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Unravelling a complex nature of eukaryotic microbes using ultrastructural analyses and sub-single cell genomics

Research Project

Project/Area Number 21H01202
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 17050:Biogeosciences-related
Research InstitutionJapan Agency for Marine-Earth Science and Technology

Principal Investigator

Nomaki Hidetaka  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(超先鋭研究開発プログラム), 上席研究員 (90435834)

Co-Investigator(Kenkyū-buntansha) HUSNIK Filip  沖縄科学技術大学院大学, 進化・細胞・共生の生物学ユニット, 准教授 (30886130)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Fiscal Year 2023: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2022: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2021: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Keywords単細胞真核生物 / 機能分化 / 真核単細胞生物 / 細胞内機能分化 / 細胞小器官 / 遺伝子発現解析 / シングルセルゲノミクス / 細胞構造
Outline of Research at the Start

単細胞でありながら細胞の大きい底生有孔虫の多くの種は、細胞質が複数の房室内にまたがって存在し、房室ごとに区切られ細胞間で、細胞小器官の分布に大きな偏りがみられる。これは、有孔虫は単細胞でありながらも房室ごとに細胞質を区切り、細胞機能を分化させ、大きな細胞内の特定の範囲内で効率的な代謝や物質貯蔵をしている可能性を示す。
この仮説を検証するため、房室ごとの細胞小器官の分布を定量的に示し、房室ごとの機能を推定する。さらに、房室ごとのトランスクリプトーム解析を行い、細胞小器官分布から推測される機能分化を遺伝子発現レベルで検証する。

Outline of Final Research Achievements

Benthic foraminifera are unicellular eukaryote but have large cell up to more than 10 cm. They have wide variety of metabolisms and symbiotic relationships and adapted diverse marine environments. We hypothesized that this metabolic diversity may have archived by a "pseudo- multicellular " manner, with each chamber containing cells having a different function. We conducted ultrastructural analysis, intracellular elemental mapping, and gene expression analysis at sub-single cell levels. The distribution of organelles varies greatly depending on the part of the cell, with some areas specialized for energy storage, symbiosis with prokaryotes, and for food digestion. Elemental distribution also confirmed these observations and presumable functions. Genes expression patterns also differ among the positions of chambers, indicating that this giant unicellular organism can have diverse metabolic functions through intracellular functional differentiation.

Academic Significance and Societal Importance of the Research Achievements

生物の進化は、「単純な単細胞生物が誕生し、それらが共生して真核生物になり、やがて多細胞になり、大型化、複雑化し、現在の動物や植物になった」というストーリーがよく知られている。本研究の成果から、有孔虫などの生物は「単細胞生物が多細胞化することなく独自の異なるメカニズムにより機能分化、大型化したことで、海洋の様々な環境で繁栄している」ことが明らかになり、生物の進化、適応がこれまで以上に複雑かつ謎に満ちたストーリーであることを示している。

Report

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

    (28 results)

All 2024 2023 2022 Other

All Int'l Joint Research (10 results) Journal Article (12 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 12 results,  Open Access: 12 results) Presentation (6 results) (of which Int'l Joint Research: 6 results)

  • [Int'l Joint Research] ハンブルグ大学(ドイツ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] マルケ工科大学(イタリア)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] ヘルシンキ大学(フィンランド)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 国立海洋研究所(英国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] サウサンプトン国立海洋研究所(英国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ウッズホール海洋学研究所(米国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] ハンブルグ大学(ドイツ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] サウサンプトン国立海洋研究所(英国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] ウッズホール海洋学研究所(米国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] ハンブルグ大学(ドイツ)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Fungal Abundance and Diversity in the Mariana Trench, the Deepest Ecosystem on Earth2024

    • Author(s)
      Varrella Stefano、Barone Giulio、Corinaldesi Cinzia、Giorgetti Alessio、Nomaki Hidetaka、Nunoura Takuro、Rastelli Eugenio、Tangherlini Michael、Danovaro Roberto、Dell’Anno Antonio
    • Journal Title

      Journal of Fungi

      Volume: 10 Issue: 1 Pages: 73-73

    • DOI

      10.3390/jof10010073

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Rapid Freezing and Cryo-SEM?EDS Imaging of Foraminifera (Unicellular Eukaryotes) Using a Conductive Viscous Cryogenic Glue2024

    • Author(s)
      Okada Satoshi、Richirt Julien、Tame Akihiro、Nomaki Hidetaka
    • Journal Title

      Microscopy and Microanalysis

      Volume: ozae026 Issue: 2 Pages: 359-367

    • DOI

      10.1093/mam/ozae026

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Composite calcite and opal test in Foraminifera (Rhizaria)2024

    • Author(s)
      Richirt Julien、Okada Satoshi、Ishitani Yoshiyuki、Uematsu Katsuyuki、Tame Akihiro、Oda Kaya、Isobe Noriyuki、Ishimura Toyoho、Tsuchiya Masashi、Nomaki Hidetaka
    • Journal Title

      EGUsphere

      Volume: 10.5194/egusphere-2024-60

    • DOI

      10.5194/egusphere-2024-60

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A deep-learning automated image recognition method for measuring pore patterns in closely related bolivinids and calibration for quantitative nitrate paleo-reconstructions2023

    • Author(s)
      Govindankutty Menon Anjaly、Davis Catherine V.、N?rnberg Dirk、Nomaki Hidetaka、Salonen Iines、Schmiedl Gerhard、Glock Nicolaas
    • Journal Title

      Scientific Reports

      Volume: 13 Issue: 1

    • DOI

      10.1038/s41598-023-46605-y

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A deep abyssal natural wood fall in the Northwestern Pacific and its associated fauna2023

    • Author(s)
      Chen Chong、Isobe Noriyuki、Nomaki Hidetaka
    • Journal Title

      Marine Biology Research

      Volume: 19 Issue: 10 Pages: 556-563

    • DOI

      10.1080/17451000.2023.2291579

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Hydrothermal vent chimney-base sediments as unique habitat for meiobenthos and nanobenthos: Observations on millimeter-scale distributions2023

    • Author(s)
      Bernhard Joan M.、Nomaki Hidetaka、Shiratori Takashi、Elmendorf Anastasia、Yabuki Akinori、Kimoto Katsunori、Tsuchiya Masashi、Shimanaga Motohiro
    • Journal Title

      Frontiers in Marine Science

      Volume: 9

    • DOI

      10.3389/fmars.2022.1033381

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Bacterivory of the hydrothermal-vent-specific copepod <i>Stygiopontius senokuchiae</i> (Dirivultidae, Siphonostomatoida) from copepodite through adult stages2023

    • Author(s)
      Nomaki Hidetaka、Kawatani Kento、Motomura Yusuke、Tame Akihiro、Uyeno Daisuke、Ogawa Nanako O.、Ohkouchi Naohiko、Shimanaga Motohiro
    • Journal Title

      Journal of the Marine Biological Association of the United Kingdom

      Volume: 103

    • DOI

      10.1017/s0025315423000139

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Foraminifera and plastic pollution: Knowledge gaps and research opportunities2023

    • Author(s)
      Bouchet Vincent M.P.、Seuront Laurent、Tsujimoto Akira、Richirt Julien、Frontalini Fabrizio、Tsuchiya Masashi、Matsuba Misako、Nomaki Hidetaka
    • Journal Title

      Environmental Pollution

      Volume: 324 Pages: 121365-121365

    • DOI

      10.1016/j.envpol.2023.121365

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The use of radiocarbon to evaluate the trophic role of geothermal bacteria in shallow hydrothermal water ecosystem2023

    • Author(s)
      Pascal Pierre-Yves、Nomaki Hidetaka、Miyairi Yosuke、Yokoyama Yusuke
    • Journal Title

      Ecological Indicators

      Volume: 148 Pages: 110108-110108

    • DOI

      10.1016/j.ecolind.2023.110108

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Microplastic particles are phagocytosed in gill cells of deep-sea and coastal mussels2022

    • Author(s)
      Ikuta Tetsuro、Tame Akihiro、Takahashi Tomoko、Nomaki Hidetaka、Nakajima Ryota
    • Journal Title

      Frontiers in Marine Science

      Volume: 9 Pages: 2132-2132

    • DOI

      10.3389/fmars.2022.1034950

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep-sea infauna with calcified exoskeletons imaged in situ using a new 3D acoustic coring system (A-core-2000)2022

    • Author(s)
      Mizuno Katsunori、Nomaki Hidetaka、Chen Chong、Seike Koji
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 1-7

    • DOI

      10.1038/s41598-022-16356-3

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Deep-sea bottom-water environment change caused by sediment resuspension on the continental slope off Sanriku, Japan, before and after the 2011 Tohoku Earthquake2022

    • Author(s)
      Wakita Masahide、Watanabe Shuichi、Yoshino Jun、Oguri Kazumasa、Nomaki Hidetaka、Kawagucci Shinsuke、Ariyoshi Keisuke、Nagano Akira、Fujikura Katsunori
    • Journal Title

      Progress in Earth and Planetary Science

      Volume: 9 Issue: 1

    • DOI

      10.1186/s40645-022-00515-1

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Abundant chitinous structures in cytoplasm of Chilostomella and their potential functions2024

    • Author(s)
      Nomaki H, Chen C, Oda K, Tsuchiya M, Tame A, Uematsu K, Salonen IS, Isobe N
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Correlative analyses of cellular structures and elemental distribution of soluble compounds: Cryo-SEM imaging coupled to EDS elemental mapping in the denitrifying species Bolivina spissa2024

    • Author(s)
      Richirt J, Okada S, Glock N, Ishitani Y, Nomaki H
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Pore detection of denitrifying benthic foraminifera Bolivina spissa through automated image analysis technique2024

    • Author(s)
      Menon AG, Davis CV, Numberg D, Nomaki H, Salonen IS, Glock N
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Ubiquitous occurrence of phosphate storage in foraminifera: Another adaptation to anaerobic environments?2024

    • Author(s)
      Glock N, Nomaki H, Woehle C, Algar C, Kienast M, Menon AG, Mutzberg A, Rakshit S, Richirt J, Schmiedl G, Steiner Z, Zhang Z
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Vacuoles size and abundance in Foraminifera: new insight about their metabolic adaptation to low oxygen environments2024

    • Author(s)
      Richirt J, Matsuzaki T, Ishitani Y, Tame A, Oda K, Nomaki H
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular insights into ecology and evolution of the deep-sea foraminifer Chilostomella ovoidea and its endobiotic plastid2024

    • Author(s)
      Salonen I, Husnik F, Naumova M, Ishitani Y, Richirt J, Nomaki H
    • Organizer
      FORAMS2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research

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

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