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- Genome analysis of Rubritalea profundi SAORIC-165T, 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 , Soochan Kim , Kangseok Lee , Jang-Cheon Cho
- J. Microbiol. 2019;57(5):413-422. Published online February 26, 2019
- DOI: https://doi.org/10.1007/s12275-019-8712-8
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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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Citations
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- Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
Mirae Kim, Jaeho Song, Seung Yeol Shin, Kazuhiro Kogure, Ilnam Kang, Jang-Cheon Cho
Frontiers in Marine Science.2024;[Epub] CrossRef - Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents
Joel Slinger, James W. Wynne, Mark B. Adams
Frontiers in Animal Science.2021;[Epub] CrossRef
- Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium
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