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

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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-165T, 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-165T, 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-165T 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-165T 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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Authors and Affiliations

  1. Department of Biological Science, Inha University, Incheon, 22212, Republic of Korea

    Jaeho Song, Ilnam Kang, Yochan Joung & Jang-Cheon Cho

  2. Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan

    Jaeho Song, Susumu Yoshizawa, Koji Hamasaki & Kazuhiro Kogure

  3. National Institute of Polar Research, Tokyo, 190-8518, Japan

    Ryo Kaneko

  4. Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan

    Kenshiro Oshima & Masahira Hattori

  5. Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan

    Masahira Hattori

  6. Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea

    Soochan Kim & Kangseok Lee

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Song, J., Kang, I., Joung, Y. et al. Genome analysis of Rubritalea profundi SAORIC-165T, the first deep-sea verrucomicrobial isolate, from the northwestern Pacific Ocean. J Microbiol. 57, 413–422 (2019). https://doi.org/10.1007/s12275-019-8712-8

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