title: Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
abstract: 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.
authors.affiliation: Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA. mmoran@uga.edu
authors.forename: Mary Ann
authors.initials: MA
authors.lastname: Moran
authors.forename: Alison
authors.initials: A
authors.lastname: Buchan
authors.forename: José M
authors.initials: JM
authors.lastname: González
authors.forename: John F
authors.initials: JF
authors.lastname: Heidelberg
authors.forename: William B
authors.initials: WB
authors.lastname: Whitman
authors.forename: Ronald P
authors.initials: RP
authors.lastname: Kiene
authors.forename: James R
authors.initials: JR
authors.lastname: Henriksen
authors.forename: Gary M
authors.initials: GM
authors.lastname: King
authors.forename: Robert
authors.initials: R
authors.lastname: Belas
authors.forename: Clay
authors.initials: C
authors.lastname: Fuqua
authors.forename: Lauren
authors.initials: L
authors.lastname: Brinkac
authors.forename: Matt
authors.initials: M
authors.lastname: Lewis
authors.forename: Shivani
authors.initials: S
authors.lastname: Johri
authors.forename: Bruce
authors.initials: B
authors.lastname: Weaver
authors.forename: Grace
authors.initials: G
authors.lastname: Pai
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: Elisha
authors.initials: E
authors.lastname: Rahe
authors.forename: Wade M
authors.initials: WM
authors.lastname: Sheldon
authors.forename: Wenying
authors.initials: W
authors.lastname: Ye
authors.forename: Todd R
authors.initials: TR
authors.lastname: Miller
authors.forename: Jane
authors.initials: J
authors.lastname: Carlton
authors.forename: David A
authors.initials: DA
authors.lastname: Rasko
authors.forename: Ian T
authors.initials: IT
authors.lastname: Paulsen
authors.forename: Qinghu
authors.initials: Q
authors.lastname: Ren
authors.forename: Sean C
authors.initials: SC
authors.lastname: Daugherty
authors.forename: Robert T
authors.initials: RT
authors.lastname: Deboy
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dodson
authors.forename: A Scott
authors.initials: AS
authors.lastname: Durkin
authors.forename: Ramana
authors.initials: R
authors.lastname: Madupu
authors.forename: William C
authors.initials: WC
authors.lastname: Nelson
authors.forename: Steven A
authors.initials: SA
authors.lastname: Sullivan
authors.forename: M J
authors.initials: MJ
authors.lastname: Rosovitz
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Haft
authors.forename: Jeremy
authors.initials: J
authors.lastname: Selengut
authors.forename: Naomi
authors.initials: N
authors.lastname: Ward
mesh_terms: 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*
chemical_list: D002352:Carrier Proteins; D012336:RNA, Ribosomal, 16S