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Title: 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

Journal Article · · Standards in Genomic Sciences
DOI:https://doi.org/10.4056/sigs.4448212· OSTI ID:1628670
 [1];  [2];  [3];  [4];  [3];  [3];  [5];  [6];  [6];  [7];  [3];  [8];  [1];  [9];  [4];  [6];  [6];  [1];  [4];  [6] more »;  [1] « less
  1. Inst. for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg (Germany)
  2. Univ. of Goettingen (Germany)
  3. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  4. Leibniz Inst. DSMZ, Braunschweig (Germany)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  9. Helmholtz Centre for Infection Research (HZI), Braunschweig (Germany)
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Strain T5T is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5T 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 T5T 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 T5T 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 T5T 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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; German Research Foundation (DFG); European Commission (EC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1628670
Journal Information:
Standards in Genomic Sciences, Vol. 9, Issue 2; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (12)

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats journal January 2017
Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour journal July 2017
Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment journal March 2016
Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill journal October 2016
Exemplar Abstract for Phaeobacter inhibens Martens et al. 2006 emend. Dogs et al. 2013. dataset January 2013
Draft genome of Leisingera aquaemixtae CECT 8399 T , a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea journal March 2016
Nonphotosynthetic Pigments as Potential Biosignatures journal May 2015
Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter journal November 2017
Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. 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 journal May 2016
The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae journal September 2017
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment journal January 2014

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59 BASIC BIOLOGICAL SCIENCES
genetics & heredity
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