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Archaeal hunting: cultivation of uncultured fastidious Archaea

Research Project

Project/Area Number 24687011
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Biodiversity/Systematics
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

IMACHI Hiroyuki  独立行政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)

Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000)
Fiscal Year 2014: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Fiscal Year 2013: ¥10,400,000 (Direct Cost: ¥8,000,000、Indirect Cost: ¥2,400,000)
Fiscal Year 2012: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Keywordsアーキア / 分離培養 / 16S rRNA遺伝子 / メタン / 古細菌 / 生態学 / 微生物 / バイオリアクター / メタン生成菌
Outline of Final Research Achievements

Cultured enrichments and isolates are important in developing 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, I attempted to cultivate and isolate uncultured Archaea using a new cultivation technique I developed and molecular techniques. As a result, I successfully obtained three anaerobic methane-oxidizing microbial communities that contain phylogenetically diverse of uncultured archaeal groups. The single cell genome analysis for one of the enriched microbial communities revealed that an uncultured archaeal group might have a unique sulfur metabolism gene. Unfortunately, isolates of the uncultured archaeal group was not obtained during the period of this study, but the enrichments and single cell genome analysis provide new information about the uncultured archaea.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (23 results)

All 2015 2014 2013 2012

All Journal Article (10 results) (of which Peer Reviewed: 9 results,  Acknowledgement Compliant: 7 results,  Open Access: 5 results) Presentation (11 results) (of which Invited: 2 results) Book (2 results)

  • [Journal Article] Presence of a novel methanogenic archaeal lineage in anaerobic digesters inferred from mcrA and 16S rRNA gene phylogenetic analyses2015

    • Author(s)
      Saito Y, Aoki M, Hatamoto M, Yamaguchi T, Takai K and Imachi H
    • Journal Title

      Journal of Water and Environmental Technology

      Volume: 13 Pages: 279-289

    • NAID

      130005076093

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta2014

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

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 64 Issue: Pt_8 Pages: 2798-2804

    • DOI

      10.1099/ijs.0.062463-0

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor2014

    • Author(s)
      Aoki M, Ehara M, Saito Y, Yoshioka H, Miyazaki M, Saito Y, Miyashita A, Kawakami S, Yamaguchi T, Ohashi A, Nunoura T, Takai K, and Imachi H
    • Journal Title

      PLOS ONE

      Volume: 9 Issue: 8 Pages: 1-14

    • DOI

      10.1371/journal.pone.0105356

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Complete genome sequence of Methanoregula formicica SMSPT, a mesophilic hydrogenotrophic methanogen isolated from a methanogenic upflow anaerobic sludge blanket reactor2014

    • Author(s)
      Yamamoto, K., H. Tamaki, H. Cadillo-Quiroz, H. Imachi, N. Kyrpides, T. Woyke, L. Goodwin, S. H. Zinder, Y. Kamagata and W-T. Liu
    • Journal Title

      Genome Annoucement

      Volume: 2 Issue: 5

    • DOI

      10.1128/genomea.00870-14

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Complete genome sequence of Methanolinea tarda NOBI-1T, a hydrogenotrophic methanogen isolated from methanogenic digester sludge2014

    • Author(s)
      Yamamoto, K., H. Tamaki, H. Cadillo-Quiroz, H. Imachi, N. Kyrpides, T. Woyke, L. Goodwin, S. H. Zinder, Y. Kamagata and W-T. Liu
    • Journal Title

      Genome Annoucement

      Volume: 2 Issue: 5

    • DOI

      10.1128/genomea.00876-14

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophlic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta2014

    • Author(s)
      Miyazaki, M., S. Sakai, K. M. Ritalahti, Yayoi Saito, Y. Yamanaka, Yumi Saito, A. Tame, K. Uematsu, F. E. Loeffler, K. Takai and H. Imachi
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 64 Issue: Pt_12 Pages: 4147-4154

    • DOI

      10.1099/ijs.0.068148-0

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] 海底堆積物中のメタン生成および酸化反応を担う微生物 (特集 地球温暖化と海洋微生物)2014

    • Author(s)
      青木仁孝、井町寛之
    • Journal Title

      生物の科学 遺伝

      Volume: 687 Pages: 486-491

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment2014

    • Author(s)
      Imachi, H., S. Sakai, J. S. Lipp, M. Miyazaki, Y. Saito, Y. Yamanaka, K.-U. Hinrichs, F. Inagaki and Ken Takai
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 64 Issue: Pt_3 Pages: 812-818

    • DOI

      10.1099/ijs.0.057547-0

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Biological CO_2 conversion to acetate in subsurface coal-sand formation using a high-pressure reactor system2013

    • Author(s)
      Ohtomo, Y., Ijiri, A., Ikegawa, Y., Tsutsumi, M., Imachi, H., Uramoto, G., Hoshino, T., Morono, Y., Sakai, S., Saito, Y., Tanikawa, W., Hirose, T., and Inagaki, F
    • Journal Title

      Frontiers in Microbiology

      Volume: Article no. 361 Pages: 4-4

    • DOI

      10.3389/fmicb.2013.00361

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detection of coenzyme F430 in deep sea sediments : A key molecule for biological methanogenesis2013

    • Author(s)
      Takano, Y.
    • Journal Title

      Organic Geochemistry

      Volume: 58 Pages: 137-140

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] 持続的CO2還元を可能にするバイオリアクターについて2015

    • Author(s)
      井町寛之
    • Organizer
      平成26年度水溶性天然ガス田の生産に係る技術検討会 第4回水溶性天然ガス(ガス田)を対象とした炭素循環の可能性検討会
    • Place of Presentation
      独立行政法人石油天然ガス・金属鉱物資源機構東京本部、東京都港区
    • Year and Date
      2015-01-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Cultivation of methanogenic microbial community from the deeply buried coalbeds in the ocean2014

    • Author(s)
      Imachi H, Tasumi E, Ijiri A, Konno U, Morono Y, Ito M, Takai K, Inagaki F and IODP Expedition 337 Scientists
    • Organizer
      9th International Symposium on Subsurface Microbiology (ISSM)
    • Place of Presentation
      Pacific Grove, CA, USA
    • Year and Date
      2014-10-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a down-flow hanging sponge bioreactor2014

    • Author(s)
      Imachi, H., Tasumi, E., Ijiri, A., Konno, U., Morono, Y., Ito, M., Takai, K., Inagaki, F. and IODP Expedition 337 Scientists
    • Organizer
      15th International Symposium on Microbial Ecology (ISME15)
    • Place of Presentation
      Seoul, South Korea
    • Year and Date
      2014-08-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] 海底下メタン菌の連続リアクター培養とCO2資源化への応用2014

    • Author(s)
      井町寛之
    • Organizer
      シンポジウム「海底下の炭化水素資源・炭素循環と地球生命工学」
    • Place of Presentation
      東京大学理学部小柴ホール、東京都文京区
    • Year and Date
      2014-01-24
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Cultivation of methanogenic community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor2013

    • Author(s)
      Imachi, H.
    • Organizer
      AGU2013 Fall Meeting
    • Place of Presentation
      San Francisco, CA, USA
    • Year and Date
      2013-12-10
    • Related Report
      2013 Annual Research Report
  • [Presentation] 深海堆積物からの嫌気共生細菌の培養とその分離の試み2013

    • Author(s)
      斎藤弥生
    • Organizer
      第29回日本微生物生態学会大会
    • Place of Presentation
      鹿児島大学郡元キャンパス、鹿児島県鹿児島市
    • Year and Date
      2013-11-23
    • Related Report
      2013 Annual Research Report
  • [Presentation] Cultivation of methanogenic microbial community from 2-km deep subseafloor coalbeds using a continuous-flow bioreactor2013

    • Author(s)
      井町寛之
    • Organizer
      第29回日本微生物生態学会大会
    • Place of Presentation
      鹿児島大学郡元キャンパス、鹿児島県鹿児島市
    • Year and Date
      2013-11-23
    • Related Report
      2013 Annual Research Report
  • [Presentation] A long-term cultivation of an anaerobic methane-oxidizing sulfate-reducing community by a down-flow hanging sponge bioreactor2013

    • Author(s)
      Aoki, M.
    • Organizer
      The 5th Taiwan-Japan-Korea International Symposium on Microbial Ecology
    • Place of Presentation
      National Central University, Jhongli, Taiwan
    • Year and Date
      2013-11-01
    • Related Report
      2013 Annual Research Report
  • [Presentation] 嫌気的メタン酸化反応に関与する海底下未知アーキアの培養2013

    • Author(s)
      青木仁孝
    • Organizer
      第47回日本水環境学会年会
    • Place of Presentation
      大阪工業大学大宮キャンパス
    • Year and Date
      2013-03-10
    • Related Report
      2012 Annual Research Report
  • [Presentation] 廃水処理リアクターを用いた嫌気的メタン酸化反応を担う未知アーキアの培養2012

    • Author(s)
      青木仁孝
    • Organizer
      第67回土木学会年次講演会
    • Place of Presentation
      名古屋大学東山キャンパス
    • Year and Date
      2012-09-05
    • Related Report
      2012 Annual Research Report
  • [Presentation] Sponges as microbial habitats : cultivation of fastidious subseafloor sedimentary microbes using continuous-flow bioreactor.2012

    • Author(s)
      Imachi, H.
    • Organizer
      International Society for Microbial Ecology 14 (ISME14)
    • Place of Presentation
      Copenhagen, Denmark
    • Year and Date
      2012-08-22
    • Related Report
      2012 Annual Research Report
  • [Book] Family Methanocellaceae. In The Prokaryotes 4th Edition. Other Major Lineages of Bacteria and The Archaea2014

    • Author(s)
      Sakai, S., R. Conrad and H. Imachi
    • Total Pages
      1028
    • Publisher
      Springer
    • Related Report
      2014 Annual Research Report
  • [Book] Chapter 2.6 Cultivation of Subseafloor Prokaryotic Life, In Earth and Life Processes Discovered from Subseafloor Environment - A Decade of Science Achieved by the Integrated Ocean Drilling Program (IODP)2014

    • Author(s)
      Engelen, B. and Imachi, H
    • Total Pages
      789
    • Publisher
      Elsevier
    • Related Report
      2014 Annual Research Report

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Published: 2012-04-24   Modified: 2019-07-29  

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