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

2011 Fiscal Year Final Research Report

• Project/Area Number: 21687006
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Biodiversity/Systematics
• Research Institution: Japan 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
• 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

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.

Research Products

• [Journal Article] Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes (2012)
  • 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
  • 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. nov (2012)
  • 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
  • Peer Reviewed
• [Journal Article] Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales (2011)
  • Author(s): Sakai, S., Y. Takaki, S. Shimamura, M. Sekine, T. Tajima, H. Kosugi, N. Ichikawa, E. Tasumi, A. T. Hiraki, A. Shimizu, Y. Kato, R. Nishiko, K. Mori, N. Fujita, H. Imachi and Ken Takai
  • Journal Title: PLoS ONE Volume: 6(7) Pages: e22898
  • DOI: doi:10.1371/journal.pone.0022898.
  • Peer Reviewed
• [Journal Article] Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Methanoregula formicica sp. nov., a novel methane-producing archaeon isolated from methanogenic sludge (2011)
  • 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
  • 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 (2010)
  • 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
  • Peer Reviewed
• [Journal Article] Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil (2010)
  • Author(s): Sakai, S., R. Conrad, W. Liesack and H. Imachi
  • Journal Title: Int. J. Syst. Evol. Microbiol Volume: 60 Pages: 2918-2923
  • 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 probes (2010)
  • Author(s): Kawakami, S., K. Kubota, H. Imachi, T. Yamaguchi, H. Harada and A. Ohashi
  • Journal Title: Microb. Environ Volume: 25 Pages: 15-21
  • 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 Japan (2009)
  • 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
  • Peer Reviewed
• [Journal Article] Sequence specific bacterial growth inhibition by peptide nucleic acid targeted to the mRNA binding site of 16S rRNA (2009)
  • Author(s): Hatamoto, M., K. Nakai, A. Ohashi and H. Imachi
  • Journal Title: Appl. Microbiol. Biotechnol Volume: 84 Pages: 1161-1168
  • Peer Reviewed
• [Journal Article] Cultivation of methanogens under low hydrogen conditions by using coculture method (2009)
  • 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
  • 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
  • Peer Reviewed
• [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
• [Presentation] Cultivation of Methanogenic Community from Marine Subsurface Sediments Using a Continuous-Flow Bioreactor (2011)
  • 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
• [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
• [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
• [Presentation] Isolation and characterization of novel bacteria which were frequently detected in marine subsurface sediments (2010)
  • 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
• [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
• [Presentation] Cultivation of methanogenic microbial community from deep subseafloor sediment using continuous-flow bioreactor (2010)
  • 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
• [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
• [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
• [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
• [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
• [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
• [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。
• [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
• [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