Logo of jbacterPermissionsJournals.ASM.orgJournalJB ArticleJournal InfoAuthorsReviewers
J Bacteriol. 2010 Oct; 192(20): 5552–5553.
Published online 2010 Aug 20. doi:  10.1128/JB.00873-10
PMCID: PMC2950497

Genome Sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the Type Strains of Two Marine Roseobacter Genera[down-pointing small open triangle]


Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T represent two marine genera in the globally significant Roseobacter clade of the Alphaproteobacteria. Here, we present the genome sequences of these organisms, isolated from the Sargasso Sea using dilution-to-extinction culturing, which offer insight into the genetic basis for the metabolic and ecological diversity of this important group.

Organisms from the Roseobacter clade of the Alphaproteobacteria are numerically significant in the world's oceans and have been found in a wide range of habitats (1, 3). Using previously described high-throughput dilution-to-extinction culturing (6, 13), the marine Roseobacter strains Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T were isolated in low-nutrient heterotrophic medium (LNHM) (4) from surface water collected at the Bermuda Atlantic Time-Series Study (BATS) site in the western Sargasso Sea (5, 9). As the type strains for two genera of this globally prolific Roseobacter group, P. bermudensis and M. alkaliphilus were selected for shotgun genome sequencing at the J. Craig Venter Institute through the Moore Foundation Microbial Genome Sequencing Project (http://www.moore.org/microgenome). Draft genomes of P. bermudensis and M. alkaliphilus, with 103 and 46 contigs, respectively, were annotated and analyzed through the Joint Genome Institute IMG/M website (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) (10).

The draft genomes of P. bermudensis and M. alkaliphilus comprise 5,425,920 and 4,529,231 bases, 5,522 and 4,764 predicted open reading frames (ORFs), and 66.44% and 64.13% G+C content, respectively. The P. bermudensis genome is predicted to contain 56 tRNA genes, five 5S rRNA genes, four 16S rRNA genes, and five 23S rRNA genes, and that of M. alkaliphilus 49 tRNA genes and one each of the 5S, 16S, and 23S rRNA genes. Both genomes have putative genes for complete glycolysis and Entner-Doudoroff pathways, a complete tricarboxylic acid cycle, and predicted metabolic pathways for the oxidation of C1 compounds. Both have predicted genes for the synthesis of most essential amino acids and some vitamins and cofactors. Each has putative genes for the utilization of fructose, sucrose, and mannose, confirmed in physiological testing of P. bermudensis (5) but not for M. alkaliphilus (9). P. bermudensis contains a predicted complete RuBisCO complex, unique to the sequenced Roseobacter species (12, 15), a complete assimilatory nitrate reduction pathway, and several type VI secretion genes. M. alkaliphilus is predicted to have complete nitrate reduction pathways to both N2 and ammonia and most type IV secretion genes. Both are predicted to have complete sec pathways and large numbers of ABC transporters (362 in P. bermudensis and 224 in M. alkaliphilus), similar to other Roseobacter strains (15).

M. alkaliphilus was named because of its alkaline growth optimum at pH 10. Na+/H+ antiporters have been shown to be involved in conferring alkaliphilic phenotypes for a variety of organisms by increasing internal cellular H+ concentrations in alkaline conditions where Na+ is present (2, 7, 8, 14, 16, 17). As expected, the genome of M. alkaliphilus contains two putative Na+/H+ antiporters, one homologous to nhaP, important for alkaliphily in several strains (2, 16, 17), and another located adjacent to predicted ABC transporter genes for capsular polysaccharide export.

Nucleotide sequence accession numbers.

The draft genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T are available in GenBank under the accession numbers AATQ00000000 and AAMT00000000, respectively. Data annotated independently by GenDB (11) 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 (www.moore.org/marinemicro) and by an individual investigator award to S.J.G.


[down-pointing small open triangle]Published ahead of print on 20 August 2010.


1. Brinkhoff, T., H. Giebel, and M. Simon. 2008. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch. Microbiol. 189:531-539. [PubMed]
2. Bualuang, A., K. Soontharapirakkul, and A. Incharoensakdi. 2010. Na+/H+ exchange activity in the alkaliphile halotolerant cyanobacterium Aphanothece halophytica. J. Appl. Phycol. 22:123-129.
3. Buchan, A., J. M. Gonzalez, and M. A. Moran. 2005. Overview of the marine Roseobacter lineage. Appl. Environ. Microbiol. 71:5665-5677. [PMC free article] [PubMed]
4. Cho, J.-C., and S. J. Giovannoni. 2003. Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria. Int. J. Syst. Evol. Microbiol. 53:1031-1036. [PubMed]
5. Cho, J.-C., and S. J. Giovannoni. 2006. Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 56:855-859. [PubMed]
6. Connon, S. A., and S. J. Giovannoni. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:3878-3885. [PMC free article] [PubMed]
7. Horikoshi, K. 1999. Alkaliphiles: some applications of their products for biotechnology. Microbiol. Mol. Biol. Rev. 63:735-750. [PMC free article] [PubMed]
8. Kitada, M., S. Kosono, and T. Kudo. 2000. The Na+/H+ antiporter of alkaliphilic Bacillus sp. Extremophiles 4:253-258. [PubMed]
9. Lee, K., Y.-J. Choo, S. J. Giovannoni, and J.-C. Cho. 2007. Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int. J. Syst. Evol. Microbiol. 57:1653-1658. [PubMed]
10. Markowitz, V. M., N. N. Ivanova, E. Szeto, K. Palaniappan, K. Chu, D. Dalevi, I.-M. A. Chen, Y. Grechkin, I. Dubchak, I. Anderson, A. Lykidis, K. Mavromatis, P. Hugenholtz, and N. C. Kyrpides. 2008. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36:D534-D538. [PMC free article] [PubMed]
11. Meyer, F., A. Goesmann, A. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, and A. PuEhler. 2003. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31:2187-2195. [PMC free article] [PubMed]
12. Newton, R. J., L. E. Griffin, K. M. Bowles, C. Meile, S. Gifford, C. E. Givens, E. C. Howard, E. King, C. A. Oakley, C. R. Reisch, J. M. Rinta-Kanto, S. Sharma, S. Sun, V. Varaljay, M. Vila-Costa, J. R. Westrich, and M. A. Moran. 2010. Genome characteristics of a generalist marine bacterial lineage. ISME J. 4:784-798. [PubMed]
13. Stingl, U., H. J. Tripp, and S. J. Giovannoni. 2007. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J. 1:361-371. [PubMed]
14. Takami, H., Y. Takaki, and I. Uchiyama. 2002. Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res. 30:3927-3935. [PMC free article] [PubMed]
15. Thrash, J. C., J.-C. Cho, K. L. Vergin, and S. J. Giovannoni. 2010. Genome sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T. J. Bacteriol. 192:3549-3550. [PMC free article] [PubMed]
16. Utsugi, J., K. Inaba, T. Kuroda, M. Tsuda, and T. Tsuchiya. 1998. Cloning and sequencing of a novel Na+/H+ antiporter gene from Pseudomonas aeruginosa. Biochim. Biophys. Acta 1398:330-334. [PubMed]
17. Wei, Y., J. Liu, Y. Ma, and T. A. Krulwich. 2007. Three putative cation/proton antiporters from the soda lake alkaliphile Alkalimonas amylolytica N10 complement an alkali-sensitive Escherichia coli mutant. Microbiology 153:2168-2179. [PMC free article] [PubMed]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)
PubReader format: click here to try


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • BioProject
    BioProject links
  • MedGen
    Related information in MedGen
  • Nucleotide
    Published Nucleotide sequences
  • Protein
    Published protein sequences
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...