title: The genomic basis of trophic strategy in marine bacteria.
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.
authors.affiliation: Environmental Microbiology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
authors.forename: Federico M
authors.initials: FM
authors.lastname: Lauro
authors.forename: Diane
authors.initials: D
authors.lastname: McDougald
authors.forename: Torsten
authors.initials: T
authors.lastname: Thomas
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Williams
authors.forename: Suhelen
authors.initials: S
authors.lastname: Egan
authors.forename: Scott
authors.initials: S
authors.lastname: Rice
authors.forename: Matthew Z
authors.initials: MZ
authors.lastname: DeMaere
authors.forename: Lily
authors.initials: L
authors.lastname: Ting
authors.forename: Haluk
authors.initials: H
authors.lastname: Ertan
authors.forename: Justin
authors.initials: J
authors.lastname: Johnson
authors.forename: Steven
authors.initials: S
authors.lastname: Ferriera
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Iain
authors.initials: I
authors.lastname: Anderson
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.forename: A Christine
authors.initials: AC
authors.lastname: Munk
authors.forename: Chris
authors.initials: C
authors.lastname: Detter
authors.forename: Cliff S
authors.initials: CS
authors.lastname: Han
authors.forename: Mark V
authors.initials: MV
authors.lastname: Brown
authors.forename: Frank T
authors.initials: FT
authors.lastname: Robb
authors.forename: Staffan
authors.initials: S
authors.lastname: Kjelleberg
authors.forename: Ricardo
authors.initials: R
authors.lastname: Cavicchioli
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000254:growth & development*; D017753:Ecosystem; D016680:Genome, Bacterial; D008386:Marine Biology; D008954:Models, Biological; D008969:Molecular Sequence Data; D010776:Photobacterium / Q000235:genetics / Q000254:growth & development; D042301:Sphingomonadaceae / Q000235:genetics / Q000254:growth & development