The genomic basis of trophic strategy in marine bacteria.
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.
Lauro
Federico M
FM
Environmental Microbiology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
McDougald
Diane
D
Thomas
Torsten
T
Williams
Timothy J
TJ
Egan
Suhelen
S
Rice
Scott
S
DeMaere
Matthew Z
MZ
Ting
Lily
L
Ertan
Haluk
H
Johnson
Justin
J
Ferriera
Steven
S
Lapidus
Alla
A
Anderson
Iain
I
Kyrpides
Nikos
N
Munk
A Christine
AC
Detter
Chris
C
Han
Cliff S
CS
Brown
Mark V
MV
Robb
Frank T
FT
Kjelleberg
Staffan
S
Cavicchioli
Ricardo
R
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