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Title: Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum ( fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsiblemore » for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. In conclusion, the genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment.« less
 [1] ;  [2] ;  [1] ;  [1] ;  [3] ;  [4] ;  [5] ;  [5] ;  [3] ;  [6] ;  [1] ;  [1]
  1. Inst. for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg (Germany)
  2. Univ. of Gottingen, Gottingen (Germany). Dept. of Genomic and Applied Microbiology and Gottingen Genomics Laboratory, Inst. of Microbiology and Genetics
  3. Leibniz Inst. DSMZ German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  4. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program; King Abdulaziz Univ., Jeddah (Saudi Arabia). Dept. of Biological Sciences, Faculty of Science
  5. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States). Genome Biology Program
  6. Newcastle Univ., Newcastle upon Tyne (United Kingdom). School of Biology
Publication Date:
Grant/Contract Number:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277
BioMed Central
Research Org:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
59 BASIC BIOLOGICAL SCIENCES; anaerobic metabolism; cell-connecting filaments; quorum quenching; flagella gene cluster; DMSP; DMSO reductase; denitrification; homoserine lactone acylase; escherichia-coli k-12; sp-nov.; emended description; rna genes; bacteria; system; clade; identification; annotation
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1379156