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

Handle URI:
http://hdl.handle.net/10754/627697
Title:
Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis
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 ( 0000-0002-4727-045X ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Watabe, Shugo
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.
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
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.
Publisher:
Elsevier BV
Journal:
Gene
KAUST Grant Number:
URF/1/1976
Issue Date:
26-Apr-2018
DOI:
10.1016/j.gene.2018.04.072
Type:
Article
ISSN:
0378-1119
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.
Additional Links:
http://www.sciencedirect.com/science/article/pii/S0378111918304542
Appears in Collections:
Articles; Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKudo, Toshiakien
dc.contributor.authorKobiyama, Atsushien
dc.contributor.authorRashid, Jonairaen
dc.contributor.authorReza, Shaheeden
dc.contributor.authorYamada, Yuichiroen
dc.contributor.authorIkeda, Yurien
dc.contributor.authorIkeda, Daisukeen
dc.contributor.authorMizusawa, Nanamien
dc.contributor.authorIkeo, Kazuhoen
dc.contributor.authorSato, Shigeruen
dc.contributor.authorOgata, Takehikoen
dc.contributor.authorJimbo, Mitsuruen
dc.contributor.authorKaga, Shinnosukeen
dc.contributor.authorWatanabe, Shihoen
dc.contributor.authorNaiki, Kimiakien
dc.contributor.authorKaga, Yoshimasaen
dc.contributor.authorSegawa, Satoshien
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorGojobori, Takashien
dc.contributor.authorWatabe, Shugoen
dc.date.accessioned2018-04-30T06:58:23Z-
dc.date.available2018-04-30T06:58:23Z-
dc.date.issued2018-04-26en
dc.identifier.citationKudo 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.en
dc.identifier.issn0378-1119en
dc.identifier.doi10.1016/j.gene.2018.04.072en
dc.identifier.urihttp://hdl.handle.net/10754/627697-
dc.description.abstractOfunato 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.en
dc.description.sponsorshipWe 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.en
dc.publisherElsevier BVen
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S0378111918304542en
dc.rightsNOTICE: this is the author’s version of a work that was accepted for publication in Gene. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Gene, [, , (2018-04-26)] DOI: 10.1016/j.gene.2018.04.072 . © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectBacterial functionsen
dc.subjectDMSP catabolic genesen
dc.subjectMetagenomicsen
dc.subjectOfunato Bayen
dc.titleSeasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysisen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.identifier.journalGeneen
dc.eprint.versionPost-printen
dc.contributor.institutionKitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japanen
dc.contributor.institutionIwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japanen
kaust.authorMineta, Katsuhikoen
kaust.authorBajic, Vladimir B.en
kaust.authorGojobori, Takashien
kaust.grant.numberURF/1/1976en
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