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Genome sequences from the prolific Roseobacter clade in the Alphaproteobacteria are beginning to reveal the genetic basis for the diverse lifestyles of these organisms. Here we present the genome sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T, two marine Roseobacter species isolated from the Sargasso Sea using dilution-to-extinction culturing, whose genomes encode for significant differences in metabolic potential.
Members of the Roseobacter clade are ecologically and physiologically diverse, occupying a wide variety of lifestyles (1, 2, 7). Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T were isolated by dilution-to-extinction culturing in low-nutrient heterotrophic media (LNHM) (4) from water collected at the Bermuda Atlantic Time-Series Study (BATS) station in the Sargasso Sea (3, 5). The genomes were shotgun sequenced by the J. Craig Venter Institute as part of the Moore Foundation Microbial Genome Sequencing Project (http://www.moore.org/microgenome). Draft genomes of O. granulosus and O. batsensis containing 85 and 23 contigs, respectively, were annotated analyzed through the Joint Genome Institute IMG/M website (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) (6). The draft genomes of O. granulosus and O. batsensis comprised 4,039,111 and 4,437,668 bases, 3,855 and 4,261 predicted open reading frames (ORFs), and 70.41% and 66.10% G+C contents, respectively. The O. granulosus genome is predicted to contain 55 tRNA genes, two 5S rRNA genes, four 16S rRNA genes, and two 23S rRNA genes; that of O. batsensis is predicted to contain 45 tRNA genes, one each of the 5S and 16S rRNA genes, and two 23S rRNA genes.
The sequencing of these and other Roseobacter genomes has directly affected the Oceanicola phylogeny. Recent phylogenetic studies of the Alphaproteobacteria and the Roseobacter clade specifically have established that the Oceanicola genus is not monophyletic (1, 7, 11). Not surprisingly, the two genomes reveal different potential capabilities for these two organisms. O. granulosus is predicted to possess several genes necessary for the Calvin cycle, including the large (but not the small) RuBisCo (ribulose-1,5-bisphosphate carboxylase) subunit. Both strains tested negative for fructose utilization (3) but contain putative genes necessary for this metabolism. Consistent with physiological tests showing glucose utilization, O. granulosus is predicted to have complete glycolysis, pentose-phosphate, and Entner-Doudoroff (ED) pathways. O. batsensis has only a putative ED pathway, but did not utilize glucose (3). Both strains were characterized as nonmotile (3), and O. batsensis has no che gene homologs, but O. granulosas is predicted to have most flagellar and che gene homologs. O. granulosus has putative genes for an aa3-type cytochrome c oxidase, and O. batsensis is predicted to have both aa3- and cbb3-type cytochrome c oxidases, the latter potentially conferring an adaptive advantage over a greater range of oxygen concentrations (8, 9).
Both organisms are predicted to have most Sec pathway genes. O. batsensis contains several putative type IV secretion genes and 6 putative TonB receptors. Each has many predicted ABC transporter genes: 239 in O. granulosus and 193 in O. batsenesis. Both organisms were observed to form polyhydroxybutyrate (PHB) in culture (3), and both organisms contain putative genes necessary for PHB synthesis (see reference 10 and references therein), including predicted copies of PHB or polyhydroxyalkanoate (PHA) polymerases and several acetyl coenzyme A (acetyl-CoA) acetyltransferases, and O. batsensis has a predicted acetoacetyl-CoA reductase.
The draft genome sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T are available in GenBank under accession no. AAOT00000000 and AAMO00000000, respectively. Data annotated independently by GenDB are accessible in the Marine Microbial Genomics database at Oregon State University (http://bioinfo.cgrb.oregonstate.edu/microbes/).
Sequencing, assembly, and annotation and data analysis were supported by the Gordon and Betty Moore Foundation Marine Microbiology Initiative, as part of its Marine Microbial Sequencing Project (http://www.moore.org/marinemicro), and by an individual investigator award to S.J.G.
Published ahead of print on 23 April 2010.