Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis

Marco Dogs; Hazuki Teshima; Jörn Petersen; Anne Fiebig; Olga Chertkov; Hajnalka Dalingault; Amy Chen; Amrita Pati; Lynne A Goodwin; Patrick Chain; John C Detter; Natalia Ivanova; Alla Lapidus; Manfred Rohde; Sabine Gronow; Nikos C Kyrpides; Tanja Woyke; Meinhard Simon; Markus Göker; Hans-Peter Klenk; Thorsten Brinkhoff

doi:10.4056/sigs.4287962

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis

Stand Genomic Sci. 2013 Oct 3;9(1):142-59. doi: 10.4056/sigs.4287962. eCollection 2013 Oct 16.

Authors

Marco Dogs¹, Hazuki Teshima², Jörn Petersen³, Anne Fiebig³, Olga Chertkov², Hajnalka Dalingault², Amy Chen⁴, Amrita Pati⁵, Lynne A Goodwin⁶, Patrick Chain⁵, John C Detter⁶, Natalia Ivanova⁵, Alla Lapidus⁵, Manfred Rohde⁷, Sabine Gronow³, Nikos C Kyrpides⁵, Tanja Woyke⁵, Meinhard Simon¹, Markus Göker³, Hans-Peter Klenk³, Thorsten Brinkhoff¹

Affiliations

¹ Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany .
² Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
³ Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
⁴ Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁵ DOE Joint Genome Institute, Walnut Creek, California, USA.
⁶ Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA.
⁷ HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.

Abstract

TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.

Keywords: Marine microbiology; Rhodobacteraceae; Roseobacter clade; facultative anaerobe; indigoidine.