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Elucidation of rhizosphere holobiont metabolic network to clarify plant growth promotion

Research Project

Project/Area Number 21H02329
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 41050:Environmental agriculture-related
Research InstitutionKyoto University

Principal Investigator

Sugiyama Akifumi  京都大学, 生存圏研究所, 教授 (20598601)

Co-Investigator(Kenkyū-buntansha) 安藤 晃規  京都大学, 農学研究科, 助教 (10537765)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2023: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000)
Fiscal Year 2022: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2021: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Keywordsホロビオント / 根圏 / イソフラボン / 遺伝子クラスター / Variovorax / Variovox属 / 微生物 / 相互作用 / 酸化酵素 / サポニン / ダイズ / ソヤサポニン
Outline of Research at the Start

植物根から影響を受ける根の近傍領域「根圏」では、植物と根圏微生物が密接な関係を構築し、ホロビオントとして機能する。本研究ではダイズ根圏ホロビオントを対象とし、植物と微生物の両方向から協奏的に、根圏の代謝物と微生物の時空間的変動を明らかにすることで、ホロビオントの形成過程と機能を分子レベルで解明する。

Outline of Final Research Achievements

The rhizosphere is defined as "soil influenced by plant roots". It is known that rhizosphere microbial communities are important for the growth of plants and crop production. But the mechanism behind the establishment of rhizosphere microbiota remains largely unclear. In this study, we analyzed metabolic genes in the holobiont, which is composed of plants and microorganisms,and revealed that the microorganisms especially Variovoras spp. that are present in the holobiont possess a group of genes for utilizing isoflavones secreted from soybean roots. Our study also revealed that these genes contribute the adaptation of Variovorax sp. in the environment where isoflavones are rich.

Academic Significance and Societal Importance of the Research Achievements

本研究ではこれまで未解明であったダイズ根圏でのイソフラボン代謝経路が明らかになった。イソフラボン代謝は腸内環境など嫌気条件では理解されていたが、土壌での好機的な環境では初めて見出されたものである。新規代謝経路の解明により、植物がどのように根圏微生物とホロビオントを形成するのかについて、代謝ネットワークの視点から解明する手がかりとなるものである。実際に他の植物でも代謝物を介した同様の相互作用が示唆されいる。また、これらの遺伝子を活用して植物の健全な生育を支える根圏微生物叢の解明や有用物質生産への活用が期待される。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (39 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (1 results) Journal Article (10 results) (of which Peer Reviewed: 9 results,  Open Access: 8 results) Presentation (26 results) (of which Int'l Joint Research: 11 results,  Invited: 8 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] the Netherlands Institute of Ecology(オランダ)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] An Isoflavone catabolism gene cluster underlying Interkingdom interactions in the soybean rhizosphere2024

    • Author(s)
      Aoki Noritaka、Shimasaki Tomohisa、Yazaki Wataru、Sato Tomoaki、Nakayasu Masaru、Ando Akinori、Kishino Shigenobu、Ogawa Jun、Masuda Sachiko、Shibata Arisa、Shirasu Ken、Yazaki Kazufumi、Sugiyama Akifumi
    • Journal Title

      ISME Communications

      Volume: - Issue: 1

    • DOI

      10.1093/ismeco/ycae052

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Application of plant specialized metabolites to modulate soil microbiota2023

    • Author(s)
      Sugiyama Akifumi
    • Journal Title

      Plant Biotechnology

      Volume: 40 Issue: 2 Pages: 123-133

    • DOI

      10.5511/plantbiotechnology.23.0227a

    • ISSN
      1342-4580, 1347-6114
    • Year and Date
      2023-06-25
    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] α‐Tomatine gradient across artificial roots recreates the recruitment of tomato root‐associated <i>Sphingobium</i>2023

    • Author(s)
      Takamatsu Kyoko、Toyofuku Miwako、Okutani Fuki、Yamazaki Shinichi、Nakayasu Masaru、Aoki Yuichi、Kobayashi Masaru、Ifuku Kentaro、Yazaki Kazufumi、Sugiyama Akifumi
    • Journal Title

      Plant Direct

      Volume: 7 Issue: 12

    • DOI

      10.1002/pld3.550

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Tomato root-associated <i>Sphingobium</i> harbors genes for catabolizing toxic steroidal glycoalkaloids2023

    • Author(s)
      Nakayasu Masaru、Takamatsu Kyoko、Kanai Keiko、Masuda Sachiko、Yamazaki Shinichi、Aoki Yuichi、Shibata Arisa、Suda Wataru、Shirasu Ken、Yazaki Kazufumi、Sugiyama Akifumi
    • Journal Title

      mBio

      Volume: 14 Issue: 5 Pages: 00599-23

    • DOI

      10.1128/mbio.00599-23

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Apoplast-Localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere2023

    • Author(s)
      Hinako Matsuda, Yumi Yamazaki, Eiko Moriyoshi, Masaru Nakayasu, Shinichi Yamazaki, Yuichi Aoki, Hisabumi Takase, Shin Okazaki, Atsushi J Nagano, Akito Kaga, Kazufumi Yazaki, Akifumi Sugiyama
    • Journal Title

      Plant and Cell Physiology

      Volume: pcad012 Issue: 5 Pages: 486-500

    • DOI

      10.1093/pcp/pcad012

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] サケ・マス類養殖の最新研究 新規脱窒材を活用したサクラマスの閉鎖循環型飼育システム-飼育試験と北海道での利活用-2023

    • Author(s)
      田園大樹, 安藤大成, 室岡瑞恵, 山口 文, 安富亮平, 後藤久典, 小川 順,安藤晃規
    • Journal Title

      月刊養殖ビジネス

      Volume: 60 Pages: 45-49

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms2022

    • Author(s)
      Nakayasu Masaru、Takamatsu Kyoko、Yazaki Kazufumi、Sugiyama Akifumi
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 87 Issue: 1 Pages: 13-20

    • DOI

      10.1093/bbb/zbac181

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Generation of Fusarium oxysporum-suppressive soil with non-soil carriers using a multiple-parallel-mineralization technique2022

    • Author(s)
      Meeboon Jamjan、Ando Akinori、Ogawa Jun、Miyamoto Kenji、Kato Yasuo、Shinohara Makoto
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 7968-7968

    • DOI

      10.1038/s41598-022-10667-1

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 複合微生物デザインによる硝化微生物コンソーシアの構築2021

    • Author(s)
      安藤 晃規、小川 順
    • Journal Title

      Seibutsu-kogaku Kaishi

      Volume: 99 Issue: 10 Pages: 526-530

    • DOI

      10.34565/seibutsukogaku.99.10_526

    • NAID

      130008107559

    • ISSN
      0919-3758, 2435-8630
    • Year and Date
      2021-10-25
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture2021

    • Author(s)
      Sugiyama Akifumi
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 85 Issue: 9 Pages: 1919-1931

    • DOI

      10.1093/bbb/zbab106

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Presentation] ダイズ根由来のイソフラボン分解菌の単離と分解特異性の解析2024

    • Author(s)
      〇佐藤 友昭、松田 陽菜子、高松 恭子、青木 愛賢、安藤 晃規、岸野 重信、小川 順、増田 幸子、柴田 ありさ、白須 賢、島﨑 智久、矢﨑 一史、杉山 暁史
    • Organizer
      日本農芸化学会2024年度大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] イソフラボン構造多様性がダイズ-根圏細菌相互作用に与える影響の探索2024

    • Author(s)
      〇佐藤 友昭、松田 陽菜子、高松 恭子、青木 愛賢、安藤 晃規、岸野 重信、小川 順、増田 幸子、柴田 ありさ、白須 賢、島﨑 智久、矢﨑 一史、杉山 暁史
    • Organizer
      第32回植物微生物研究会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Quantification of flavones and flavonols in different cultivars of soybean2024

    • Author(s)
      〇Koshiro Matsumura,Hinako Matsuda,Kyoko Takamatsu,Shinichi Yamazaki,Hisabumi Takase,Yoshiharu Fujii,Yuichi Aoki,Nozomu Sakurai, Kazufumi Yazaki,Akifumi Sugiyama
    • Organizer
      7th International Symposium of the Kyoto Biomolecular Mass Spectrometry Society
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Analysis of isoflavone catabolism pathway of bacteria isolated from soybean roots2024

    • Author(s)
      〇Tomoaki Sato, Hinako Matsuda, Kyoko Takamatsu, Noritaka Aoki, Akinori Ando, Shigenobu Kishino, Jun Ogawa, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Tomohisa Shimasaki, Kazufumi Yazaki, Akifumi Sugiyama
    • Organizer
      7th International Symposium of the Kyoto Biomolecular Mass Spectrometry Society
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Apoplastic beta-glucosidase increases the accumulation of isoflavones in the soybean rhizosphere2023

    • Author(s)
      ○Hinako Matsuda, Yumi Yamazaki, Eiko Moriyoshi, Masaru Nakayasu, Shinichi Yamazaki, Yuichi Aoki, Hisabumi Takase, Shin Okazaki, Atsushi J Nagano, Akito Kaga, Kazufumi Yazaki and Akifumi Sugiyama
    • Organizer
      2023 IS-MPMI CONGRESS
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Metabolic capacity of rhizosphere bacteria enriched by isoflavones in soybean rhizosphere2023

    • Author(s)
      Akifumi Sugiyama
    • Organizer
      2023 IS-MPMI CONGRESS
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Construction of a microbial consortium and evaluation of its activities on ammonification and nitrification of organic nitrogen2023

    • Author(s)
      ○Htun Inzali、Akinori Ando、Sakuntala Saijai、Wakako Okada、Kenji Miyamoto、Makoto Shinohara、Yasuo Kato、Masao Takano、Jun Ogawa
    • Organizer
      酵素工学研究会 第87回講演会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Construction of a microbial co-culture and evaluation of its activities on ammonification and nitrification of organic nitrogen2023

    • Author(s)
      ○Htun Inzali, Akinori Ando, Sakuntala Saijai, Wakako Okada, Kenji Miyamoto, Makoto Shinohara, Yasuo Kato, Masao Takano, Jun Ogawa
    • Organizer
      3rd Japan-Germany-Switzerland Workshop for Enzyme Technology and Bioprocess Development
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Construction of a microbial co-culture and evaluation of its activities on ammonification and nitrification of organic nitrogen2023

    • Author(s)
      ○Htun Inzali, Akinori Ando, Sakuntala Saijai, Wakako Okada, Kenji Miyamoto, Makoto Shinohara, Yasuo Kato, Masao Takano, Jun Ogawa
    • Organizer
      KANSAI JSBBA 10th Student Forum
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The Effect of Isoflavone Structural Diversity on Soybean-Rhizosphere Bacteria Interactions2023

    • Author(s)
      〇Tomoaki Sato, Hinako Matsuda, Kyoko Takamatsu, Noritaka Aoki, Akinori Ando, Shigenobu Kishino, Jun Ogawa, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Tomohisa Shimasaki, Kazufumi Yazaki, Akifumi Sugiyama
    • Organizer
      KANSAI JSBBA 10th Student Forum
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effects of flavones and flavonols on the bacterial community in soybean rhizosphere2023

    • Author(s)
      〇Koshiro Matsumura,Hinako Matsuda,Kyoko Takamatsu,Shinichi Yamazaki,Hisabumi Takase,Yoshiharu Fujii,Yuichi Aoki,Nozomu Sakurai, Kazufumi Yazaki,Akifumi Sugiyama
    • Organizer
      KANSAI JSBBA 10th Student Forum
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ダイズ根圏細菌 Variovorax sp. におけるイソフラボン分解に関与する遺伝子の同定2022

    • Author(s)
      ◯青木愛賢、島﨑智久、矢崎渉、中安大、安藤晃規、岸野重信、小川順、増田幸子、柴田ありさ、須田亙、白須賢、矢﨑一史、杉山暁史
    • Organizer
      第31回植物微生物研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ダイズ根圏細菌のイソフラボン代謝遺伝子の同定と機能解析2022

    • Author(s)
      ○青木 愛賢、島﨑 智久、矢崎 渉、中安 大、安藤 晃規、岸野 重信、小川 順、増田 幸子、柴田 ありさ、須田 亙、白須 賢、矢﨑 一史、杉山 暁史
    • Organizer
      第64回日本植物生理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 作物頑健性に寄与する 根圏ケミカルワールドの機能2022

    • Author(s)
      杉山 暁史
    • Organizer
      日本学術会議農芸化学分科会・植物科学分科会シンポジウム「SDGs達成に向けた農芸化学の挑戦」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 根圏での植物-微生物代謝ネットワーク2022

    • Author(s)
      杉山 暁史
    • Organizer
      農薬バイオサイエンス研究会シンポジウム
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Rhizosphere metabolome for the robustness of crops2022

    • Author(s)
      Akifumi Sugiyama
    • Organizer
      Unveiling the secret of underground: technologies for visualizing root and rhizosphere
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ダイズ根圏のイソフラボン蓄積に関与するβ-グルコシダーゼの解析2022

    • Author(s)
      松田 陽菜子 山﨑 由実 森吉 英子 中安 大 山﨑 真一 青木 裕一 高瀬 尚文 岡崎 伸 永野 惇 加賀 秋人 矢﨑 一史 ○杉山 暁史
    • Organizer
      日本農芸化学会2023広島大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ダイズ根から根圏へのイソフラボン分泌を促進するアポプラスト局在のβ-グルコシダーゼの解析2022

    • Author(s)
      〇松田陽菜子、山﨑由実、森吉英子、中安 大、山﨑真一、青木裕一、高瀨尚文、永野 惇、岡崎 伸、加賀秋人、矢﨑一史、杉山暁史
    • Organizer
      第39回日本植物バイオテクノロジー学会(堺)大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Metabolic capacities of rhizosphere bacteria that respond to plant specialized metabolites2022

    • Author(s)
      Akifumi Sugiyama
    • Organizer
      NWO-JSPS seminar
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 「植物微生物×オミクス」 根圏メタボローム解析2022

    • Author(s)
      杉山暁史
    • Organizer
      第二回植物微生物シンバイオロジー協議会シンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] ダイズ根圏でのイソフラボン分解に関与する遺伝子の同定2022

    • Author(s)
      青木愛賢、島﨑智久、矢崎渉、中安大、安藤晃規、岸野重信、小川順、増田幸子、柴田ありさ、須田亙、白須賢、矢﨑一史、杉山暁史
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 根分泌モデル実験系を用いたトマチンによるトマト根圏微生物叢形成の解析2022

    • Author(s)
      高松 恭子、豊福 美和子、奥谷 芙季、中安 大、矢﨑 一史、杉山 暁史
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 創出土壌を対象とした X 線 CT による土壌物理性解析の試み2022

    • Author(s)
      西田 亮也、鈴木 飛鳥、宮本 憲二、加藤 康夫、安藤 晃規、小川 順、篠原 信 、高野 雅夫
    • Organizer
      日本農芸化学会2022年度大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Dynamics and functions of plant specialized metabolites in shaping rhizosphere microbiota2021

    • Author(s)
      Akifumi Sugiyama
    • Organizer
      第94回日本生化学会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 作物生産を支える根圏ケミカルの 機能・動態・可視化2021

    • Author(s)
      杉山暁史
    • Organizer
      令和3年度 農業・工業原材料生産と光技術研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Analysis of the effects of amino acids and derivatives on root growth2021

    • Author(s)
      Huang Ying, Naito Kumiko, Kato Yasuo, Shinohara Makoto, Ando Akinori, Ogawa Jun, Miyamoto Kenji
    • Organizer
      Pacifichem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Book] 独立栄養微生物によるCO2資源化技術 "第14章 硝化微生物群を活用した人工土壌創製"2023

    • Author(s)
      安藤晃規, 野崎 守, 小川 順
    • Total Pages
      232
    • Publisher
      シーエムシー出版
    • ISBN
      9784781317564
    • Related Report
      2023 Annual Research Report
  • [Remarks]

    • URL

      https://www.rish.kyoto-u.ac.jp/lpge/index.html

    • Related Report
      2022 Annual Research Report

URL: 

Published: 2021-04-28   Modified: 2025-01-30  

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