Genome sequence of Phaeobacter inhibens type strain (T5T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

Dogs, Marco; Voget, Sonja; Teshima, Hazuki; Petersen, Jörn; Davenport, Karen; Dalingault, Hajnalka; Chen, Amy; Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.; Standfest, Sonja; Rohde, Manfred; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Simon, Meinhard; Klenk, Hans-Peter; Göker, Markus; Brinkhoff, Thorsten

doi:10.4056/sigs.4448212

Genome sequence of Phaeobacter inhibens type strain (T5^T), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens

Journal Article · Fri Dec 20 00:00:00 EST 2013 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.4448212· OSTI ID:1628670

Dogs, Marco ^[1]; Voget, Sonja ^[2]; Teshima, Hazuki ^[3]; Petersen, Jörn ^[4]; Davenport, Karen ^[3]; Dalingault, Hajnalka ^[3]; Chen, Amy ^[5]; Pati, Amrita ^[6]; Ivanova, Natalia ^[6]; Goodwin, Lynne A. ^[7]; Chain, Patrick ^[3]; Detter, John C. ^[8]; Standfest, Sonja ^[9]; Rohde, Manfred ^[10]; Gronow, Sabine ^[4]; Kyrpides, Nikos C. ^[6]; Woyke, Tanja ^[6]; Simon, Meinhard ^[9]; Klenk, Hans-Peter ^[4]; Göker, Markus ^[6] more »

Inst. for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg (Germany); DOE/OSTI
Univ. of Goettingen (Germany)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Leibniz Inst. DSMZ, Braunschweig (Germany)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Inst. for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg (Germany)
Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany)

Strain T5^T is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5^T was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5^T comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5^T possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5^T a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: European Commission; German Research Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628670

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 2 Vol. 9; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment Kanukollu, Saranya; Voget, Sonja; Pohlner, Marion Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0143-0	journal	March 2016
Exemplar Abstract for Phaeobacter inhibens Martens et al. 2006 emend. Dogs et al. 2013. Parker, Charles Thomas; Taylor, Dorothea; Garrity, George M. https://doi.org/10.1601/ex.10132	dataset	January 2013
Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Breider, Sven; Scheuner, Carmen; Schumann, Peter Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00416	journal	August 2014
Gene Flow Across Genus Barriers – Conjugation of Dinoroseobacter shibae’s 191-kb Killer Plasmid into Phaeobacter inhibens and AHL-mediated Expression of Type IV Secretion Systems Patzelt, Diana; Michael, Victoria; Päuker, Orsola Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00742	journal	May 2016
The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae Bartling, Pascal; Brinkmann, Henner; Bunk, Boyke Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01787	journal	September 2017
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment Breider, Sven; Teshima, Hazuki; Petersen, Jörn Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.3828824	journal	January 2014
Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour Breider, Sven; Freese, Heike M.; Spröer, Cathrin International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 7 https://doi.org/10.1099/ijsem.0.001879	journal	July 2017
Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill Giebel, Helge-Ansgar; Klotz, Franziska; Voget, Sonja Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0201-7	journal	October 2016

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Rhodobacteraceae
Rhodobacterales
anaerobic
genetics & heredity
microbiology
motile
rod-shaped
secondary metabolites
tropodithietic acid