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3D visualization of microbes and surrounding environment by nano-xCT

Research Project

Project/Area Number 20K20952
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 17:Earth and planetary science and related fields
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

MORONO Yuki  国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(高知コア研究所), 主任研究員 (30421845)

Co-Investigator(Kenkyū-buntansha) 山村 雅幸  東京工業大学, 情報理工学院, 教授 (00220442)
浦本 豪一郎  高知大学, 教育研究部総合科学系複合領域科学部門, 講師 (70612901)
谷川 亘  国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(高知コア研究所), 主任研究員 (70435840)
Project Period (FY) 2020-07-30 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2021: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2020: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000)
Keywords海底下生命圏 / 生存空間 / CT / X線断層撮影 / X線断層
Outline of Research at the Start

本研究ではナノスケールで物質の三次元構造観察を可能とするコンピューター断層撮影(XCT)を活用し、環境試料中に存在する微生物及びその生息空間の三次元観察を実現する。地球バイオマスの数~10%程度を占め、その生態が謎に包まれる海底下微生物について、極限環境における生命存続戦略や地球規模の元素循環に果たす役割を明らかにすることを最終目的とする。微生物のみならず、地層中の微小鉱物との相互作用、相互配置を含めた総合的な地層環境の解析を可能とする技術へとつながるものである。

Outline of Final Research Achievements

In this study, we investigated the subseafloor sedimentary biosphere through the approach aimed to visualize microbes and their surrounding environment in a 3D manner by using an X-ray CT scanning approach. The chemical addition of heavy elements to microbial cells and impregnating ionic liquids enabled the microbe-scale visualization of natural marine sediment samples. Also, we further tried element-specific contrast enhancements and identified issues for future.

Academic Significance and Societal Importance of the Research Achievements

「環境と相互作用しながら生きる微生物とその周辺環境の三次元可視化・観察」これが本研究での挑戦であり、その意義である。海底下に限らず、微生物が生育する環境では微生物自身が行う代謝反応により様々な化学グラジエントが形成され、その結果として物理的な生息環境の改変も起こる。このような海底下の持続的物質動態を本質的に理解する上で、主体となる生命活動とその周辺環境を観察することこそが必要なアプローチである。これまで二次元的な観察またはその連続によって可視化されてきた微生物と生息空間を3次元的に解析するために必須の研究であると自負している。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (12 results)

All 2023 2022 2021 2020

All Journal Article (7 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 6 results,  Open Access: 6 results) Presentation (3 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Book (1 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] A simple method for taxon-specific purification of diatom frustules from ocean sediments using a cell sorter2023

    • Author(s)
      Kato Yuji、Morono Yuki、Ijiri Akira、Terada Takeshi、Ikehara Minoru
    • Journal Title

      Progress in Earth and Planetary Science

      Volume: 10 Issue: 1 Pages: 13-13

    • DOI

      10.1186/s40645-023-00543-5

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Label-Free Identification of Spore-Forming Bacteria Using Ultrabroadband Multiplex Coherent Anti-Stokes Raman Scattering Microspectroscopy2023

    • Author(s)
      Tanaka, K., R. Oketani, T. Terada, P. Leproux, Y. Morono and H. Kano
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 127 Issue: 9 Pages: 1940-1946

    • DOI

      10.1021/acs.jpcb.2c07291

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Simple In-liquid Staining of Microbial Cells for Flow Cytometry Quantification of the Microbial Population in Marine Subseafloor Sediments2021

    • Author(s)
      Mori Fumiaki、Nishimura Tomoya、Wakamatsu Taisuke、Terada Takeshi、Morono Yuki
    • Journal Title

      Microbes and Environments

      Volume: 36 Issue: 3 Pages: n/a

    • DOI

      10.1264/jsme2.ME21031

    • NAID

      130008077315

    • ISSN
      1342-6311, 1347-4405
    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bringing 100 million-year-old marine microbes back to life2021

    • Author(s)
      Morono Yuki
    • Journal Title

      TheScienceBreaker

      Volume: 07 Issue: 02

    • DOI

      10.25250/thescbr.brk532

    • Related Report
      2021 Research-status Report
    • Open Access
  • [Journal Article] Temperature limits to deep subseafloor life in the Nankai Trough subduction zone2020

    • Author(s)
      Heuer Verena B.、Inagaki Fumio、Morono Yuki、Kubo Yusuke、Spivack Arthur J.、Viehweger Bernhard、Treude Tina、Beulig Felix、Schubotz Florence、Tonai Satoshi、Bowden Stephen A.、Cramm Margaret、Henkel Susann、Hirose Takehiro、Homola Kira、Hoshino Tatsuhiko、Ijiri Akira、Imachi Hiroyuki、Kamiya Nana、et al.
    • Journal Title

      Science

      Volume: 370 Issue: 6521 Pages: 1230-1234

    • DOI

      10.1126/science.abd7934

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years2020

    • Author(s)
      Morono Yuki、Ito Motoo、Hoshino Tatsuhiko、Terada Takeshi、Hori Tomoyuki、Ikehara Minoru、D’Hondt Steven、Inagaki Fumio
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 3626-3626

    • DOI

      10.1038/s41467-020-17330-1

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence <i>in situ</i> Hybridization (FISH) for Environmental Samples2020

    • Author(s)
      Morono, Y., K. Kubota, D. Tsukagoshi and T. Terada
    • Journal Title

      Microbes and Environments

      Volume: 35 Issue: 3 Pages: 1-1

    • DOI

      10.1264/jsme2.me20062

    • NAID

      130007865781

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 白亜紀の超貧栄養海底下堆積物から生きて発見された生命2021

    • Author(s)
      Morono Y, Ito M, Hoshino T, Terada T, Hori T, Ikehara M, D'Hondt S, Inagaki F.
    • Organizer
      日本農芸化学会2021年度大会
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] EDTA-FISH:環境試料のFluorescence in situ Hybridization (FISH)において非特異的プローブ吸着を抑制する効果的かつシンプルなアプローチ2020

    • Author(s)
      諸野祐樹、久保田健吾、塚越大介、寺田武志
    • Organizer
      第21回極限環境生物学会年会
    • Related Report
      2020 Research-status Report
  • [Presentation] Aerobic microbial life in oxic sediment of South Pacific Gyre persists up to 101.5 million years2020

    • Author(s)
      Morono Y, Ito M, Hoshino T, Terada T, Hori T, Ikehara M, D'Hondt S, Inagaki F.
    • Organizer
      American Geophysical Union Fall meeting 2020
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Book] 生物がすむ果てはどこだ?2022

    • Author(s)
      諸野祐樹
    • Total Pages
      96
    • Publisher
      くもん出版
    • ISBN
      9784774327112
    • Related Report
      2021 Research-status Report
  • [Patent(Industrial Property Rights)] 試料の空隙を可視化する方法2020

    • Inventor(s)
      諸野祐樹, 浦本豪一郎
    • Industrial Property Rights Holder
      諸野祐樹, 浦本豪一郎
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2020-201369
    • Filing Date
      2020
    • Related Report
      2020 Research-status Report

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Published: 2020-08-03   Modified: 2024-01-30  

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