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Development of a simultaneous analysis system for multispecies breeding regimes with environmental DNA analysis

Research Project

Project/Area Number 20H03326
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 InstitutionKobe University

Principal Investigator

Minamoto Toshifumi  神戸大学, 人間発達環境学研究科, 教授 (50450656)

Co-Investigator(Kenkyū-buntansha) 山中 裕樹  龍谷大学, 先端理工学部, 准教授 (60455227)
Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2022: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2021: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000)
Fiscal Year 2020: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Keywords環境DNA / 環境RNA / 繁殖レジーム / メタバーコーディング / コイ / ゼブラフィッシュ
Outline of Research at the Start

近年急速に発展する環境DNA分析は、主に種の在不在を検知するツールとして用いられている。本研究ではさらなる発展系として、環境DNA中の核DNA/ミトコンドリアDNAの比(核/Mt比)を利用して水中生物の繁殖レジームを多種同時に把握する手法を確立する。本研究では、(1)種特異的な環境DNAの定量によって核/Mt比から繁殖レジームを推定する手法の開発と野外適用、(2)定量的メタバーコーディングによって、多種の繁殖レジームをまとめて推定する手法の開発と野外適用を行う。また、繁殖期に特異的なRNAマーカーの探索を通じて、(3)環境RNAによって繁殖レジームを推定するさらに新たな手法の基礎的研究を行う。

Outline of Final Research Achievements

The study was conducted to obtain information other than distribution, such as reproduction of aquatic organisms, by analyzing nucleic acids in the environment including environmental DNA (eDNA) and environmental RNA (eRNA). We found that it is possible to understand the reproductive regimes of specific species by using nuclear and mitochondrial eDNA, that it is possible to understand the reproductive regimes of multiple species simultaneously using quantitative eDNA metabarcoding, and that it is potentially possible to understand the reproductive regimes from environmental messenger RNA (emRNA) information. These results indicate that we can obtain reproductive information, which is important for the conservation of rare and valuable fishery species, by using environmental biomolecules, eDNA and eRNA.

Academic Significance and Societal Importance of the Research Achievements

野生生物の繁殖に関わる情報は、生物の保全上貴重である。このような情報を水をすくうだけで得ることができるようになれば、希少種や水産有用魚種の保全のための保護区域の設定などに役立つことが期待される。30 by 30における保護区域の設定においても有用な科学的知見を提供するためのツールとなりうるだろう

Report

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

    (37 results)

All 2023 2022 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (14 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 14 results,  Open Access: 12 results) Presentation (20 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Book (2 results)

  • [Int'l Joint Research] 上海交通大学(中国)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] An efficient environmental DNA detection method for rare species: a case study of a small salamander (Hynobius boulengeri)2023

    • Author(s)
      Sakata Masayuki K.、Takeshita Daiki、Nishizawa Ryohei、Sato Takuya、Minamoto Toshifumi
    • Journal Title

      Analytical Sciences

      Volume: 39 Issue: 5 Pages: 721-728

    • DOI

      10.1007/s44211-023-00289-6

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Warm temperature and alkaline conditions accelerate environmental <scp>RNA</scp> degradation2022

    • Author(s)
      Jo Toshiaki、Tsuri Kenji、Hirohara Takaya、Yamanaka Hiroki
    • Journal Title

      Environmental DNA

      Volume: - Issue: 5 Pages: 836-848

    • DOI

      10.1002/edn3.334

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Environmental DNA analysis for macro-organisms: species distribution and more2022

    • Author(s)
      Minamoto Toshifumi
    • Journal Title

      DNA Research

      Volume: 29 Issue: 3

    • DOI

      10.1093/dnares/dsac018

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Spatiotemporal changes in environmental DNA concentrations caused by fish spawning activity.2022

    • Author(s)
      Wu, L., Yamamoto, Y., Yamaguchi, S., Minamoto, T.
    • Journal Title

      Ecological Indicators

      Volume: 142 Pages: 109213-109213

    • DOI

      10.1016/j.ecolind.2022.109213

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia2022

    • Author(s)
      Sakata Masayuki K.、Kawata Mone U.、Kurabayashi Atsushi、Kurita Takaki、Nakamura Masatoshi、Shirako Tomoyasu、Kakehashi Ryosuke、Nishikawa Kanto、Hossman Mohamad Yazid、Nishijima Takashi、Kabamoto Junichi、Miya Masaki、Minamoto Toshifumi
    • Journal Title

      Metabarcoding and Metagenomics

      Volume: 6 Pages: 15-26

    • DOI

      10.3897/mbmg.6.76534

    • NAID

      120007193008

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes2021

    • Author(s)
      Jo Toshiaki、Takao Kenta、Minamoto Toshifumi
    • Journal Title

      Environmental DNA

      Volume: 4 Issue: 2 Pages: 271-283

    • DOI

      10.1002/edn3.253

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Environmental DNA detection of an invasive ant species (Linepithema humile) from soil samples2021

    • Author(s)
      Yasashimoto Tetsu、Sakata Masayuki K.、Sakita Tomoya、Nakajima Satoko、Ozaki Mamiko、Minamoto Toshifumi
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1 Pages: 10712-10712

    • DOI

      10.1038/s41598-021-89993-9

    • NAID

      120007097071

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel2021

    • Author(s)
      Takahashi Sayaka、Takada Shingo、Yamanaka Hiroki、Masuda Reiji、Kasai Akihide
    • Journal Title

      PLOS ONE

      Volume: 16 Issue: 9 Pages: e0255576-e0255576

    • DOI

      10.1371/journal.pone.0255576

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance2021

    • Author(s)
      Hirohara Takaya、Tsuri Kenji、Miyagawa Koichi、Paine Robert T. R.、Yamanaka Hiroki
    • Journal Title

      Frontiers in Ecology and Evolution

      Volume: 9 Pages: 632973-632973

    • DOI

      10.3389/fevo.2021.632973

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river2020

    • Author(s)
      Sakata Masayuki K.、Watanabe Takeshi、Maki Nobutaka、Ikeda Kousuke、Kosuge Toshihiro、Okada Hiroaki、Yamanaka Hiroki、Sado Tetsuya、Miya Masaki、Minamoto Toshifumi
    • Journal Title

      Limnology

      Volume: 22 Issue: 2 Pages: 221-235

    • DOI

      10.1007/s10201-020-00645-9

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Projection range of eDNA analysis in marshes: a suggestion from the Siberian salamander (Salamandrella keyserlingii) inhabiting the Kushiro marsh, Japan2020

    • Author(s)
      Takeshita Daiki、Terui Shigeharu、Ikeda Kousuke、Mitsuzuka Takashi、Osathanunkul Maslin、Minamoto Toshifumi
    • Journal Title

      PeerJ

      Volume: 8 Pages: e9764-e9764

    • DOI

      10.7717/peerj.9764

    • NAID

      120006884198

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout2020

    • Author(s)
      Imamura Akio、Hayami Kana、Sakata Masayuki、Minamoto Toshifumi
    • Journal Title

      Biodiversity Data Journal

      Volume: 8

    • DOI

      10.3897/bdj.8.e56876

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Seasonal monitoring of Hida salamander Hynobius kimurae using environmental DNA with a genus-specific primer set2020

    • Author(s)
      Toshiaki Jo, Sei Tomita, Yukihiro Kohmatsu, Maslin Osathanunkul, Atushi Ushimaru, Toshifumi Minamoto
    • Journal Title

      Endang Species Res

      Volume: 43 Pages: 341-352

    • DOI

      10.3354/esr01073

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Messenger RNA typing of environmental RNA (eRNA): A case study on zebrafish tank water with perspectives for the future development of eRNA analysis on aquatic vertebrates2020

    • Author(s)
      Tsuri Kenji、Ikeda Shizuya、Hirohara Takaya、Shimada Yasuhito、Minamoto Toshifumi、Yamanaka Hiroki
    • Journal Title

      Environmental DNA

      Volume: 3 Issue: 1 Pages: 14-21

    • DOI

      10.1002/edn3.169

    • NAID

      120007028974

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 絶滅危惧種の保全と外来種対策における環境DNA分析の有効性2023

    • Author(s)
      源利文, 木原菜摘
    • Organizer
      スイゲンゼニタナゴの保全を考えるワークショップ
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 夜間の光は魚の生態に影響を及ぼすのか?ー環境DNA技術を用いた種組成調査よりー2022

    • Author(s)
      大藪愛紗, 源利文
    • Organizer
      日本陸水学会第86回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 定量メタバーコーディングを用いた魚類生態調査2022

    • Author(s)
      呉盧漢, 稲川崇史, 沖津二朗, 坂本正吾, 源利文
    • Organizer
      環境DNA学会「あなたが主役のワークショップ」
    • Related Report
      2022 Annual Research Report
  • [Presentation] 河川横断構造物がニホンウナギの河川遡上に与える影響の解明2022

    • Author(s)
      國政祐太, 木原菜摘, 源利文
    • Organizer
      環境DNA学会「あなたが主役のワークショップ」
    • Related Report
      2022 Annual Research Report
  • [Presentation] 琵琶湖における廃川の魚類ハビタットとしての活用可能性2022

    • Author(s)
      東坂波也翔, 松本岳大, 坂田雅之, 源利文
    • Organizer
      第69回日本生態学会大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 核DNAをマーカーとする魚類環境DNAメタバーコーディング法の野外適用2022

    • Author(s)
      佐々木大介, 伊藤玄, 山中裕樹, 坂田雅之, 源利文
    • Organizer
      第69回日本生態学会大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 定量的環境DNAメタバーコーディングを用いた魚類の繁殖期の同時モニタリング2022

    • Author(s)
      呉盧漢, 稲川崇史, 沖津二朗, 坂本正吾, 源利文
    • Organizer
      第69回日本生態学会大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] アオコの発生した湖における環境DNAメタバーコーディングの試み2022

    • Author(s)
      ウ倩倩, 坂田雅之, 呉德意, 山中裕樹, 源利文
    • Organizer
      環境DNA学会第4回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 両生類を対象とした環境DNAメタバーコーディング検出系の開発と評価2022

    • Author(s)
      坂田雅之, 河田萌音, 倉林敦, 栗田隆気, 中村匡聡, 白子智康, 掛橋竜祐, 西川完途, モハメド ヤジット ホスマン, 西島太加志, 樺元淳一, 宮正樹, 源利文
    • Organizer
      環境DNA学会第4回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 魚類の核環境DNAメタバーコーディング手法の開発2022

    • Author(s)
      佐々木大介, 山中裕樹, 坂田雅之, 源利文
    • Organizer
      環境DNA学会第4回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 魚類繁殖活動による環境DNA濃度の時間と距離に伴う変化2022

    • Author(s)
      呉盧漢, 山本義彦, 山口翔吾, 源利文
    • Organizer
      環境DNA学会第4回大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Understanding eDNA characteristics and dynamics for fisheries management and conservation2021

    • Author(s)
      Toshiaki Jo
    • Organizer
      American Fisheries Society 151st Annual Meeting 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Basic knowledge accumulation in eDNA/eRNA analysis for mining more biological information from the environmental medium with more reliability2021

    • Author(s)
      Hiroki Yamanaka
    • Organizer
      American Fisheries Society 151st Annual Meeting 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 魚類環境RNAの検出最適化のためのプロトコル検証および野外適用2021

    • Author(s)
      高尾健太, 徐寿明, 源利文
    • Organizer
      日本生態学会第68回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境核酸分析によるコイの栄養状態の評価2021

    • Author(s)
      姜明揚, 山本義彦, 源利文
    • Organizer
      日本生態学会第68回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 核DNAをマーカーとした魚類環境DNAメタバーコーディングの新規手法の開発2021

    • Author(s)
      佐々木大介, 山中裕樹, 源利文
    • Organizer
      日本生態学会第68回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNAを用いたダム湖における魚類繁殖期の推定2021

    • Author(s)
      呉盧漢, 稲川崇史, 沖津二郎, 源利文
    • Organizer
      日本生態学会第68回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNAとRNAの分解に及ぼす温度とpHの影響2021

    • Author(s)
      釣健司, 廣原嵩也, 島田康人, 源利文, 山中裕樹
    • Organizer
      日本生態学会第68回大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNAによる魚類の繁殖期推定2020

    • Author(s)
      呉盧漢, 稲川崇史, 沖津二朗, 源利文
    • Organizer
      環境DNA学会第3回大会・第36回個体群生態学会大会合同大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 環境DNA分析手法を用いたコイ科魚類の産卵行動の検出2020

    • Author(s)
      佐々木大介, 渡部健, 源利文
    • Organizer
      環境DNA学会第3回大会・第36回個体群生態学会大会合同大会
    • Related Report
      2020 Annual Research Report
  • [Book] 環境DNA入門2022

    • Author(s)
      源 利文
    • Total Pages
      120
    • Publisher
      岩波書店
    • ISBN
      4000297155
    • Related Report
      2022 Annual Research Report
  • [Book] 環境DNA2021

    • Author(s)
      一般社団法人 環境DNA学会、土居 秀幸、近藤 倫生
    • Total Pages
      300
    • Publisher
      共立出版
    • ISBN
      9784320058163
    • Related Report
      2020 Annual Research Report

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Published: 2020-04-28   Modified: 2024-01-30  

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