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dc.contributor.authorReza, Md. Shaheed
dc.contributor.authorKobiyama, Atsushi
dc.contributor.authorYamada, Yuichiro
dc.contributor.authorIkeda, Yuri
dc.contributor.authorIkeda, Daisuke
dc.contributor.authorMizusawa, Nanami
dc.contributor.authorIkeo, Kazuho
dc.contributor.authorSato, Shigeru
dc.contributor.authorOgata, Takehiko
dc.contributor.authorJimbo, Mitsuru
dc.contributor.authorKudo, Toshiaki
dc.contributor.authorKaga, Shinnosuke
dc.contributor.authorWatanabe, Shiho
dc.contributor.authorNaiki, Kimiaki
dc.contributor.authorKaga, Yoshimasa
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorWatabe, Shugo
dc.date.accessioned2018-04-30T06:58:24Z
dc.date.available2018-04-30T06:58:24Z
dc.date.issued2018-04-27
dc.identifier.citationReza MS, Kobiyama A, Yamada Y, Ikeda Y, Ikeda D, et al. (2018) Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay. Gene. Available: http://dx.doi.org/10.1016/j.gene.2018.04.075.
dc.identifier.issn0378-1119
dc.identifier.pmid29705124
dc.identifier.doi10.1016/j.gene.2018.04.075
dc.identifier.urihttp://hdl.handle.net/10754/627698
dc.description.abstractThe Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27–0.34 Gb WGS library, 0.9 × 106–1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0–19.6% Planktomarina (Family Rhodobacteraceae) and 13.7–17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5–6.1%), Flavobacterium (1.8–2.6%), Sphingobacterium (1.4–1.6%) and Cellulophaga (1.4–2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8–15.2%, 3.6–4.9% and 2.1–3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.
dc.description.sponsorshipWe thank Dr. Tomoko Sakami, Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, for helping establish our sampling and DNA extraction systems. The research reported in this publication was supported in part by the King Abdullah University of Science and Technology (KAUST), under award number URF/1/1976.
dc.publisherElsevier BV
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S0378111918304578
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, [, , (2018-04-27)] DOI: 10.1016/j.gene.2018.04.075 . © 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/
dc.subjectMetagenomics
dc.subjectBacterial diversity
dc.subjectOfunato Bay
dc.subjectWhole genome sequencing
dc.subject16S rRNA
dc.titleTaxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.identifier.journalGene
dc.eprint.versionPost-print
dc.contributor.institutionKitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
dc.contributor.institutionIwate Fisheries Technology Center, Kamaishi, Iwate 026-0001, Japan
kaust.personMineta, Katsuhiko
kaust.personBajic, Vladimir B.
kaust.personGojobori, Takashi
kaust.grant.numberURF/1/1976
refterms.dateFOA2019-04-27T00:00:00Z
dc.date.published-online2018-04-27
dc.date.published-print2018-07


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