The genomic basis of trophic strategy in marine bacteria

Federico M. Lauro, Diane McDougald, Torsten Thomas, Timothy J. Williams, Suhelen Egan, Scott Rice, Matthew Z. DeMaere, Lily Ting, Haluk Ertan, Justin Johnson, Steven Ferriera, Alla Lapidus, Iain Anderson, Nikos Kyrpides, A. Christine Munkf, Chris Detterg, Cliff S. Hang, Mark V. Brown, Frank T. Robb, Staffan KjellebergRicardo Cavicchioli*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

407 Citations (Scopus)

Abstract

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, Photobacterium angustum S14 and Sphingopyxis alaskensis 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.

Original languageEnglish
Pages (from-to)15527-15533
Number of pages7
JournalProceedings of the National Academy of Sciences of the United States of America
Volume106
Issue number37
DOIs
Publication statusPublished - 15 Sep 2009
Externally publishedYes

Keywords

  • Microbial adaptation and ecology
  • Microbial genomics and metagenomics
  • Monitoring environmental health
  • Trophic adaptation

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