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

Lauro FM,McDougald D,Thomas T,Williams TJ,Egan S,Rice S,DeMaere MZ,Ting L,Ertan H,Johnson J,Ferriera S,Lapidus A,Anderson I,Kyrpides N,Munk AC,Detter C,Han CS,Brown MV,Robb FT,Kjelleberg S,Cavicchioli R

doi

10.1073/pnas.0903507106

subject

Has Abstract

pub_date

2009-09-15 00:00:00

pages

15527-33

issue

37

eissn

0027-8424

issn

1091-6490

pii

0903507106

journal_volume

106

pub_type

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