title: Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m.
abstract: Viruses play important roles in aquatic ecosystems, but deep-sea bacteriophages remain largely unexplored. A temperate bacteriophage (termed vB_PstS-1) was identified from the psychrotolerant gammaproteobacterium Pseudomonas stutzeri 1-1-1b, which was isolated from hadopelagic water (depth of 7000 m) of the Japan Trench in the Northwest Pacific Ocean. The genome size of PstS-1 was 48,666 bp; its genome displayed a 59.8% G + C content and a total of 79 coding sequences were identified in its genome. The PstS-1 phage belongs to the family Siphoviridae, but its genomic sequence and organization are distinct from those of any other well-known Siphoviridae phage. The mosaic genomic structure of PstS-1 suggests the occurrence of genetic exchange between distinct temperate phages in deep-sea Pseudomonas populations. The PstS-1 genome also harbors three distinct sequence regions corresponding to spacers within a single clustered regularly interspaced short palindromic repeat (CRISPR) locus in the rhizosphere-associated diazotrophic P. stutzeri A1501 genome. The extension of these spacers to the soil environment and the presence of many homologs of both the hadal deep-sea phage PstS-1 and terrestrial Pseudomonas phages suggest the early co-evolution of temperate phages and their host genus Pseudomonas prior to the divergence of their habitational and physiological adaptation.
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: mityoshi@jamstec.go.jp.
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Yoshida
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
authors.forename: Yukari
authors.initials: Y
authors.lastname: Yoshida-Takashima
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
authors.forename: Takuro
authors.initials: T
authors.lastname: Nunoura
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Takai
mesh_terms: D016679:Genome, Viral; D023281:Genomics; D007564:Japan; D009792:Oceans and Seas; D010802:Phylogeny; D017105:Pseudomonas Phages / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000648:ultrastructure; D044223:Pseudomonas stutzeri / Q000821:virology*; D012623:Seawater / Q000382:microbiology* / Q000821:virology; D017422:Sequence Analysis, DNA; D017906:Siphoviridae / Q000235:genetics / Q000302:isolation & purification*
keywords: Deep sea; Genome sequence; Pseudomonas; Temperate bacteriophage