {2009-10-15 14:43:58}, priority = {2}, title = {The genomic basis of trophic strategy in marine bacteria}, url = {http://dx.doi.org/10.1073/pnas.0903507106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:5792317 L3 - citeulike-article-id:5792317 N2 - 10.1073/pnas.0903507106 Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, S14 and RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining. IS - 37 JF - Proceedings of the National Academy of Sciences EP - 15533 TI - The genomic basis of trophic strategy in marine bacteria VL - 106 SP - 15527 KW - genome KW - metagenomics KW - niche AU - Lauro, Federico AU - McDougald, Diane AU - Thomas, Torsten AU - Williams, Timothy AU - Egan, Suhelen AU - Rice, Scott AU - DeMaere, Matthew AU - Ting, Lily AU - Ertan, Haluk AU - Johnson, Justin AU - Ferriera, Steven AU - Lapidus, Alla AU - Anderson, Iain AU - Kyrpides, Nikos AU - Munk, Christine AU - Detter, Chris AU - Han, Cliff AU - Brown, Mark AU - Robb, Frank AU - Kjelleberg, Staffan AU - Cavicchioli, Ricardo PY - 2009/09/15/ UR - http://dx.doi.org/10.1073/pnas.0903507106 ER -