title: Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment.
abstract: 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 responsible 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. 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.
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
authors.forename: Saranya
authors.initials: S
authors.lastname: Kanukollu
authors.affiliation: Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
authors.forename: Sonja
authors.initials: S
authors.lastname: Voget
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
authors.forename: Marion
authors.initials: M
authors.lastname: Pohlner
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
authors.forename: Verona
authors.initials: V
authors.lastname: Vandieken
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Petersen
authors.affiliation: Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, California USA ; Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, California USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, California USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Shapiro
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: School of Biology, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
authors.forename: Heribert
authors.initials: H
authors.lastname: Cypionka
authors.affiliation: Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
authors.forename: Bert
authors.initials: B
authors.lastname: Engelen
keywords: Anaerobic metabolism; Cell-connecting filaments; DMSO reductase; DMSP; Denitrification; Flagella gene cluster; Quorum quenching