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- Federico M. Lauro
- Environmental Microbiology Initiative,
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- Diane McDougald
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney NSW 2052, Australia;
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- Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney NSW 2052, Australia;
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- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, and
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- Suhelen Egan
- School of Biotechnology and Biomolecular Sciences, and
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- Scott Rice
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney NSW 2052, Australia;
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- Matthew Z. DeMaere
- School of Biotechnology and Biomolecular Sciences, and
-
- Lily Ting
- School of Biotechnology and Biomolecular Sciences, and
-
- Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, and
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- Justin Johnson
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850;
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- Steven Ferriera
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850;
-
- Alla Lapidus
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598;
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- Iain Anderson
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598;
-
- Nikos Kyrpides
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598;
-
- A. Christine Munk
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598;
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- Chris Detter
- Department of Energy Joint Genome Institute Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545;
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- Cliff S. Han
- Department of Energy Joint Genome Institute Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545;
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- Mark V. Brown
- Environmental Microbiology Initiative,
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- Frank T. Robb
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202; and
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- Staffan Kjelleberg
- Environmental Microbiology Initiative,
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- Ricardo Cavicchioli
- Environmental Microbiology Initiative,
書誌事項
- 公開日
- 2009-09-15
- DOI
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- 10.1073/pnas.0903507106
- 公開者
- Proceedings of the National Academy of Sciences
この論文をさがす
説明
<jats:p> 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, <jats:italic>Photobacterium angustum</jats:italic> S14 and <jats:italic>Sphingopyxis alaskensis</jats:italic> 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. </jats:p>
収録刊行物
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- Proceedings of the National Academy of Sciences
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Proceedings of the National Academy of Sciences 106 (37), 15527-15533, 2009-09-15
Proceedings of the National Academy of Sciences
