title: Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments.
abstract: Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.
authors.affiliation: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Aono
authors.forename: Tomoya
authors.initials: T
authors.lastname: Baba
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ara
authors.forename: Tatsunari
authors.initials: T
authors.lastname: Nishi
authors.forename: Tomoko
authors.initials: T
authors.lastname: Nakamichi
authors.forename: Eiji
authors.initials: E
authors.lastname: Inamoto
authors.forename: Hiromi
authors.initials: H
authors.lastname: Toyonaga
authors.forename: Miki
authors.initials: M
authors.lastname: Hasegawa
authors.forename: Yuki
authors.initials: Y
authors.lastname: Takai
authors.forename: Yoshiko
authors.initials: Y
authors.lastname: Okumura
authors.forename: Miki
authors.initials: M
authors.lastname: Baba
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.forename: Chiaki
authors.initials: C
authors.lastname: Kato
authors.forename: Taku
authors.initials: T
authors.lastname: Oshima
authors.forename: Kaoru
authors.initials: K
authors.lastname: Nakasone
authors.forename: Hirotada
authors.initials: H
authors.lastname: Mori
mesh_terms: D000332:Aerobiosis; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004270:DNA, Circular / Q000737:chemistry / Q000235:genetics; D005618:Fresh Water / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics*; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D009566:Nitrates / Q000378:metabolism; D009573:Nitrites / Q000378:metabolism; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D020592:Shewanella / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D013045:Species Specificity; D026801:Synteny; D014871:Water Microbiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004270:DNA, Circular; D009566:Nitrates; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases