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methanogenesis from root organic matters in deep subsurface

Research Project

Project/Area Number 18H05295
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Review Section Broad Section K
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

鎌形 洋一  国立研究開発法人産業技術総合研究所, 生命工学領域, 招聘研究員 (70356814)

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, 研究グループ長 (00421842)
眞弓 大介  国立研究開発法人産業技術総合研究所, 地質調査総合センター, 主任研究員 (30549861)
坂田 将  国立研究開発法人産業技術総合研究所, 地質調査総合センター, 招聘研究員 (70357101)
Project Period (FY) 2018-06-11 – 2023-03-31
Project Status Granted (Fiscal Year 2022)
Budget Amount *help
¥193,440,000 (Direct Cost: ¥148,800,000、Indirect Cost: ¥44,640,000)
Fiscal Year 2022: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2021: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2020: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2019: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2018: ¥41,600,000 (Direct Cost: ¥32,000,000、Indirect Cost: ¥9,600,000)
Keywordsメタン生成古細菌 / 地下圏微生物 / メタゲノム / 根源有機物 / 芳香族化合物 / 未知微生物 / 地下微生物 / 陸域地下圏 / 培養 / 環境ゲノム情報解析 / メタン / 生理生態 / 炭素循環 / 原油 / 石炭 / メタン生成アーキア / 共生微生物 / メタゲノム解析 / 根源有機化合物 / 芳香属分解代謝 / 絶対嫌気性微生物 / メタン生成菌 / 有機根源物質 / 石炭・原油分解 / 微生物共生ネットワーク
Outline of Annual Research Achievements

深部地下圏における生物的メタン生成は 1) 複雑な高分子堆積有機物が熱化学反応などによって溶解性有機物に変換される反応、2) 発酵微生物群がこれらを分解し、メタン生成菌ための主要基質を生成する反応 3) メタン生成菌によるメタン産生、から成り立っていると考えられる。しかし生物反応と非生物反応の境界線は不明瞭で、介在する有機物ならびに微生物を含めプロセスの全容は明らかになっていない。本提案では、提案者らの絶対嫌気高圧培養法・安定同位体質量分析法・分子遺伝学的代謝予測法などを駆使し、深部陸域地下圏に広がる微生物生存圏とそれを支える有機物群を俯瞰的かつ精細に捉えることによって生物起源メタンの成因解明を目指している。本年度は、深部地下圏の高温域における根源有機物の高温高圧反応生成物の同定に取組み、褐炭の熟成過程では炭化水素成分では中長鎖の直鎖アルカンやイソプレノイドアルカン、アルキルナフタレンが生成され、また極性成分では脂肪酸、グリセロール、安息香酸類、フェノール・ナフトール類が生成されることを明らかにした。これらの有機物は、根源有機物の熱分解生成物として深部地下生命圏を支える基質である可能性が示唆された。こうした根源有機物を利用する地下微生物の集積培養にも成功しつつある。中でも、Actinobacteria門の目もしくは科レベルで新規な地下バクテリアや門レベルの未培養アーキアの集積培養に成功するとともに、集積培養系を対象としたオミクス解析を実施し、代謝機能の解明を進めた。さらに石炭を単独でメタンに転換する地下メタン生成アーキアについて、その代謝経路をオミクス解析等により明らかにした。また深部地下圏から門レベルで新規な微生物の純粋分離に成功し、本微生物が本来真核生物の特徴とされるゲノムを包む膜をもつことを明らかにし、Nature Communications誌に論文発表するなど大きな成果を挙げた。

Current Status of Research Progress
Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

深部地下圏の高温域における根源有機物の高温高圧反応生成物の同定に成功し、深部地下生物圏のゲノム遺伝子情報データの獲得も順調に進んでいる。さらに、系統学的新規性の高い、機能的にもユニークな可能性のある新規地下微生物の集積培養化と機能解明でも想定以上の成果が得られている。さらに、石炭を単独でメタンに変換する深部地下圏由来のメタン生成アーキアについては、その未知の代謝経路をオミクス解析等により解き明かすとともに、深部地下圏から純粋分離に成功した新門微生物の特徴付けとユニークな細胞構造の解明についてNature姉妹誌に論文発表するなど、大きな成果を上げたことから、順調に進展していると考えている。

Strategy for Future Research Activity

本提案で主軸としている5つの項目(1. 「深部地下圏の高温域における根源有機物の高温高圧反応生成物の同定」、2. 「深部地下生物圏の大規模DNAシークエンシングによる多様性と代謝特性の解析」、3. 「高圧・常圧培養法を用いた根源有機物分解に関わる地下圏微生物の集積・分離・培養」、4. 「発酵微生物とメタン生成菌の共生系の高圧培養で生成するメタンの安定同位体比の測定」、5. 「芳香族メトキシ化合物を分解しメタンを生成する機構の解明」)について、いずれも順調に推移していることから、今の取組みを継続実施するとともに、特に、5の石炭由来成分からのメタン生成経路の解明については論文発表するとともに、それ以外の成果についても着実に国際誌に論文発表してゆく予定である。

Assessment Rating
Interim Assessment Comments (Rating)

A: In light of the aim of introducing the research area into the research categories, the expected progress has been made in research.

Report

(7 results)
  • 2020 Abstract (Interim Assessment) ( PDF )   Annual Research Report   Interim Assessment (Comments) ( PDF )
  • 2019 Annual Research Report
  • 2018 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report

Research Products

(32 results)

All 2021 2020 2019 2018 Other

All Int'l Joint Research (5 results) Journal Article (17 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 17 results,  Open Access: 13 results) Presentation (9 results) (of which Int'l Joint Research: 6 results,  Invited: 7 results) Remarks (1 results)

  • [Int'l Joint Research] University of Dusseldorf/Max-Planck-Institut Kohlenforschung/Universittsmedizin Berlin(ドイツ)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Oklahoma/University of Illinois(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Sichuan University/City University of Hong Kong(中国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Strasbourg(フランス)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Imperial College, London(英国)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N,2021

    • Author(s)
      Sakamoto S, Nobu MK, Mayumi D, Tamazawa S, Kusada H, Yonebayashi H, Iwama H, Ikarashi M, Wakayama T, Maeda H, Sakata S, Tamura T, Nomura N,
    • Journal Title

      Syst Appl Microbiol

      Volume: 44 Pages: 126154-126154

    • DOI

      10.1016/j.syapm.2020.126154

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Desulfovibrio subterraneus sp. nov., a mesophilic sulfate-reducing deltaproteobacterium isolated from a deep siliceous mudstone formation2021

    • Author(s)
      Ueno Akio、Tamazawa Satoshi、Tamamura Shuji、Murakami Takuma、Kiyama Tamotsu、Inomata Hidenori、Amano Yuki、Miyakawa Kazuya、Tamaki Hideyuki、Naganuma Takeshi、Kaneko Katsuhiko
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 71 Pages: 004683-004683

    • DOI

      10.1099/ijsem.0.004683

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Parallel Evolution of Enhanced Biofilm Formation and Phage-Resistance in Pseudomonas aeruginosa during Adaptation Process in Spatially Heterogeneous Environments2021

    • Author(s)
      Yamamoto Kyosuke、Kusada Hiroyuki、Kamagata Yoichi、Tamaki Hideyuki
    • Journal Title

      Microorganisms

      Volume: 9 Pages: 569-569

    • DOI

      10.3390/microorganisms9030569

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] An iron corrosion-assisted H2-supplying system: a culture method for methanogens and acetogens under low H2 pressures2020

    • Author(s)
      Souichiro Kato, Motoko Takashino, Kensuke Igarashi, Hanako Mochimaru, Daisuke Mayumi, Hideyuki Tamaki
    • Journal Title

      Scientific Reports

      Volume: 10 Pages: 19124-19124

    • DOI

      10.1038/s41598-020-76267-z

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Isolation of a member of the candidate phylum ‘Atribacteria’ reveals a unique cell membrane structure2020

    • Author(s)
      Katayama Taiki、Nobu Masaru K.、Kusada Hiroyuki、Meng Xian-Ying、Hosogi Naoki、Uematsu Katsuyuki、Yoshioka Hideyoshi、Kamagata Yoichi、Tamaki Hideyuki
    • Journal Title

      Nature Communications

      Volume: 11 Pages: 6381-6381

    • DOI

      10.1038/s41467-020-20149-5

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses2020

    • Author(s)
      Nobu Masaru K.、Narihiro Takashi、Mei Ran、Kamagata Yoichi、Lee Patrick K. H.、Lee Po-Heng、McInerney Michael J.、Liu Wen-Tso
    • Journal Title

      Microbiome

      Volume: 8 Pages: 111-111

    • DOI

      10.1186/s40168-020-00885-y

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism2020

    • Author(s)
      Preiner Martina、Igarashi Kensuke、Muchowska Kamila B.、Yu Mingquan、Varma Sreejith J.、Kleinermanns Karl、Nobu Masaru K.、Kamagata Yoichi、T?ys?z Harun、Moran Joseph、Martin William F.
    • Journal Title

      Nature Ecology & Evolution

      Volume: 4 Pages: 534-542

    • DOI

      10.1038/s41559-020-1125-6

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Different Interspecies Electron Transfer Patterns during Mesophilic and Thermophilic Syntrophic Propionate Degradation in Chemostats2020

    • Author(s)
      Chen Ya-Ting、Zeng Yan、Wang Hui-Zhong、Zheng Dan、Kamagata Yoichi、Narihiro Takashi、Nobu Masaru Konishi、Tang Yue-Qin
    • Journal Title

      Microbial Ecology

      Volume: 80 Pages: 120-132

    • DOI

      10.1007/s00248-020-01485-x

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Improved Isolation of Uncultured Anaerobic Bacteria using Medium Prepared with Separate Sterilization of Agar and Phosphate2020

    • Author(s)
      Kato Souichiro、Terashima Mia、Yama Ayano、Sato Megumi、Kitagawa Wataru、Kawasaki Kosei、Kamagata Yoichi
    • Journal Title

      Microb. Environ.

      Volume: 35 Issue: 1 Pages: n/a

    • DOI

      10.1264/jsme2.me19060

      10.1264/jsme2.ME19060

    • NAID

      130007793538

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Isolation of an archaeon at the prokaryote-eukaryote interface2020

    • Author(s)
      Imachi H., Nobu M. K., Nakahara N., Morono Y., Ogawara M., Takaki Y., Takano Y., Uematsu K., Ikuta T., Ito M., Matsui Y., Miyazaki M., Murata K., Saito Y., Sakai S., Song C., Tasumi E., Yamanaka Y., Yamaguchi T., Kamagata Y., Tamaki H., Takai K.
    • Journal Title

      Nature

      Volume: 577 Pages: 519-525

    • DOI

      10.1038/s41586-019-1916-6

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old2019

    • Author(s)
      Tamaki Hideyuki
    • Journal Title

      Microb. Environ.

      Volume: 34 Issue: 2 Pages: 117-120

    • DOI

      10.1264/jsme2.me3402rh

      10.1264/jsme2.ME3402rh

    • NAID

      130007668647

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Improvement of terrestrial groundwater sampling method affects microbial community analysis2019

    • Author(s)
      Akio Ueno, Satoshi Tamazawa, Shuji Tamamura, Noritaka Aramaki, A. K. M. Alam Badrul, Takuma Murakami, Shinji Yamaguchi, Junya Yamagishi, Hideyuki Tamaki, Daisuke Mayumi, Takeshi Naganuma & Katsuhiko Kaneko
    • Journal Title

      Geomicrobiology Journal

      Volume: 36 Pages: 303-316

    • DOI

      10.1080/01490451.2018.1534900

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tripartite Symbiosis of an Anaerobic Scuticociliate with Two Hydrogenosome-Associated Endosymbionts, a Holospora-Related Alphaproteobacterium and a Methanogenic Archaeon2019

    • Author(s)
      Takeshita Kazutaka、Yamada Takanori、Kawahara Yuto、Narihiro Takashi、Ito Michihiro、Kamagata Yoichi、Shinzato Naoya
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 85 Pages: 24-24

    • DOI

      10.1128/aem.00854-19

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [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 Pages: 1185-1194

    • DOI

      10.1099/ijsem.0.003291

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conductive Iron Oxides Promote Methanogenic Acetate Degradation by Microbial Communities in a High-Temperature Petroleum Reservoir2019

    • Author(s)
      加藤創一郎、和田薫、北川航、眞弓大介、五十嵐雅之、曽根輝夫、浅野孝蔵、鎌形洋一
    • Journal Title

      Microb. Environ.

      Volume: 34 Issue: 1 Pages: 95-98

    • DOI

      10.1264/jsme2.me18140

      10.1264/jsme2.ME18140

    • NAID

      130007627745

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [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 Pages: 4503-4511

    • DOI

      10.1111/1462-2920.14388

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Isolation of previously uncultured slow-growing bacteria by using a simple modification in the preparation of agar media2018

    • Author(s)
      Souichiro Kato, Ayasa Yamagishi, Serina Daimon, Kosei Kawasaki, Hideyuki Tamaki, Wataru Kitagawa, Ayumi Abe, Michiko Tanaka, Teruo Sone, Kozo Asano, Yoichi Kamagata
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 84

    • DOI

      10.1128/aem.00807-18

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Presentation] 深部地下圏でメトキシ芳香族化合物分解を担う新規共生細菌の生存戦略2021

    • Author(s)
      坂本 幸子、NOBU MASARU KONISHI、眞弓 大介、玉澤 聡、米林英治、岩間弘樹、五十嵐雅之、若山樹、前田 治男、坂田 将、田村 具博、野村暢彦、鎌形 洋一、玉木 秀幸
    • Organizer
      日本農芸化学会2021年度仙台大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 深部地下圏でメトキシ芳香族化合物分解を担う新規共生細菌の発見及び生存戦略の解明2021

    • Author(s)
      坂本 幸子、NOBU MASARU KONISHI、眞弓 大介、玉澤 聡、米林英治、岩間弘樹、五十嵐雅之、若山樹、前田 治男、坂田 将、田村 具博、野村暢彦、鎌形 洋一、玉木 秀幸
    • Organizer
      第15回日本ゲノム微生物学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Deep subsurface microbes involved in the degradation of complex organic materials2021

    • Author(s)
      鎌形洋一
    • Organizer
      8TH INTERNATIONAL SYMPOSIUM ON APPLIED MICROBIOLOGY AND MOLECULAR BIOLOGY IN OIL SYSTEMS
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Importance of isolation in metagenomic era2019

    • Author(s)
      Kamagata, Y
    • Organizer
      Annual Conference and International Symposium, Chinese Society of Microbial Ecology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cultivation of fastidious anaerobes2019

    • Author(s)
      Kamagata, Y
    • Organizer
      EMBO workshop, Wageningen, The Netherlands
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Exploring novel and functionally important organisms in natural environments2019

    • Author(s)
      Kamagata, Y
    • Organizer
      International Meeting of the Microbiological Society of Korea
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Syntrophic/symbiotic associations with different species of microbes2018

    • Author(s)
      Kamagata, Y
    • Organizer
      Conference and International Symposium, Chinese Society of Microbial Ecology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cultivation-based microbial ecology2018

    • Author(s)
      Kamagata, Y
    • Organizer
      Plenary talk at the 17thInternational Symposium on Microbial Ecology, Leipzig, Germany
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 未知の微生物を”培養”して深淵な生命機能を探る2018

    • Author(s)
      玉木秀幸
    • Organizer
      第32回日本微生物生態学会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Remarks] 地下で発見!ゲノムが膜で包まれたバクテリア

    • URL

      https://www.aist.go.jp/aist_j/press_release/pr2020/pr20201214/pr20201214.html

    • Related Report
      2020 Annual Research Report

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Published: 2018-06-12   Modified: 2022-12-28  

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