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Nanogeomicrobiology

Research Project

Project/Area Number 19H03310
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 45040:Ecology and environment-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Shingo Kato  国立研究開発法人理化学研究所, バイオリソース研究センター, 上級研究員 (40554548)

Co-Investigator(Kenkyū-buntansha) 鈴木 庸平  東京大学, 大学院理学系研究科(理学部), 准教授 (00359168)
伊藤 隆  国立研究開発法人理化学研究所, バイオリソース研究センター, 特別嘱託研究員 (80321727)
Project Period (FY) 2019-04-01 – 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: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2022: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2021: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2020: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2019: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Keywords鉄酸化菌 / 鉄還元菌 / 分離培養 / メタゲノム / バイオミネラル / 生物地球化学的循環 / ナノ鉱物 / 微生物ダークマター / 鉄バクテリア / 生物地球化学循環 / 鉄酸化微生物 / 鉄還元微生物 / バイオミネラリゼーション / 微生物
Outline of Research at the Start

微生物による鉄の酸化還元及び酸化鉄ナノ鉱物の生成溶解、それに伴う様々な元素の吸着溶脱は、地球規模での物質循環や生態系の成り立ちを理解する上で、鍵となる反応である。本研究では、「多種多様な未培養微生物が、酸化鉄ナノ鉱物の生成と溶解を駆動し、地球表層環境における様々な元素の挙動・循環を支配している」という作業仮説を立て、分離培養を基軸として、最先端の分子生物学および鉱物学的手法を駆使して、その検証を行う。本研究は、地球規模での元素循環を理解する上でのパラダイムシフトとなる可能性を秘めている。

Outline of Final Research Achievements

This study aimed to elucidate the formation and dissolution of iron oxide nanominerals in the Earth's surface environment through the isolation and cultivation of microorganisms. We obtained phylogenetically novel and diverse isolates of iron-oxidizing and iron-reducing microorganisms from various environments. For the first time, we report the existence of microorganisms capable of oxidizing and reducing iron at circumneutral pH. Through culture experiments, we demonstrated that these iron-oxidizing and iron-reducing microorganisms produce and dissolve iron oxide nanominerals. Thus, we showed the contributions of microorganisms to the biogeochemical cycling of iron and related elements in natural environments.

Academic Significance and Societal Importance of the Research Achievements

本研究は、鉄循環を駆動する新規微生物の存在を実証しただけでなく、まだ同定されていない鉄駆動微生物が自然界には多種存在していることを示唆している。本研究で獲得した新規微生物は、公的菌株保存機関に寄託され、一部は一般の研究者にすでに公開されているため、さらなる基礎・応用研究に利用可能である。本研究によって得られた成果は、自然界の元素循環に対する新たな視点を提示するものであり、さらには資源枯渇や環境汚染問題解決へ向けた応用バイオ技術の飛躍的な発展に貢献する可能性を秘めている。

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (24 results)

All 2023 2022 2021 2020 2019 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 8 results) Presentation (8 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results) Remarks (5 results)

  • [Journal Article] Bullet-shaped magnetosomes and metagenomic-based magnetosome gene profiles in a deep-sea hydrothermal vent chimney2023

    • Author(s)
      Nakano Shinsaku、Furutani Hitoshi、Kato Shingo、Kouduka Mariko、Yamazaki Toshitsugu、Suzuki Yohey
    • Journal Title

      Frontiers in Microbiology

      Volume: 14 Pages: 1174899-1174899

    • DOI

      10.3389/fmicb.2023.1174899

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics2022

    • Author(s)
      Kato Shingo、Masuda Sachiko、Shibata Arisa、Shirasu Ken、Ohkuma Moriya
    • Journal Title

      Frontiers in Microbiology

      Volume: 13 Pages: 1045931-1045931

    • DOI

      10.3389/fmicb.2022.1045931

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sideroxyarcus emersonii gen. nov. sp. nov., a neutrophilic, microaerobic iron- and thiosulfate-oxidizing bacterium isolated from iron-rich wetland sediment2022

    • Author(s)
      Kato Shingo、Itoh Takashi、Iino Takao、Ohkuma Moriya
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 72 Issue: 4 Pages: 005347-005347

    • DOI

      10.1099/ijsem.0.005347

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Single Bacterium Capable of Oxidation and Reduction of Iron at Circumneutral pH2021

    • Author(s)
      Kato Shingo、Ohkuma Moriya
    • Journal Title

      Microbiology Spectrum

      Volume: 9 Issue: 1

    • DOI

      10.1128/spectrum.00161-21

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conexivisphaera calida gen. nov., sp. nov., a thermophilic sulfur- and iron-reducing archaeon, and proposal of Conexivisphaeraceae fam. nov., Conexivisphaerales ord. nov., and Conexivisphaeria class. nov. in the phylum Thaumarchaeota2021

    • Author(s)
      Kato Shingo、Ohnishi Masafumi、Nagamori Mai、Yuki Masahiro、Takashina Tomonori、Ohkuma Moriya、Itoh Takashi
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 71 Issue: 1 Pages: 004595-004595

    • DOI

      10.1099/ijsem.0.004595

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Complete Genome Sequence of Athalassotoga saccharophila Strain NAS-01, a Deep-Branching Thermophilic Lineage in the Phylum Thermotogae2020

    • Author(s)
      Kato Shingo、Itoh Takashi、Ohkuma Moriya
    • Journal Title

      Microbiology Resource Announcements

      Volume: 9 Issue: 16

    • DOI

      10.1128/mra.00322-20

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Sulfuracidifex tepidarius gen. nov., sp. nov. and transfer of Sulfolobus metallicus Huber and Stetter 1992 to the genus Sulfuracidifex as Sulfuracidifex metallicus comb. nov.2020

    • Author(s)
      Itoh Takashi、Miura Tatsuki、Sakai Hiroyuki D.、Kato Shingo、Ohkuma Moriya、Takashina Tomonori
    • Journal Title

      International Journal of Systematic and Evolutionary Microbiology

      Volume: 70 Issue: 3 Pages: 1837-1842

    • DOI

      10.1099/ijsem.0.003981

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modern precipitation of hydrogenetic ferromanganese minerals during on-site 15-year exposure tests2020

    • Author(s)
      Usui A., Hino H., Suzushima D., Tomioka N., Suzuki Y., Sunamura M., Kato S., Kashiwabara T., Kikuchi S., Uramoto G.-I., Suzuki K., Yamaoka K.
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 1-10

    • DOI

      10.1038/s41598-020-60200-5

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Metabolic Potential of As-yet-uncultured Archaeal Lineages of <i>Candidatus</i> Hydrothermarchaeota Thriving in Deep-sea Metal Sulfide Deposits2019

    • Author(s)
      Kato Shingo、Nakano Shinsaku、Kouduka Mariko、Hirai Miho、Suzuki Katsuhiko、Itoh Takashi、Ohkuma Moriya、Suzuki Yohey
    • Journal Title

      Microbes and Environments

      Volume: 34 Issue: 3 Pages: 293-303

    • DOI

      10.1264/jsme2.ME19021

    • NAID

      130007711469

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics2019

    • Author(s)
      Kato Shingo、Hirai Miho、Ohkuma Moriya、Suzuki Katsuhiko
    • Journal Title

      PLOS ONE

      Volume: 14 Issue: 11 Pages: e0224888-e0224888

    • DOI

      10.1371/journal.pone.0224888

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring2019

    • Author(s)
      Kato Shingo、Itoh Takashi、Yuki Masahiro、Nagamori Mai、Ohnishi Masafumi、Uematsu Katsuyuki、Suzuki Katsuhiko、Takashina Tomonori、Ohkuma Moriya
    • Journal Title

      The ISME Journal

      Volume: 13 Issue: 10 Pages: 2465-2474

    • DOI

      10.1038/s41396-019-0447-3

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Novel bacterial players driving iron cycle in freshwater sediments2022

    • Author(s)
      Shingo Kato, Ohkuma Moriya
    • Organizer
      JpGU 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Exploration of Iron Reducing, Thermoacidophilic Archaea in Oku-Shiobara Hot Spring2022

    • Author(s)
      Sora Sakasai, Takashi Itoh, Shingo Kato, Moriya Ohkuma, Tomonori Takashina
    • Organizer
      13th International Congress on Extremophiles
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 鉄代謝微生物研究の最前線とアストロバイオロジーへの展開2022

    • Author(s)
      加藤真悟
    • Organizer
      2021年度 ISAS宇宙生命探査シンポジウム
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Oxidation and reduction of iron by a single Rhodoferax isolate at circumneutral pH2021

    • Author(s)
      Shingo Kato, Takashi Itoh, and Moriya Ohkuma
    • Organizer
      JpGU2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 淡水性環境中の鉄サイクルを駆動する新規鉄酸化・還元細菌の探索2021

    • Author(s)
      加藤真悟, 大熊盛也
    • Organizer
      日本微生物資源学会第27回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] シングルセルソーティングの威力~鉄サイクルを駆動する微生物生態の新展開~2021

    • Author(s)
      加藤真悟
    • Organizer
      新学術領域シンポジウム「ポストコッホ型の生態を見る・知る」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] ロングリードメタゲノミクスによる未培養性温泉微生物の完全ゲノム再構築2021

    • Author(s)
      加藤真悟、増田幸子、柴田ありさ、白須賢、大熊盛也
    • Organizer
      日本微生物生態学会第34回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Research and resource development of archaea/extremophiles in RIKEN-JCM2020

    • Author(s)
      Shingo Kato, Takashi Itoh and Moriya Ohkuma
    • Organizer
      生物工学Webシンポジウム2020
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Remarks]

    • URL

      https://www.jcm.riken.jp/JCM/staff/skato/index.html

    • Related Report
      2023 Annual Research Report
  • [Remarks] 単独で鉄を酸化も還元もできる微生物の発見 -微生物による鉄代謝の新たな一面-

    • URL

      https://www.riken.jp/press/2021/20210902_2/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] “微生物ダークマター”を追え!

    • URL

      https://www.riken.jp/pr/closeup/2021/20211201_1/index.html

    • Related Report
      2021 Annual Research Report
  • [Remarks] 研究成果等を紹介するホームページ

    • URL

      https://www.jcm.riken.jp/JCM/staff/skato/index.html

    • Related Report
      2020 Annual Research Report
  • [Remarks]

    • URL

      https://jcm.brc.riken.jp/ja/

    • Related Report
      2019 Annual Research Report

URL: 

Published: 2019-04-18   Modified: 2025-01-30  

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