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Cultivation and characterization of archaeal dark matters

Research Project

Project/Area Number 15H02419
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biodiversity/Systematics
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

IMACHI Hiroyuki  国立研究開発法人海洋研究開発機構, 深海・地殻内生物圏研究分野, 主任研究員 (20361933)

Co-Investigator(Kenkyū-buntansha) 玉木 秀幸  国立研究開発法人産業技術総合研究所, 生命工学領域, 研究グループ付 (00421842)
高木 善弘  国立研究開発法人海洋研究開発機構, 深海・地殻内生物圏研究分野, 主任技術研究員 (10399561)
諸野 祐樹  国立研究開発法人海洋研究開発機構, 高知コア研究所, グループリーダー代理 (30421845)
Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥40,170,000 (Direct Cost: ¥30,900,000、Indirect Cost: ¥9,270,000)
Fiscal Year 2018: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Fiscal Year 2017: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
Fiscal Year 2016: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Fiscal Year 2015: ¥13,130,000 (Direct Cost: ¥10,100,000、Indirect Cost: ¥3,030,000)
Keywordsアーキア / 培養 / バイオリアクター / 海底堆積物 / 嫌気性微生物 / 微生物 / 生物多様性 / 古細菌
Outline of Final Research Achievements

Cultivation of microorganisms is crucial to develop our understanding of microbial physiology, genetics and ecology. However, many microorganisms, particularly members of the domain Archaea, remain uncultured under laboratory conditions. In this study, we attempted to cultivate and isolate fastidious but ecologically important uncultured Archaea. To isolate such archaeal members, we used bioreactor enrichment containing such uncultured archaea as inoculum, which we established from deep-sea methane seep sediment during our previous JSPS KAKENHI projects. After many cultivation attempts combined with molecular-based techniques, we successfully enriched several uncultured archaea and eventually obtained an archaeon belonging to the DSAG group. In addition, we revealed a part of physiology and genetic properties of the DSAG archaeon.

Academic Significance and Societal Importance of the Research Achievements

微生物を培養し、その詳細な性状を調べることは生物学を基礎とするあらゆる学術・産業分野において重要な課題である。しかしながら、環境中に生息する微生物の多くは人為的に培養されておらず、特にドメイン・アーキアに属する微生物の培養例は少ない。本研究では、これまで環境中に普遍的かつ優占的に存在する事が予見されていた複数種のアーキアの培養に成功した。特に進化学的観点から現在大きな注目を集めているDSAGアーキアの培養に世界で初めて成功したことは画期的な成果である。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (43 results)

All 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (12 results) Journal Article (16 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 16 results,  Open Access: 8 results,  Acknowledgement Compliant: 3 results) Presentation (10 results) (of which Int'l Joint Research: 7 results,  Invited: 4 results) Book (5 results)

  • [Int'l Joint Research] カリフォルニア工科大学(米国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] ブレーメン大学(ドイツ)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] 国立台湾大学/国立成功大学(台湾)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] カリフォルニア工科大学(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ブレーメン大学(ドイツ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] 国立台湾大学(台湾)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Bremen(Germany)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] National Taiwan University(Taiwan)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] California Institute of Technology/Craig J. Vender Institute/University of Illinoi(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Bremen(Germany)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] National Taiwan University/National Cheng Kung University(Taiwan)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] California Institute of Technology/Craig J. Vender Institute/University of South California(米国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation2019

    • Author(s)
      Imachi Hiroyuki、Tasumi Eiji、Takaki Yoshihiro、Hoshino Tatsuhiko、Schubotz Florence、Gan Shuchai、Tu Tzu-Hsuan、Saito Yumi、Yamanaka Yuko、Ijiri Akira、Matsui Yohei、Miyazaki Masayuki、Morono Yuki、Takai Ken、Hinrichs Kai-Uwe、Inagaki Fumio
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1

    • DOI

      10.1038/s41598-019-38754-w

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi2019

    • Author(s)
      Nakahara Nozomi、Nobu Masaru K.、Takaki Yoshihiro、Miyazaki Masayuki、Tasumi Eiji、Sakai Sanae、Ogawara Miyuki、Yoshida Naoko、Tamaki Hideyuki、Yamanaka Yuko、Katayama Arata、Yamaguchi Takashi、Takai Ken、Imachi Hiroyuki
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 69 Issue: 4 Pages: 1185-1194

    • DOI

      10.1099/ijsem.0.003291

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex2018

    • Author(s)
      Ijiri Akira et al.
    • Journal Title

      Science Advances

      Volume: 4 Issue: 6 Pages: 4631-4631

    • DOI

      10.1126/sciadv.aao4631

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Insight into anaerobic methanotrophy from 13C/12C-amino acids and 14C/12C-ANME cells in seafloor microbial ecology2018

    • Author(s)
      Takano Yoshinori、Chikaraishi Yoshito、Imachi Hiroyuki、Miyairi Yosuke、Ogawa Nanako O.、Kaneko Masanori、Yokoyama Yusuke、Kr?ger Martin、Ohkouchi Naohiko
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 14070-14070

    • DOI

      10.1038/s41598-018-31004-5

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism2018

    • Author(s)
      Hidalgo‐Ahumada Catalina A. P.、Nobu Masaru K.、Narihiro Takashi、Tamaki Hideyuki、Liu Wen‐Tso、Kamagata Yoichi、Stams Alfons J M、Imachi Hiroyuki、Sousa Diana Z
    • Journal Title

      Environmental Microbiology

      Volume: 20 Issue: 12 Pages: 4503-4511

    • DOI

      10.1111/1462-2920.14388

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater2018

    • Author(s)
      Matsushita Shuji、Komizo Daisuke、Cao Linh Thi Thuy、Aoi Yoshiteru、Kindaichi Tomonori、Ozaki Noriatsu、Imachi Hiroyuki、Ohashi Akiyoshi
    • Journal Title

      Water Research

      Volume: 130 Pages: 224-233

    • DOI

      10.1016/j.watres.2017.11.063

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fractionation of nitrogen isotopes during amino acid metabolism in heterotrophic and chemolithoautotrophic microbes across Eukarya, Bacteria, and Archaea: Effects of nitrogen sources and metabolic pathways2017

    • Author(s)
      Yamaguchi Yasuhiko T.、Chikaraishi Yoshito、Takano Yoshinori、Ogawa Nanako O.、Imachi Hiroyuki、Yokoyama Yusuke、Ohkouchi Naohiko
    • Journal Title

      Organic Geochemistry

      Volume: 111 Pages: 101-112

    • DOI

      10.1016/j.orggeochem.2017.04.004

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Biotic manganese oxidation coupled with methane oxidation using a continuous-flow bioreactor system under marine conditions2017

    • Author(s)
      Kato Shingo、Miyazaki Masayuki、Kikuchi Sakiko、Kashiwabara Teruhiko、Saito Yumi、Tasumi Eiji、Suzuki Katsuhiko、Takai Ken、Cao Linh Thi Thuy、Ohashi Akiyoshi、Imachi Hiroyuki
    • Journal Title

      Water Science and Technology

      Volume: 76 Issue: 7 Pages: 1781-1795

    • DOI

      10.2166/wst.2017.365

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Microbial Community Composition and Functional Capacity in a Terrestrial Ferruginous, Sulfate-Depleted Mud Volcano2017

    • Author(s)
      Tu Tzu-Hsuan、Wu Li-Wei、Lin Yu-Shih、Imachi Hiroyuki、Lin Li-Hung、Wang Pei-Ling
    • Journal Title

      Frontiers in Microbiology

      Volume: 8

    • DOI

      10.3389/fmicb.2017.02137

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan2016

    • Author(s)
      Takuro Nunoura, Yoshihiro Takaki, Shigeru Shimamura, Jungo Kakuta, Hiromi Kazama, Miho Hirai, Noriaki Masui, Hitoshi Tomaru, Yuki Morono, Hiroyuki Imachi, Fumio Inagaki, Ken Takai
    • Journal Title

      Environmental Microbiology

      Volume: 18 Issue: 6 Pages: 1-16

    • DOI

      10.1111/1462-2920.13096

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino acids-utilizing bacterium isolated from marine subsurface sediment2016

    • Author(s)
      Imachi H, Sakai S, Kubota K, Miyazaki M, Saito Y and Takai K
    • Journal Title

      International Journal of Systematic and Evoltionary Microbiology

      Volume: 66 Issue: 3 Pages: 1293-1300

    • DOI

      10.1099/ijsem.0.000878

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Hydrogen and carbon isotope systematics in hydrogenotrophic methanogenesis under H2-limited and -enriched conditions: Implications for the origin of methane and its isotopic diagnosis.2016

    • Author(s)
      Okumura T., Kawagucci S., Saito Y., Matsui Y., Takai K., Imachi H.
    • Journal Title

      Progress in Earth and Planetary Science.

      Volume: 3 Issue: 1 Pages: 14-14

    • DOI

      10.1186/s40645-016-0088-3

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Nitrogen and oxygen isotope effects of ammonia oxidation by thermophilic Thaumarchaeota from a geothermal water stream2016

    • Author(s)
      Nishizawa M, Sakai S, Konno U, Nakahara N, Takaki Y, Saito Y, Imachi H, Tasumi E, Makabe A, Koba K and Takai K
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 82 Issue: 15 Pages: 4492-4504

    • DOI

      10.1128/aem.00250-16

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments2016

    • Author(s)
      Browne P, Tamaki H, Kyrpides N, Woyke T, Goodwin L, Imachi H, Brauer, S Yavitt J B, Liu W-T, Zinder S and Cadillo-Quiroz H
    • Journal Title

      The ISME Journal

      Volume: 11 Issue: 1 Pages: 87-99

    • DOI

      10.1038/ismej.2016.104

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Methanomicrobium antiquum sp. nov., a hydrogenotrophic methanogen isolated from deep sedimentary aquifers in a natural gas field2016

    • Author(s)
      Mochimaru H, Tamaki H, Katayama T, Imachi H, Sakata S and Kamagata Y
    • Journal Title

      International Journal of Systematic and Evoltionary Microbiology

      Volume: 66 Issue: 11 Pages: 4873-4877

    • DOI

      10.1099/ijsem.0.001444

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exploring deep microbial life in coal-bearing sediments down to ~2.5km below the seafloor2015

    • Author(s)
      INAGAKI FUMIO, Kai-Uwe Hinrichs,KUBO YUSUKE,Marshall W. Bowles,Verena B. Heuer,Wei-Li Hong,HOSHINO TATSUHIKO,IJIRI AKIRA,IMACHI HIROYUKI,ITO MOTOO,KANEKO MASANORI,Mark A. Lever,Lin Yu-Shin,Barbara A. Methe,Morita Sumito,MORONO YUKI,et al.
    • Journal Title

      SCIENCE/AAAS/

      Volume: 349 Issue: 6246 Pages: 420-424

    • DOI

      10.1126/science.aaa6882

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Cultivation of microbial dark matters in subseafloor biosphere2018

    • Author(s)
      Hiroyuki Imachi
    • Organizer
      The 6th DSM 2018 International Workshop on Deep-Sea Microbiology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 微生物暗黒物質は暗黒ではない-海底下生命圏からの未培養微生物の培養を例として-2017

    • Author(s)
      井町寛之
    • Organizer
      環境微生物系学会合同大会2017
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Cultivation of uncultured subseafloor microbes using down-flow hanging sponge (DHS) bioreactors2017

    • Author(s)
      Imachi H
    • Organizer
      Deep Life Cultivation workshop
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cultivation of microbial dark matters from marine sediments: novel bacteria affiliated with uncultured groups of the phylum Chloroflexi.2017

    • Author(s)
      Nakahara N, Yoshida N, Tasumi E, Nobu M, Miyazaki M, Takaki Y, Sakai S, Tamaki H, Yamaguchi T, Takai K and Imachi H
    • Organizer
      JpGU-AGU Joint Meeting 2017
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 海底堆積物から分離した新規Chlorolexi門細菌の生理代謝機能の解明2017

    • Author(s)
      中原望・吉田奈央子・田角栄二・高木善弘・酒井早苗・宮崎征行・山口隆司・高井研・井町寛之
    • Organizer
      環境微生物系学会合同大会2017
    • Related Report
      2016 Annual Research Report
  • [Presentation] 海底堆積物に生息する微生物ダークマターChloroflexi門細菌の分離・培養2016

    • Author(s)
      中原望・小西優・高木善弘・酒井早苗・玉木秀幸・山口隆司・高井研・井町寛之
    • Organizer
      第31回日本微生物生態学会大会
    • Place of Presentation
      横須賀市文化会館 (横須賀、神奈川)
    • Year and Date
      2016-10-23
    • Related Report
      2015 Annual Research Report
  • [Presentation] Cultivation of uncultured Chloroflexi bacteria, a microbial dark matter in subseafloor biosphere2016

    • Author(s)
      Nakahara N, Takai Y, Konishi M, Tamaki H, Yamaguchi T, Takai K and Imachi H
    • Organizer
      The 8th Asian Symposium on Microbial Ecology
    • Place of Presentation
      National Taiwan University (Taipei, Taiwan)
    • Year and Date
      2016-10-01
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identifying methanogenic community members obtained from 2-km deep coalbed2016

    • Author(s)
      Identifying methanogenic community members obtained from 2-km deep coalbed
    • Organizer
      International Symposium on Microbial Ecology (ISME) 2016
    • Place of Presentation
      Palais des congres de Montreal (Montreal, Canada)
    • Year and Date
      2016-08-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cultivation of previously uncultured Chloroflexi, a bacterial dark matter in subseafloor biosphere2016

    • Author(s)
      Nakahara N, Takai Y, Konishi M, Tamaki H, Yamaguchi T, Takai K and Imachi H
    • Organizer
      International Symposium on Microbial Ecology (ISME) 2016
    • Place of Presentation
      Palais des congres de Montreal (Montreal, Canada)
    • Year and Date
      2016-08-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identifying 2 km-deep methanogenic community members using a long-term bioreactor cultivation2016

    • Author(s)
      Imachi H, Tasumi E, Tu T-H, Ijiri A, Morono Y, Ishii S, Methe BA, Takai K and Inagaki F
    • Organizer
      Goldschimidt2016
    • Place of Presentation
      Pacifico Yokohama (Yokohama, Japan)
    • Year and Date
      2016-06-29
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Book] Methanocellales. In Bergey’s Manual of Systematics of Archaea and Bacteria2016

    • Author(s)
      Sakai S and Imachi H
    • Total Pages
      1
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2015 Annual Research Report
  • [Book] Methanocellaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria2016

    • Author(s)
      Sakai S and Imachi H
    • Total Pages
      1
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2015 Annual Research Report
  • [Book] Methanocella. In Bergey’s Manual of Systematics of Archaea and Bacteria2016

    • Author(s)
      Sakai S and Imachi H
    • Total Pages
      6
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2015 Annual Research Report
  • [Book] Methanoregulaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria2016

    • Author(s)
      Imachi H and Sakai S
    • Total Pages
      4
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2015 Annual Research Report
  • [Book] Methanolinea. In Bergey’s Manual of Systematics of Archaea and Bacteria2016

    • Author(s)
      Imachi H and Sakai S
    • Total Pages
      4
    • Publisher
      John Wiley & Sons, Inc.
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-08-25  

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