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Archaeal hunting : explore new metabolic functions of uncultured Archaea by using new culturing techniques

Research Project

Project/Area Number 21687006
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
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, 海洋・極限環境生物圏領域, 主任研究員 (20361933)

Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥27,170,000 (Direct Cost: ¥20,900,000、Indirect Cost: ¥6,270,000)
Fiscal Year 2011: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Fiscal Year 2010: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Fiscal Year 2009: ¥11,570,000 (Direct Cost: ¥8,900,000、Indirect Cost: ¥2,670,000)
Keywordsアーキア / 分離培養 / 16S rRNA遺伝子 / メタン / 嫌気的メタン酸化 / 古細菌 / 分離
Research Abstract

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. In this study, I attempted to cultivate and isolate uncultured Archaea from various environmental samples using new cultivation techniques I developed. As a result, I successfully cultivated and isolated methanogenic and methanotrophic Archaea. These results strongly suggest that the culturing methods I developed are effective ways to cultivate fastidious but ecologically important archaeal species that would otherwise escape conventional isolation strategies. Also, these isolates obtained in this study would promote to understand carbon cycle on earth and to develop new environmental technologies.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (56 results)

All 2012 2011 2010 2009 Other

All Journal Article (28 results) (of which Peer Reviewed: 27 results) Presentation (25 results) Remarks (3 results)

  • [Journal Article] Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes2012

    • Author(s)
      Kawakami, S., T. Hasegawa, H. Imachi, T. Yamaguchi, H. Harada, A. Ohashi and K. Kubota
    • Journal Title

      J. Microbiol. Methods

      Volume: 88 Pages: 218-223

    • NAID

      120005308241

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Methanolinea mesophila, sp. nov., a hydrogenotrophic methanogen isolated from a rice field in Taiwan, and proposal of the new archaeal family Methanoregulaceae fam. nov2012

    • Author(s)
      Sakai, S., M. Ehara, I-C. Tseng, T. Yamaguchi, S. L. Brauer, H. Cadillo-Quiroz, S. H. Zinder and H. Imachi
    • Journal Title

      Int. J. Syst

      Volume: 62 Pages: 1389-1395

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Geofilum rubicundum gen.nov.sp.nov., isolated from a deep subseafloor sediment off the Shimokita Peninsula2012

    • Author(s)
      Miyazaki, M.
    • Journal Title

      International Journal of Systematic Evolutionary of Microbiology

      Volume: 61 Pages: 1076-1081

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales2011

    • Author(s)
      Sanae Sakai
    • Journal Title

      PLoS ONE

      Volume: 6 Issue: 7 Pages: e22898-e22898

    • DOI

      10.1371/journal.pone.0022898

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor2011

    • Author(s)
      Imachi, H., K. Aoi, E. Tasumi, Y. Saito, Y. Yamanaka, Y. Saito, T. Yamaguchi, H. Tomaru, R. Takeuchi, Y. Morono, F. Inagaki and K. Takai
    • Journal Title

      ISME J.

      Volume: 5 Pages: 1913-1925

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Methanoregula formicica sp. nov., a novel methane-producing archaeon isolated from methanogenic sludge2011

    • Author(s)
      Yashiro, Y., S. Sakai, M. Ehara, M. Miyazaki, T. Yamaguchi and H. Imachi
    • Journal Title

      Int. J. Syst.

      Volume: 61 Pages: 53-59

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor2011

    • Author(s)
      Imachi, H.
    • Journal Title

      The ISME Journal

      Volume: 5 Pages: 1913-1925

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative study of subseafloor microbial community structures in deeply buried coral fossils and sediment matrices from the Challenger Mound in the Porcupine Seabight2011

    • Author(s)
      Hoshino, T.
    • Journal Title

      Frontiers in Microbiology

      Volume: 2

    • DOI

      10.3389/fmicb.2011.00231

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Partial nitrification in an airlift activated sludge reactor with experimental and theoretical assessments of the pH gradient inside the sponge support medium2011

    • Author(s)
      Uemura, S.
    • Journal Title

      International Journal of Environmental Research

      Volume: 5 Pages: 33-40

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef2010

    • Author(s)
      Nunoura, T., M. Hirai, H. Imachi, M. Miyazaki, H. Makita, H. Hirayama, Y. Furushima, H. Yamamoto and K. Takai
    • Journal Title

      Arch. Microbiol

      Volume: 192 Pages: 811-819

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil2010

    • Author(s)
      Sakai, S., R. Conrad, W. Liesack and H. Imachi
    • Journal Title

      Int. J. Syst. Evol. Microbiol

      Volume: 60 Pages: 2918-2923

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Detection of single copy genes by two-pass tyramide signal amplification fluorescence in situ hybridization(two-pass TSA-FISH) with single oligonucleotide probes2010

    • Author(s)
      Kawakami, S., K. Kubota, H. Imachi, T. Yamaguchi, H. Harada and A. Ohashi
    • Journal Title

      Microb. Environ

      Volume: 25 Pages: 15-21

    • NAID

      10025921485

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb.nov., and emended description of the genus Kosmotoga.2010

    • Author(s)
      Nunoura, T.
    • Journal Title

      Archives of Microbiology

      Volume: 192 Pages: 811-819

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Two-pass TSA-FISH法を用いた微生物機能遺伝子の視覚的検出技術2010

    • Author(s)
      長谷川拓也
    • Journal Title

      環境バイオテクノロジー学会誌

      Volume: 10 Pages: 97-103

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Methanoregula formicica sp. nov., a novel methane-producing archaeon isolated from methanogenic sludge2010

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

      International Journal of Systematic and Evolutionary Microbilogy (印刷中)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Peptide nucleic acids (PNAs) antisense effect to bacterial growth and their application potentiality in biotechnology2010

    • Author(s)
      Hatamoto, M.
    • Journal Title

      Applied Microbiology and Biotechnology 86

      Pages: 397-402

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Detection of single copy genes by two-pass tyramide signal amplification fluorescence in situ hybridization(two-pass TSA-FISH) with single olig onucleotide probes2010

    • Author(s)
      Kawakami, S.
    • Journal Title

      Microbes and Environments 25

      Pages: 15-21

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen, isolated from Italian rice field soil2010

    • Author(s)
      Sakai, S
    • Journal Title

      Intemational Journal of Systematic and Evolutionary Microbilogy (印刷中)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular characterization of potential nitrogen fixation by anaerobic methane oxidizing archaea in the methane-seep sediments at the No.8 Kumano Knoll in the Kumano Basin, offshore of Japan2009

    • Author(s)
      Miyazaki, J., R. Higa, T. Toki, J. Ashi, U. Tsunogai, T. Nunoura, H. Imachi and K. Takai
    • Journal Title

      Appl. Environ. Microbiol

      Volume: 75 Pages: 7153-7162

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Sequence specific bacterial growth inhibition by peptide nucleic acid targeted to the mRNA binding site of 16S rRNA2009

    • Author(s)
      Hatamoto, M., K. Nakai, A. Ohashi and H. Imachi
    • Journal Title

      Appl. Microbiol. Biotechnol

      Volume: 84 Pages: 1161-1168

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cultivation of methanogens under low hydrogen conditions by using coculture method2009

    • Author(s)
      Sakai, S., H. Imachi, Y. Sekiguchi, I-C. Tseng, A. Ohashi, H. Harada and Y. Kamagata
    • Journal Title

      Appl. Environ. Microbiol

      Volume: 75 Pages: 4892-4896

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs(ANMEs)2009

    • Author(s)
      Miyashita, A., H. Mochimaru, H. Kazama, A. Ohashi, T. Yamaguchi, T. Nunoura, K. Horikoshi, K. Takai and H. Imachi
    • Journal Title

      FEMS Microbiol

      Volume: 297 Pages: 31-37

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Development of 16S rRNA gene-targeted primers for detection of archaeal anaerobic methanotrophs (ANMEs)2009

    • Author(s)
      Miyashita, A.
    • Journal Title

      FEMS Microbiology Letters 297

      Pages: 31-37

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cultivation of methanogens under low hydrogen conditions by using coculture method2009

    • Author(s)
      Sakai, S.
    • Journal Title

      Applied and Environmental Microbiology 75

      Pages: 4892-4896

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sequence specific bacterial growth inhibition by peptide nucleic acid tareted to the mRNA binding site of 16S rRNA2009

    • Author(s)
      Hatamoto, M.
    • Journal Title

      Applied Microbiology and Biotechnology 84

      Pages: 1161-1168

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular characterization of potential nitrogen fixation by anaerobic methane oxidizing archaea in the methane-seep sediments at the No. 8 Kumano Knoll in the Kumano Basin, offshore of Japan2009

    • Author(s)
      Miyazaki, J.
    • Journal Title

      Applied and Environmental Microbiology 75

      Pages: 7153-7162

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 排水処理リアクターを利用した難培養性深海底メタン生成菌の培養2009

    • Author(s)
      井町寛之
    • Journal Title

      用水と廃水 51

      Pages: 53-76

    • NAID

      40016710039

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 有新規微生物間共生培養法によるメタン生成古細菌の分離培養と系統分類2009

    • Author(s)
      井町寛之
    • Journal Title

      IFO Research Communications 23

      Pages: 39-56

    • Related Report
      2009 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2011

    • Author(s)
      青木仁孝
    • Organizer
      第28回土木学会新潟会研究調査発表会
    • Place of Presentation
      ハイブ長岡、長岡
    • Year and Date
      2011-11-22
    • Related Report
      2011 Final 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2011

    • Author(s)
      青木仁孝
    • Organizer
      第28回土木学会新潟会研究調査発表会
    • Place of Presentation
      新潟県長岡市ハイブ長岡
    • Year and Date
      2011-11-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Cultivation of Methanogenic Community from Marine Subsurface Sediments Using a Continuous-Flow Bioreactor2011

    • Author(s)
      Imachi, H
    • Organizer
      8th International Symposium for Subsurface Microbiology ISSM 2011
    • Place of Presentation
      Garmisch-Partenkirchen, Germany
    • Year and Date
      2011-09-12
    • Related Report
      2011 Final Research Report
  • [Presentation] Cultivation of methanogenic community from marine subsurface sediments using a continuous-flow bioreactor2011

    • Author(s)
      Imachi, H.
    • Organizer
      8th International Symposium for Subsurface Microbiology
    • Place of Presentation
      Garmisch-partenkirchen, Germany
    • Year and Date
      2011-09-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] 深海底堆積物環境に生息する難培養性アーキアの分離培養の試み2011

    • Author(s)
      青木仁孝
    • Organizer
      第24回日本Archaea研究会
    • Place of Presentation
      慶應義塾大学先端生命科学研究所メタボロームキャンパス、鶴岡
    • Year and Date
      2011-09-02
    • Related Report
      2011 Final Research Report
  • [Presentation] 深海底堆積物環境に生息する難培養性アーキアの分離培養の試み2011

    • Author(s)
      青木仁孝
    • Organizer
      第24回日本Archaea研究会
    • Place of Presentation
      慶應義塾大学先端生命科学研究所メタボロームキャンパス
    • Year and Date
      2011-09-02
    • Related Report
      2011 Annual Research Report
  • [Presentation] 嫌気的メタン酸化反応を担う深海底未培養アーキアの培養2011

    • Author(s)
      江原真之
    • Organizer
      第45回日本水環境学会年会
    • Place of Presentation
      北海道大学
    • Year and Date
      2011-03-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] 深海堆積物から分離したメタン生成アーキアの菌学的特徴とその圧力応答2010

    • Author(s)
      田角栄二
    • Organizer
      第26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学大学会館、つくば
    • Year and Date
      2010-11-25
    • Related Report
      2011 Final Research Report
  • [Presentation] Isolation and characterization of novel bacteria which were frequently detected in marine subsurface sediments2010

    • Author(s)
      酒井早苗
    • Organizer
      26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学大学会館、つくば
    • Year and Date
      2010-11-25
    • Related Report
      2011 Final Research Report
  • [Presentation] FISH法による深海底未知アーキアの検出2010

    • Author(s)
      江原真之
    • Organizer
      第26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学大学会館、つくば
    • Year and Date
      2010-11-25
    • Related Report
      2011 Final Research Report
  • [Presentation] FISH法による深海底未知アーキアの検出2010

    • Author(s)
      江原真之
    • Organizer
      第26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学 大学会館
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] Isolation and characterization of novel bacteria which were frequently detected in marine subsurface sediments.2010

    • Author(s)
      酒井早苗
    • Organizer
      第26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学 大学会館
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] 深海堆積物から分離したメタン生成アーキアの菌学的特徴とその圧力応答2010

    • Author(s)
      田角栄二
    • Organizer
      第26回日本微生物生態学会大会
    • Place of Presentation
      筑波大学 大学会館
    • Year and Date
      2010-11-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] 難培養性微生物の培養技術2010

    • Author(s)
      井町寛之
    • Organizer
      第13回日本水環境学会シンポジウム
    • Place of Presentation
      京都大学吉田キャンパス
    • Year and Date
      2010-09-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] 深海底未知アーキアの純粋分離株取得に向けて2010

    • Author(s)
      江原真之
    • Organizer
      第23回日本Archaea研究会
    • Place of Presentation
      名古屋大学ベンチャーホール
    • Year and Date
      2010-07-10
    • Related Report
      2010 Annual Research Report
  • [Presentation] Cultivation of methanogenic microbial community from deep subseafloor sediment using continuous-flow bioreactor2010

    • Author(s)
      Imachi, H.
    • Organizer
      110th ASM(American Society for Microbiology) annual meeting
    • Place of Presentation
      San Diego, USA
    • Year and Date
      2010-05-22
    • Related Report
      2011 Final Research Report
  • [Presentation] 嫌気的メタン酸化反応を担う深海底未培養アーキアの培養2010

    • Author(s)
      江原真之
    • Organizer
      第45回日本水環境学会年会
    • Place of Presentation
      北海道大学、札幌
    • Year and Date
      2010-03-17
    • Related Report
      2011 Final Research Report
  • [Presentation] 微生物学的廃水処理リアクターを利用した難培養性深海メタン生成アーキアの培養2010

    • Author(s)
      青井健
    • Organizer
      第44回日本水環境学会年会
    • Place of Presentation
      福岡大学七隈キャンパス、福岡
    • Year and Date
      2010-03-16
    • Related Report
      2011 Final Research Report
  • [Presentation] 微生物学的廃水処理リアクターを利用した難培養性深海メタン生成アーキアの培養2010

    • Author(s)
      青井健
    • Organizer
      第44回日本水環境学会年会
    • Place of Presentation
      福岡大学七隈キャンパス
    • Year and Date
      2010-03-16
    • Related Report
      2009 Annual Research Report
  • [Presentation] 微生物学的廃水処理リアクターを利用した深海底メタン生成菌の培養の試み2009

    • Author(s)
      青井健
    • Organizer
      第25回日本微生物生態学会
    • Place of Presentation
      大学東広島キャンパス、東広島
    • Year and Date
      2009-11-21
    • Related Report
      2011 Final Research Report
  • [Presentation] 嫌気的メタン酸化アーキアの培養の試み2009

    • Author(s)
      井町寛之
    • Organizer
      第25回日本微生物生態学会
    • Place of Presentation
      広島大学東広島キャンパス、東広島
    • Year and Date
      2009-11-21
    • Related Report
      2011 Final Research Report
  • [Presentation] 嫌気的メタシ酸化アーキアの培養の試み2009

    • Author(s)
      井町寛之
    • Organizer
      第25回日本微生物生態学会年会
    • Place of Presentation
      広島大学東広島キャンパス
    • Year and Date
      2009-11-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] 微生物学的廃水処理リアクターを利用した深海底メタン生成菌の培養の試み2009

    • Author(s)
      青井健
    • Organizer
      第25回日本微生物生態学会年会
    • Place of Presentation
      広島大学東広島キャンパス
    • Year and Date
      2009-11-21
    • Related Report
      2009 Annual Research Report
  • [Presentation] 廃水処理リアクターを用いた深海底未知アーキアの培養2009

    • Author(s)
      江原真之
    • Organizer
      第27回土木学会新潟会研究調査発表会
    • Place of Presentation
      朱鷺メッセ、新潟
    • Year and Date
      2009-11-10
    • Related Report
      2011 Final Research Report
  • [Presentation] 深海底堆積物からの難培養性メタン生成アーキアの培養-石の上にも3年物語-2009

    • Author(s)
      井町寛之
    • Organizer
      日本Archaea研究会第22回大会
    • Place of Presentation
      産業技術総合研究所北海道センター
    • Year and Date
      2009-07-11
    • Related Report
      2009 Annual Research Report
  • [Remarks] (1)プレス発表、「新しい培養手法により効率的にメタン生成菌を培養することに成功.海底下における天然バイオガス発生メカニズムの解明や応用開発研究に糸口」、2011年6月7日に文部科学省にてレク付きプレス発表を行った。翌朝の日刊工業新聞や日経産業新聞等で記事として紹介された。

    • Related Report
      2011 Final Research Report
  • [Remarks] (2) TV出演、中京テレビ、トヨタエコスペシャル、2010年7月19日放送

    • Related Report
      2011 Final Research Report
  • [Remarks] (3) TV出演、NHK、サイエンスZERO「二酸化炭素を資源に変える」、2010年5月15日放送

    • Related Report
      2011 Final Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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