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    Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

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    Type
    Article
    Authors
    Kudo, Toshiaki
    Kobiyama, Atsushi
    Rashid, Jonaira
    Reza, Shaheed
    Yamada, Yuichiro
    Ikeda, Yuri
    Ikeda, Daisuke
    Mizusawa, Nanami
    Ikeo, Kazuho
    Sato, Shigeru
    Ogata, Takehiko
    Jimbo, Mitsuru
    Kaga, Shinnosuke
    Watanabe, Shiho
    Naiki, Kimiaki
    Kaga, Yoshimasa
    Segawa, Satoshi
    Mineta, Katsuhiko cc
    Bajic, Vladimir B. cc
    Gojobori, Takashi cc
    Watabe, Shugo
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Applied Mathematics and Computational Science Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    KAUST Grant Number
    URF/1/1976
    Date
    2018-04-26
    Online Publication Date
    2018-04-26
    Print Publication Date
    2018-07
    Permanent link to this record
    http://hdl.handle.net/10754/627697
    
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    Abstract
    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.
    Citation
    Kudo T, Kobiyama A, Rashid J, Reza S, Yamada Y, et al. (2018) Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis. Gene. Available: http://dx.doi.org/10.1016/j.gene.2018.04.072.
    Sponsors
    We thank Dr. Toshiya Iida and Dr. Masahiro Yuki of RIKEN for their helpful advice regarding the bioinformatic analysis. This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No URF/1/1976.
    Publisher
    Elsevier BV
    Journal
    Gene
    DOI
    10.1016/j.gene.2018.04.072
    PubMed ID
    29705130
    Additional Links
    http://www.sciencedirect.com/science/article/pii/S0378111918304542
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.gene.2018.04.072
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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