Genome analysis of Rubritalea profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean

Jaeho Song, Ilnam Kang, Yochan Joung, Susumu Yoshizawa, Ryo Kaneko, Kenshiro Oshima, Masahira Hattori, Koji Hamasaki, Kazuhiro Kogure, Soochan Kim, Kangseok Lee, Jang Cheon Cho

    Research output: Contribution to journalArticle

    Abstract

    Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165 T , a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165 T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165 T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

    Original languageEnglish
    JournalJournal of Microbiology
    DOIs
    Publication statusPublished - 2019 Jan 1

    Fingerprint

    Pacific Ocean
    Oceans and Seas
    Genome
    Verrucomicrobia
    Genes
    Pentose Phosphate Pathway
    Untranslated RNA
    Niacinamide
    Citric Acid Cycle
    Niacin
    Base Composition
    Carbohydrate Metabolism
    Glycolysis
    Coenzyme A
    Metabolic Networks and Pathways
    rRNA Genes
    Folic Acid
    Sulfates
    Life Style
    Signal Transduction

    Keywords

    • 16S rRNA
    • deep sea
    • genome
    • particle-associated
    • Rubritalea
    • Verrucomicrobia

    ASJC Scopus subject areas

    • Microbiology
    • Applied Microbiology and Biotechnology

    Cite this

    Genome analysis of Rubritalea profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean . / Song, Jaeho; Kang, Ilnam; Joung, Yochan; Yoshizawa, Susumu; Kaneko, Ryo; Oshima, Kenshiro; Hattori, Masahira; Hamasaki, Koji; Kogure, Kazuhiro; Kim, Soochan; Lee, Kangseok; Cho, Jang Cheon.

    In: Journal of Microbiology, 01.01.2019.

    Research output: Contribution to journalArticle

    Song, Jaeho ; Kang, Ilnam ; Joung, Yochan ; Yoshizawa, Susumu ; Kaneko, Ryo ; Oshima, Kenshiro ; Hattori, Masahira ; Hamasaki, Koji ; Kogure, Kazuhiro ; Kim, Soochan ; Lee, Kangseok ; Cho, Jang Cheon. / Genome analysis of Rubritalea profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean In: Journal of Microbiology. 2019.
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    abstract = "Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165 T , a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5{\%}. The SAORIC-165 T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165 T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.",
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    AU - Song, Jaeho

    AU - Kang, Ilnam

    AU - Joung, Yochan

    AU - Yoshizawa, Susumu

    AU - Kaneko, Ryo

    AU - Oshima, Kenshiro

    AU - Hattori, Masahira

    AU - Hamasaki, Koji

    AU - Kogure, Kazuhiro

    AU - Kim, Soochan

    AU - Lee, Kangseok

    AU - Cho, Jang Cheon

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    N2 - Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165 T , a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165 T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165 T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

    AB - Although culture-independent studies have shown the presence of Verrucomicrobia in the deep sea, verrucomicrobial strains from deep-sea environments have been rarely cultured and characterized. Recently, Rubritalea profundi SAORIC-165 T , a psychrophilic bacterium of the phylum Verrucomicrobia, was isolated from a depth of 2,000 m in the northwestern Pacific Ocean. In this study, the genome sequence of R. profundi SAORIC-165 T , the first deep-sea verrucomicrobial isolate, is reported with description of the genome properties and comparison to surface-borne Rubritalea genomes. The draft genome consisted of four contigs with an entire size of 4,167,407 bp and G+C content of 47.5%. The SAORIC-165 T genome was predicted to have 3,844 proteincoding genes and 45 non-coding RNA genes. The genome contained a repertoire of metabolic pathways, including the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, tricarboxylic acid cycle, assimilatory sulfate reduction, and biosynthesis of nicotinate/nicotinamide, pantothenate/coenzyme A, folate, and lycopene. The comparative genomic analyses with two surface-derived Rubritalea genomes showed that the SAORIC-165 T genome was enriched in genes involved in transposition of mobile elements, signal transduction, and carbohydrate metabolism, some of which might be related to bacterial enhancement of ecological fitness in the deep-sea environment. Amplicon sequencing of 16S rRNA genes from the water column revealed that R. profundi-related phylotypes were relatively abundant at 2,000 m and preferred a particle-associated life style in the deep sea. These findings suggest that R. profundi represents a genetically unique and ecologically relevant verrucomicrobial group well adapted to the deep-sea environment.

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