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Characterization of ubiquitous but previously-overlooked nitrogen-fixing bacteria in soil ecosystems

Research Project

Project/Area Number 18K19165
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 38:Agricultural chemistry and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

Keishi Senoo  東京大学, 大学院農学生命科学研究科(農学部), 教授 (40206652)

Co-Investigator(Kenkyū-buntansha) 伊藤 英臣  国立研究開発法人産業技術総合研究所, 生命工学領域, 主任研究員 (70748425)
Project Period (FY) 2018-06-29 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2019: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2018: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords窒素固定微生物 / 鉄還元細菌 / 陸域土壌 / Anaeromyxobacter / Geobacter / 生物的窒素固定 / 鉄還元菌 / 窒素固定活性 / 土壌圏 / 窒素固定 / 水田土壌 / 土壌 / 微生物 / 陸域生態系
Outline of Final Research Achievements

Nitrogen fixation genes in Geobacter and Anaeromyxobacter were frequently detected in our metagenomic analysis of soils in Japan (paddy, upland, forest, sediment) and in the world (agricultural soils, sediment, forest, desert, polar), suggesting ubiquitous distribution of nitrogen-fixing iron-reducing bacteria in terrestrial environments. We isolated Geobacter and Anaeromyxobacter strains from soils and confirmed their nitrogen-fixing activity. Based on Geobacter isolates from paddy soils, we proposed new genera, Geomonas and Oryzomonas. Nitrogen fixation of iron reducing bacteria might be active under anaerobic condition in various soil environments.

Academic Significance and Societal Importance of the Research Achievements

窒素固定は大気中の窒素ガスを生物が利用できる形態の窒素に変換して土壌に供給する、自然生態系を支える重要な反応である。19世紀末に窒素固定が発見されて以降、「土壌の窒素固定は植物共生細菌や光合成細菌が担う」というのが一般常識として定着していた。本研究により、窒素固定できる鉄還元細菌が地球規模で普遍的に分布していること、そして従来の窒素固定微生物よりも存在量が多い傾向も見出された。このことは窒素固定に関する定説を刷新して自然生態系の支持基盤の本質に迫るものであり、その波及効果は土壌学分野に留まることなく、微生物学、地球科学、生態学まで広く自然科学分野全般に及ぶ。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (33 results)

All 2021 2020 2019 2018 Other

All Journal Article (7 results) (of which Peer Reviewed: 6 results,  Open Access: 1 results) Presentation (25 results) (of which Int'l Joint Research: 10 results,  Invited: 9 results) Remarks (1 results)

  • [Journal Article] Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas2021

    • Author(s)
      Itoh Hideomi、Xu Zhenxing、Masuda Yoko、Ushijima Natsumi、Hayakawa Chie、Shiratori Yutaka、Senoo Keishi
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 71 Issue: 1

    • DOI

      10.1099/ijsem.0.004607

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Ideal agriculture: Basic research and field technology supporting sustainable and innovative crop production2020

    • Author(s)
      妹尾啓史・増田曜子・伊藤英臣・野田口理孝・田畑 亮・岡安浩次・ 澤井 優・鈴木孝征・黒谷賢一・藤 雅子・Yuniar Devi Utami・清水幸子・ 西條雄介・大森良弘・藤原 徹・白鳥 豊・太田沙由理
    • Journal Title

      Japanese Journal of Soil Science and Plant Nutrition

      Volume: 91 Issue: 2 Pages: 94-98

    • DOI

      10.20710/dojo.91.2_94

    • NAID

      130007831579

    • ISSN
      0029-0610, 2424-0583
    • Year and Date
      2020-04-05
    • Related Report
      2019 Research-status Report
  • [Journal Article] DiazotrophicAnaeromyxobacterIsolates from Soils2020

    • Author(s)
      Masuda Yoko、Yamanaka Haruka、Xu Zhen-Xing、Shiratori Yutaka、Aono Toshihiro、Amachi Seigo、Senoo Keishi、Itoh Hideomi
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 86 Issue: 16

    • DOI

      10.1128/aem.00956-20

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov.2020

    • Author(s)
      Xu Zhenxing、Masuda Yoko、Hayakawa Chie、Ushijima Natsumi、Kawano Keisuke、Shiratori Yutaka、Senoo Keishi、Itoh Hideomi
    • Journal Title

      Microorganisms

      Volume: 8 Issue: 5 Pages: 634-634

    • DOI

      10.3390/microorganisms8050634

    • Related Report
      2020 Annual Research Report 2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] 水田土壌における鉄還元菌窒素固定の発見と応用 オミクス解析から低窒素農業へ2020

    • Author(s)
      増田曜子・ 伊藤英臣・白鳥豊・妹尾啓史
    • Journal Title

      化学と生物

      Volume: 58(3) Pages: 143-150

    • NAID

      130007993004

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Journal Article] Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., four ferric-reducing bacteria isolated from paddy soil, and reclassification of three species of the genus Geobacter as members of the genus Geomonas gen. nov.2019

    • Author(s)
      Zhenxing Xu, Yoko Masuda, Hideomi Itoh, Natsumi Ushijima, Yutaka Shiratori, Keishi Senoo
    • Journal Title

      Frontiers in Microbiology

      Volume: 10 Pages: 2201-2201

    • DOI

      10.3389/fmicb.2019.02201

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 日本農芸化学会との合同企画シンポジウム「植物・微生物機能の解析・制御と食糧・バイオマス生産への応用展開」2019

    • Author(s)
      浅見忠男・安藤康雄・森川正章・Jog Rahul・三輪京子・池田成志・松井章浩・佐古香織・上田実・Khurram Bashir・砂押裕司・Sultana Rasheed・田中真帆・石田順子・金鍾明・Huong Mai Nguyen・吉田稔・土生芳樹・関原明・野尻秀昭・妹尾啓史
    • Journal Title

      日本土壌肥料学雑誌

      Volume: 90(1) Pages: 82-87

    • Related Report
      2019 Research-status Report
    • Peer Reviewed
  • [Presentation] 増田曜子、石田敬典、山中遥加、Zhenxing Xu、伊藤英臣、白鳥豊、大峡広智、妹尾啓史2020

    • Author(s)
      水田土壌における鉄還元菌窒素固定の発見・検証と鉄・稲わら添加による増強
    • Organizer
      日本土壌肥料学会2020年度岡山大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 増田曜子、石田敬典、伊藤英臣、早川智恵、白鳥豊、妹尾啓史2020

    • Author(s)
      水田土壌の鉄還元菌窒素固定の増強-稲わらと鉄添加の効果
    • Organizer
      日本土壌微生物学会2020年度大会(大阪)
    • Related Report
      2020 Annual Research Report
  • [Presentation] Nitrogen fixation by iron reducing bacteria - previously overlooked diazotrophs essential for sustainable soil-plant ecosystems2019

    • Author(s)
      Yoko Masuda, Haruka Yamanaka, Hideomi Itoh, Zhenxing Xu, Yutaka Shiratori, Seigo Amachi, Toshihiro Aono, Keishi Senoo
    • Organizer
      11th Asian Symposium of Microbial Ecology
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Nitrogen fixation of iron reducing bacteria in paddy soils - previously overlooked diazotroph essential for sustainable soil nitrogen fertility -2019

    • Author(s)
      Yoko Masuda, Haruka Yamanaka, Hideomi Itoh, Zhenxing Xu, Yutaka Shiratori, Seigo Amachi, Toshihiro Aono, Keishi Senoo
    • Organizer
      5th Asian Conference on Plant-Microbe Symbiosis & Nitrogen Fixation Program
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Boosting nitrogen fixation of iron-reducing bacteria in paddy soil by Fe(iii) and rice straw application2019

    • Author(s)
      Takanori Ishida, Yoko Masuda, Yutaka Shiratori, Hideomi Itoh, Keishi Senoo
    • Organizer
      5th Asian Conference on Plant-Microbe Symbiosis & Nitrogen Fixation Program
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Nitrogen fixation of iron reducing bacteria in rice paddy soils - potent agents for sustainable crop production with low nitrogen input2019

    • Author(s)
      Y. Masuda, H. Yamanaka, H. Itoh, Y. Shiratori, S. Amachi, T. Aono, K. Senoo
    • Organizer
      15th symposium on Bacterial Genetics and Ecology
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Nitrogen fixation of iron reducing bacteria in rice paddy soils - discovery, verification and application to low-nitrogen agriculture -2019

    • Author(s)
      Keishi Senoo
    • Organizer
      Seminar at National Engineering Research Center for Biotechnology and School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] Soil microbial ecology for sustainable agriculture2019

    • Author(s)
      Keishi Senoo
    • Organizer
      Seminar at Nanjing University of Information Science and Technology
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] 水田土壌における鉄還元菌窒素固定の発見と応用-マイクロバイオーム解析から低窒素農業へ-2019

    • Author(s)
      増田曜子・伊藤英臣・白鳥豊・妹尾啓史
    • Organizer
      日本土壌微生物学会 2019 年度大会
    • Related Report
      2019 Research-status Report
    • Invited
  • [Presentation] 水田土壌における鉄還元菌窒素固定の発見と低窒素農業への応用の試み -オミクス解析からサステイナブル農業へ-2019

    • Author(s)
      妹尾啓史・増田曜子・伊藤英臣・白鳥豊
    • Organizer
      日本土壌肥料学会2019年度大会シンポジウム 理想の農業を追求する-サステイナブルで革新的な食糧生産を支える基礎研究と現場技術
    • Related Report
      2019 Research-status Report
  • [Presentation] 水田土壌における鉄還元菌窒素固定:鉄添加による窒素固定活性の増強2019

    • Author(s)
      高野諒・石田敬典・増田曜子・伊藤英臣・白鳥豊・妹尾啓史
    • Organizer
      日本土壌肥料学会2019年度大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 水田土壌を集積培地として用いた鉄還元細菌の単離2019

    • Author(s)
      河野圭丞・Zhenxing Xu・増田曜子・白鳥豊・妹尾啓史・伊藤英臣
    • Organizer
      日本土壌肥料学会2019年度大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 水田土壌における鉄還元菌窒素固定の発見と検証2019

    • Author(s)
      増田曜子・Zhenxing Xu・山中遥加・伊藤英臣・白鳥豊・妹尾啓史
    • Organizer
      日本微生物生態学会第33回大会
    • Related Report
      2019 Research-status Report
  • [Presentation] Isolation and characterization of Geomonas species, a novel genus involved in reductive nitrogen transformation in paddy soils2019

    • Author(s)
      Zhenxing Xu, Yoko Masuda, Hideomi Itoh, Keishi Senoo
    • Organizer
      日本微生物生態学会第33回大会
    • Related Report
      2019 Research-status Report
  • [Presentation] Identification and isolation of active N2O reducers in rice paddy soil, and application to N2O mitigation2018

    • Author(s)
      Keishi Senoo
    • Organizer
      China-Japan Symposium on Rhizosphere Cross-talk (NFSC-JST Cooperative Research Projects)
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Microbial Drivers of Nitrogen Transformation in Rice Paddy Soil: Identification, Isolation and Application to N2O Mitigation2018

    • Author(s)
      Keishi Senoo
    • Organizer
      Seminar at Nanjing University of Information Science and Technology
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Microbial Drivers of Nitrogen Transformation in Rice Paddy Soil: Identification, Isolation and Application to N2O Mitigation2018

    • Author(s)
      Keishi Senoo
    • Organizer
      Seminar at Nanjing Agricultural University
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Microbial Ecology of Nitrogen Dynamics in Agricultural Soils: Key Drivers of Reductive Nitrogen Transformation in Paddy Field and N2O Generation in Upland Field2018

    • Author(s)
      Keishi SENOO
    • Organizer
      2018 International Symposium and Annual Meeting of the KSABC
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Nitrogen fixing activity of iron reducing bacteria in paddy soils: potent agents for low nitrogen rice production in East Asia2018

    • Author(s)
      Yoko Masuda, Hideomi Itoh, Yutaka Shiratori, Keishi Senoo
    • Organizer
      NARO-MARCO International Symposium on Nitrogen Cycling and Its Environmental Impacts in East Asia
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 農耕地土壌の窒素循環微生物の群集構造と機能、環境保全型農業への応用2018

    • Author(s)
      妹尾啓史
    • Organizer
      (一財)バイオインダストリー協会 植物バイオ研究会 第16回会合「植物バイオの先端技術(1)セミナー」
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 陸域土壌における鉄還元菌窒素固定遺伝子の分布-水田だけではない!?鉄還元菌による窒素固定-2018

    • Author(s)
      増田曜子、伊藤英臣、白鳥豊、天知誠吾、妹尾啓史
    • Organizer
      日本微生物生態学会、10th Asian Symposium on Microbial Ecology
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 鉄還元細菌の窒素固定能の検証2018

    • Author(s)
      山中遥加、増田曜子、伊藤英臣、青野俊裕、天知誠吾、白鳥豊、妹尾啓史
    • Organizer
      日本土壌肥料学会2018年度神奈川大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 還元的な陸域環境下における鉄還元細菌の窒素固定活性の検証2018

    • Author(s)
      松島賢吾、藤村玲子、増田曜子、山中遥加、伊藤英臣、白鳥豊、青野俊裕、大塚重人、妹尾啓史
    • Organizer
      日本土壌肥料学会2018年度神奈川大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 水田土壌の優占種、鉄還元細菌の新機能 ~窒素肥沃度を支えるキープレーヤー~2018

    • Author(s)
      増田曜子、伊藤英臣、白鳥豊、妹尾啓史
    • Organizer
      第11回北陸バイオシンポジウム
    • Related Report
      2018 Research-status Report
  • [Presentation] Isolation and characterization of Geobacter species, potential drivers of reductive nitrogen transformation in paddy soils2018

    • Author(s)
      Zhenxing Xu, Yoko Masuda, Hideomi Itoh, Keishi Senoo
    • Organizer
      日本農芸化学会2019年度大会
    • Related Report
      2018 Research-status Report
  • [Remarks] Yayoi Highlight 「鉄で土を肥やす! 低窒素農業」

    • URL

      https://www.a.u-tokyo.ac.jp/pr-yayoi/70yh.pdf

    • Related Report
      2019 Research-status Report

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Published: 2018-07-25   Modified: 2022-01-27  

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