Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.
Moran
Mary Ann
MA
Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA. mmoran@uga.edu
Buchan
Alison
A
González
José M
JM
Heidelberg
John F
JF
Whitman
William B
WB
Kiene
Ronald P
RP
Henriksen
James R
JR
King
Gary M
GM
Belas
Robert
R
Fuqua
Clay
C
Brinkac
Lauren
L
Lewis
Matt
M
Johri
Shivani
S
Weaver
Bruce
B
Pai
Grace
G
Eisen
Jonathan A
JA
Rahe
Elisha
E
Sheldon
Wade M
WM
Ye
Wenying
W
Miller
Todd R
TR
Carlton
Jane
J
Rasko
David A
DA
Paulsen
Ian T
IT
Ren
Qinghu
Q
Daugherty
Sean C
SC
Deboy
Robert T
RT
Dodson
Robert J
RJ
Durkin
A Scott
AS
Madupu
Ramana
R
Nelson
William C
WC
Sullivan
Steven A
SA
Rosovitz
M J
MJ
Haft
Daniel H
DH
Selengut
Jeremy
J
Ward
Naomi
N
D000222:Adaptation, Physiological / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D008386:Marine Biology; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D010802:Phylogeny; D010933:Plankton / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D041904:Roseobacter / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D012623:Seawater / Q000382:microbiology*
D002352:Carrier Proteins; D012336:RNA, Ribosomal, 16S