Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Mary Ann Moran (), Alison Buchan, José M. González, John F. Heidelberg, William B. Whitman, Ronald P. Kiene, James R. Henriksen, Gary M. King, Robert Belas, Clay Fuqua, Lauren Brinkac, Matt Lewis, Shivani Johri, Bruce Weaver, Grace Pai, Jonathan A. Eisen, Elisha Rahe, Wade M. Sheldon, Wenying Ye, Todd R. Miller, Jane Carlton, David A. Rasko, Ian T. Paulsen, Qinghu Ren, Sean C. Daugherty, Robert T. Deboy, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, William C. Nelson, Steven A. Sullivan, M. J. Rosovitz, Daniel H. Haft, Jeremy Selengut and Naomi Ward
Additional contact information
Mary Ann Moran: University of Georgia
Alison Buchan: Yale University
José M. González: Universidad de La Laguna
John F. Heidelberg: The Institute for Genomic Research
William B. Whitman: University of Georgia
Ronald P. Kiene: University of South Alabama
James R. Henriksen: University of Georgia
Gary M. King: Darling Marine Center, University of Maine
Robert Belas: University of Maryland Biotechnology Institute
Clay Fuqua: Indiana University
Lauren Brinkac: The Institute for Genomic Research
Matt Lewis: The Institute for Genomic Research
Shivani Johri: The Institute for Genomic Research
Bruce Weaver: The Institute for Genomic Research
Grace Pai: The Institute for Genomic Research
Jonathan A. Eisen: The Institute for Genomic Research
Elisha Rahe: Indiana University
Wade M. Sheldon: University of Georgia
Wenying Ye: University of Georgia
Todd R. Miller: University of Maryland Biotechnology Institute
Jane Carlton: The Institute for Genomic Research
David A. Rasko: The Institute for Genomic Research
Ian T. Paulsen: The Institute for Genomic Research
Qinghu Ren: The Institute for Genomic Research
Sean C. Daugherty: The Institute for Genomic Research
Robert T. Deboy: The Institute for Genomic Research
Robert J. Dodson: The Institute for Genomic Research
A. Scott Durkin: The Institute for Genomic Research
Ramana Madupu: The Institute for Genomic Research
William C. Nelson: The Institute for Genomic Research
Steven A. Sullivan: The Institute for Genomic Research
M. J. Rosovitz: The Institute for Genomic Research
Daniel H. Haft: The Institute for Genomic Research
Jeremy Selengut: The Institute for Genomic Research
Naomi Ward: The Institute for Genomic Research

Nature, 2004, vol. 432, issue 7019, 910-913

Abstract: Abstract Since the recognition of prokaryotes as essential components of the oceanic food web1, 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 cultured2 or have only been grown to low densities in sea water3,4. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10–20% of coastal and oceanic mixed-layer bacterioplankton2,5,6,7. 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. Figure 1 Phylogenetic tree of 16S rRNA gene sequences from the Roseobacter clade and other major marine taxa. Sequences include those from uncultured bacterioplankton (open square) and from cultured bacterioplankton isolated at very low nutrient concentrations (filled circle). Scale bar shows Jukes–Cantor evolutionary distance.

Date: 2004
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DOI: 10.1038/nature03170

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