{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360021391875895424.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1128/msphere.00337-23"}},{"identifier":{"@type":"URI","@value":"https://journals.asm.org/doi/pdf/10.1128/msphere.00337-23"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>ABSTRACT</jats:title>\n          <jats:p>\n            Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth’s carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445–8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with\n            <jats:italic>in situ</jats:italic>\n            methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.\n          </jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE</jats:title>\n            <jats:p>The Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.</jats:p>\n          </jats:sec>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380021391875895454","@type":"Researcher","foaf:name":[{"@value":"Kana Jitsuno"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895448","@type":"Researcher","foaf:name":[{"@value":"Tatsuhiko Hoshino"}],"jpcoar:affiliationName":[{"@value":"Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895433","@type":"Researcher","foaf:name":[{"@value":"Yohei Nishikawa"}],"jpcoar:affiliationName":[{"@value":"CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895449","@type":"Researcher","foaf:name":[{"@value":"Masato Kogawa"}],"jpcoar:affiliationName":[{"@value":"Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895303","@type":"Researcher","foaf:name":[{"@value":"Katsuhiko Mineta"}],"jpcoar:affiliationName":[{"@value":"CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Marine Open Innovation Institute, Shizuoka, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895309","@type":"Researcher","foaf:name":[{"@value":"Michael Strasser"}],"jpcoar:affiliationName":[{"@value":"Department of Geology, University of Innsbruck, Innsbruck, Austria"}]},{"@id":"https://cir.nii.ac.jp/crid/1420001326220392320","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"40356423"},{"@type":"NRID","@value":"1000040356423"},{"@type":"NDL_AUTHOR_ID","@value":"00884527"},{"@type":"NRID","@value":"9000021563626"},{"@type":"NRID","@value":"9000386336934"},{"@type":"NRID","@value":"9000254061942"},{"@type":"NRID","@value":"9000262362945"},{"@type":"NRID","@value":"9000391784965"},{"@type":"NRID","@value":"9000347136123"},{"@type":"NRID","@value":"9000018366682"},{"@type":"NRID","@value":"9000365017237"},{"@type":"NRID","@value":"9000002496683"},{"@type":"NRID","@value":"9000006909446"},{"@type":"NRID","@value":"9000370281520"},{"@type":"NRID","@value":"9000002479732"},{"@type":"NRID","@value":"9000386338342"},{"@type":"NRID","@value":"9000386336844"},{"@type":"NRID","@value":"9000241768267"},{"@type":"NRID","@value":"9000018706973"},{"@type":"NRID","@value":"9000391785294"},{"@type":"NRID","@value":"9000386336810"},{"@type":"NRID","@value":"9000254262707"},{"@type":"NRID","@value":"9000409996117"},{"@type":"NRID","@value":"9000018657099"},{"@type":"NRID","@value":"9000020575420"},{"@type":"NRID","@value":"9000245917819"},{"@type":"NRID","@value":"9000389942736"},{"@type":"NRID","@value":"9000403550595"},{"@type":"NRID","@value":"9000399571587"},{"@type":"NRID","@value":"9000009939105"},{"@type":"NRID","@value":"9000018350496"},{"@type":"NRID","@value":"9000386338335"},{"@type":"NRID","@value":"9000345426790"},{"@type":"NRID","@value":"9000399376861"},{"@type":"NRID","@value":"9000018862115"},{"@type":"NRID","@value":"9000019030045"},{"@type":"NRID","@value":"9000004617781"},{"@type":"NRID","@value":"9000316693026"},{"@type":"NRID","@value":"9000283115991"},{"@type":"NRID","@value":"9000018393723"},{"@type":"NRID","@value":"9000001058157"},{"@type":"NRID","@value":"9000014233943"},{"@type":"NRID","@value":"9000391785124"},{"@type":"NRID","@value":"9000014442973"},{"@type":"NRID","@value":"9000403551372"},{"@type":"NRID","@value":"9000258409947"},{"@type":"NRID","@value":"9000254585792"},{"@type":"NRID","@value":"9000389439277"},{"@type":"NRID","@value":"9000386338042"},{"@type":"NRID","@value":"9000403550288"},{"@type":"NRID","@value":"9000410949824"},{"@type":"NRID","@value":"9000240102741"},{"@type":"NRID","@value":"9000403550195"},{"@type":"NRID","@value":"9000009972636"},{"@type":"NRID","@value":"9000001086746"},{"@type":"NRID","@value":"9000237765739"},{"@type":"NRID","@value":"9000398150798"},{"@type":"NRID","@value":"9000016658940"},{"@type":"NRID","@value":"9000414373459"},{"@type":"NRID","@value":"9000386337059"},{"@type":"NRID","@value":"9000386337056"},{"@type":"NRID","@value":"9000386337032"},{"@type":"NRID","@value":"9000258408389"},{"@type":"NRID","@value":"9000241764500"},{"@type":"NRID","@value":"9000254585910"},{"@type":"NRID","@value":"9000414200628"},{"@type":"NRID","@value":"9000410949823"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/linkike00"}],"foaf:name":[{"@value":"Ken Ikehara"}],"jpcoar:affiliationName":[{"@value":"Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895430","@type":"Researcher","foaf:name":[{"@value":"Jeremy Everest"}],"jpcoar:affiliationName":[{"@value":"British Geological Survey, Edinburgh, United Kingdom"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895453","@type":"Researcher","foaf:name":[{"@value":"Lena Maeda"}],"jpcoar:affiliationName":[{"@value":"Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895425","@type":"Researcher","foaf:name":[{"@value":"Fumio Inagaki"}],"jpcoar:affiliationName":[{"@value":"Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan"},{"@value":"Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895300","@type":"Researcher","foaf:name":[{"@value":"Haruko Takeyama"}],"jpcoar:affiliationName":[{"@value":"Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan"},{"@value":"Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895446","@type":"Researcher","foaf:name":[{"@value":"Piero Bellanova"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895452","@type":"Researcher","foaf:name":[{"@value":"Morgane Brunet"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895434","@type":"Researcher","foaf:name":[{"@value":"Zhirong Cai"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895443","@type":"Researcher","foaf:name":[{"@value":"Antonio Cattaneo"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895437","@type":"Researcher","foaf:name":[{"@value":"Katharina Hochmuth"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895301","@type":"Researcher","foaf:name":[{"@value":"Kanhsi Hsiung"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895304","@type":"Researcher","foaf:name":[{"@value":"Takashi Ishizawa"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895428","@type":"Researcher","foaf:name":[{"@value":"Takuya Itaki"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895438","@type":"Researcher","foaf:name":[{"@value":"Joel Johnson"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895435","@type":"Researcher","foaf:name":[{"@value":"Toshiya Kanamatsu"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895298","@type":"Researcher","foaf:name":[{"@value":"Myra Keep"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895431","@type":"Researcher","foaf:name":[{"@value":"Arata Kioka"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895442","@type":"Researcher","foaf:name":[{"@value":"Christian Maerz"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895299","@type":"Researcher","foaf:name":[{"@value":"Cecilia McHugh"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895445","@type":"Researcher","foaf:name":[{"@value":"Aaron Micallef"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895439","@type":"Researcher","foaf:name":[{"@value":"Luo Min"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895444","@type":"Researcher","foaf:name":[{"@value":"Dhananjai Pandey"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895424","@type":"Researcher","foaf:name":[{"@value":"Jean Noel Proust"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895307","@type":"Researcher","foaf:name":[{"@value":"Troy Rasbury"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895308","@type":"Researcher","foaf:name":[{"@value":"Natascha Riedinger"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895432","@type":"Researcher","foaf:name":[{"@value":"Rui Bao"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895440","@type":"Researcher","foaf:name":[{"@value":"Yasufumi Satoguchi"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895305","@type":"Researcher","foaf:name":[{"@value":"Derek Sawyer"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895450","@type":"Researcher","foaf:name":[{"@value":"Chloe Seibert"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895451","@type":"Researcher","foaf:name":[{"@value":"Maxwell Silver"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895302","@type":"Researcher","foaf:name":[{"@value":"Susanne Straub"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895447","@type":"Researcher","foaf:name":[{"@value":"Joonas Virtasalo"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895297","@type":"Researcher","foaf:name":[{"@value":"Yonghong Wang"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895426","@type":"Researcher","foaf:name":[{"@value":"Ting-Wei Wu"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895306","@type":"Researcher","foaf:name":[{"@value":"Sarah Zellers"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895436","@type":"Researcher","foaf:name":[{"@value":"Martin Kölling"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895441","@type":"Researcher","foaf:name":[{"@value":"Jyh-Jaan Steven Huang"}]},{"@id":"https://cir.nii.ac.jp/crid/1380021391875895296","@type":"Researcher","foaf:name":[{"@value":"Yoshitaka Nagahashi"}]}],"contributor":[{"@id":"https://cir.nii.ac.jp/crid/1380021391875895427","@type":"Researcher","foaf:name":[{"@value":"Xiyang Dong"}],"role":"editor"}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"23795042"}],"prism:publicationName":[{"@value":"mSphere"}],"dc:publisher":[{"@value":"American Society for Microbiology"}],"prism:publicationDate":"2024-01-30","prism:volume":"9","prism:number":"1"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["https://creativecommons.org/licenses/by/4.0/","https://journals.asm.org/non-commercial-tdm-license"],"url":[{"@id":"https://journals.asm.org/doi/pdf/10.1128/msphere.00337-23"}],"createdAt":"2024-01-03","modifiedAt":"2024-01-30","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=Research%20Article","dc:title":"Research Article"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040010457587966080","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"22H00429"},{"@type":"JGN","@value":"JP22H00429"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22H00429/"}],"notation":[{"@language":"ja","@value":"日本海溝乱泥流物質供給システムと超深海・海底下微生物生態系との広域時空相関の解明"},{"@language":"en","@value":"Exploring the spatiotemporal distribution and interrelationships between hadal microbial ecosystems and turbidite systems in the Japan Trench"}]},{"@id":"https://cir.nii.ac.jp/crid/1040299826878732672","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"23K22586"},{"@type":"JGN","@value":"JP23K22586"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23K22586/"}],"notation":[{"@language":"ja","@value":"統合層序・年代モデル構築に基づく日本海溝の過去数万年間の地震履歴の解明"},{"@language":"en","@value":"Paleoseismology of the Japan Trench over the past tens of thousands of years based on the construction of an integrated stratigraphic and chronological model"}]},{"@id":"https://cir.nii.ac.jp/crid/1040862776832167424","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"23K22618"},{"@type":"JGN","@value":"JP23K22618"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-23K22618/"}],"notation":[{"@language":"ja","@value":"海底下の「静かな」微生物進化"},{"@language":"en","@value":"Microbial evolution below the seafloor"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360001114074605696","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Methanogenesis from Methylated Amines in a Hypersaline Algal Mat"}]},{"@id":"https://cir.nii.ac.jp/crid/1360005744245282688","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Event Stratigraphy in a Hadal Oceanic Trench: The Japan Trench as Sedimentary Archive Recording Recurrent Giant Subduction Zone Earthquakes and Their Role 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