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

Journal Article · · Standards in Genomic Sciences
DOI:https://doi.org/10.4056/sigs.4287962· OSTI ID:1628666
 [1];  [2];  [3];  [4];  [2];  [2];  [5];  [6];  [7];  [6];  [7];  [6];  [6];  [8];  [4];  [6];  [6];  [9];  [4];  [4] more »;  [9] « less
  1. Univ. of Oldenburg (Germany). Inst. for Chemistry and Biology of the Marine Environment; DOE/OSTI
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division
  3. Leibniz Inst. DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  4. Leibniz Inst. DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Data Management and Technology Center
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. HZI – Helmholtz Centre for Infection Research, Braunschweig (Germany)
  9. Univ. of Oldenburg (Germany). Inst. for Chemistry and Biology of the Marine Environment
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TF-218T 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-218T 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-218T 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.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1628666
Journal Information:
Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 9; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (10)

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
Exemplar Abstract for Phaeobacter daeponensis Yoon et al. 2007 emend. Dogs et al. 2013 and Leisingera daeponensis (Yoon et al. 2007) Breider et al. 2014. dataset January 2013
Nomenclature Abstract for Phaeobacter daeponensis Yoon et al. 2007 emend. Dogs et al. 2013. dataset January 2013
Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. journal August 2014
Comparative genomics of Roseobacter clade bacteria isolated from the accessory nidamental gland of Euprymna scolopes journal February 2015
Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment journal January 2014
Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336T), a representative of the Roseobacter clade journal October 2013
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 December 2013
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T) journal March 2014
Genome sequence of Epibacterium ulvae strain DSM 24752T, an indigoidine-producing, macroalga-associated member of the marine Roseobacter group journal August 2019

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Related Subjects

Roseobacter clade
59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity
Marine microbiology
Microbiology
Rhodobacteraceae
facultative anaerobe
indigoidine