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Development of novel biological survey method using environmental DNA/RNA: estimating the behavior and states of underwater organisms

Research Project

Project/Area Number 17H03735
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Ecology/Environment
Research InstitutionKobe University

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) 山中 裕樹  龍谷大学, 理工学部, 講師 (60455227)
Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥16,900,000 (Direct Cost: ¥13,000,000、Indirect Cost: ¥3,900,000)
Fiscal Year 2019: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2018: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2017: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Keywords環境DNA / 環境RNA / 繁殖 / 生理状態 / RNA-seq / ゼブラフィッシュ / コイ / オオサンショウウオ / 繁殖行動 / RNA/DND比 / 分子生態 / 齢構成
Outline of Final Research Achievements

In this study, we developed a technique to understand the behavior and physiological state of an organism using environmental nucleic acids (environmental DNA and RNA). The results showed that increased environmental DNA could be a marker of reproductive behavior, that environmental RNA was detectable, that a large number of cytoskeleton-related genes were detected in environmental water, and that mRNAs that could be candidate reproductive markers were present in the environment. This is the first study to demonstrate the applicability of environmental nucleic acids to the detection of animal physiological states and behaviors in the field. These results are particularly noteworthy because they expand the applicability of environmental nucleic acid analysis in the future.

Academic Significance and Societal Importance of the Research Achievements

環境DNAなどの核酸を用いることで生物の状態を明らかにできる技術開発に成功したことは、希少種が再生産しているかなど生物多様性保全に関わる情報を非侵襲的に得ることなどを可能にする。また、環境中のmRNAなどは生物の生理状態を反映すると考えられ、水産養殖環境における感染症の早期発見など、応用的な利用も可能であると考えられる。このように本研究では基礎生物学的にも応用生物学的にも重要な手法の開発に成功した。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (50 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (4 results) Journal Article (16 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 9 results,  Open Access: 7 results) Presentation (30 results) (of which Int'l Joint Research: 7 results,  Invited: 3 results)

  • [Int'l Joint Research] 上海交通大学/浙江海洋大学/温州大学(中国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] チェンマイ大学(タイ)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] 上海交通大学/浙江海洋大学/温州大学(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] チェンマイ大学(タイ)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] The life history with seasonal migration of the lacustrine shrimp Palaemon paucidens in an ancient lake in Japan2019

    • Author(s)
      Wu, Q., Takami, Y., Minamoto, T. and Ishikawa, T.
    • Journal Title

      ECOSPHERE

      Volume: 10 Issue: 4

    • DOI

      10.1002/ecs2.2628

    • NAID

      120006624240

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Habitat selection and migration of the common shrimp, Palaemon paucidens in Lake Biwa, Japan - An eDNA - based study.2019

    • Author(s)
      Wu, Q., Kawano, K., Ishikawa, T, Sakata, M. K., Nakao, R., Hiraiwa, M. K., Tsuji, S., Yamanaka, H. and Minamoto, T.
    • Journal Title

      Environmental DNA

      Volume: - Issue: 1 Pages: 1-10

    • DOI

      10.1002/edn3.6

    • NAID

      120007002615

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys2019

    • Author(s)
      Toshifumi Minamoto, Kana Hayami, Masayuki K. Sakata, Akio Imamura
    • Journal Title

      Ecological Resaerch

      Volume: 24 Issue: 1 Pages: 237-242

    • DOI

      10.1111/1440-1703.1018

    • NAID

      120006767919

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters2018

    • Author(s)
      Qianqian Wu, Ken Kawano, Yoshitoshi Uehara, Noboru Okuda, Masamichi Hongo, Satsuki Tsuji, Hiroki Yamanaka, Toshifumi Minamoto
    • Journal Title

      Freshwater Science

      Volume: 37 Issue: 2 Pages: 307-314

    • DOI

      10.1086/697542

    • NAID

      120006604618

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 環境DNAとは何か2018

    • Author(s)
      源利文
    • Journal Title

      海洋と生物

      Volume: 40 Pages: 3-8

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 環境DNAによる個体数・生物量推定の可能性2018

    • Author(s)
      深谷肇一、長田穣、源利文
    • Journal Title

      海洋と生物

      Volume: 40 Pages: 47-53

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 環境DNAの有効性:水槽実験とフィールドでの検証2018

    • Author(s)
      益田玲爾、村上弘章、高橋宏司、源利文、宮正樹
    • Journal Title

      海洋と生物

      Volume: 40 Pages: 17-22

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 海と川との接続性を環境DNA分析で診る:河川横断構造物の影響評価2018

    • Author(s)
      山中裕樹
    • Journal Title

      海洋と生物

      Volume: 40 Pages: 54-59

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance2017

    • Author(s)
      Tsuji Satsuki、Ushio Masayuki、Sakurai Sho、Minamoto Toshifumi、Yamanaka Hiroki
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 4 Pages: e0176608-e0176608

    • DOI

      10.1371/journal.pone.0176608

    • NAID

      120006313617

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant2017

    • Author(s)
      Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsui, S., Motozawa, H., Hongo, M., Sogo, Y., Kakimi, N., Teramura, I., Sugita, M., Baba, M., Kondo, A.
    • Journal Title

      Limnology

      Volume: 17 Issue: 2 Pages: 233-241

    • DOI

      10.1007/s10201-016-0508-5

    • NAID

      120006220788

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 環境DNA分析を用いた高校生による生物調査2017

    • Author(s)
      源利文
    • Journal Title

      兵庫県高等学校教育研究会生物部会

      Volume: 41 Pages: 2-5

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 水域生態系における環境DNAモニタリング手法開発の現在2017

    • Author(s)
      源利文
    • Journal Title

      環境技術

      Volume: 46 Pages: 624-629

    • Related Report
      2017 Annual Research Report
  • [Journal Article] 境DNAモニタリング手法の課題と展望2017

    • Author(s)
      源利文、内井喜美子、高原輝彦、土居秀幸
    • Journal Title

      環境技術

      Volume: 46 Pages: 648-652

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan2017

    • Author(s)
      Sakata Masayuki K.、Maki Nobutaka、Sugiyama Hideki、Minamoto Toshifumi
    • Journal Title

      The Science of Nature

      Volume: 104 Issue: 11-12 Pages: 100-100

    • DOI

      10.1007/s00114-017-1521-1

    • NAID

      120006541929

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Environmental DNA enables detection of terrestrial mammals from forest pond water2017

    • Author(s)
      Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, and Masaki Miya
    • Journal Title

      Molecular Ecology Resources

      Volume: 17(6):e Issue: 6 Pages: 63-75

    • DOI

      10.1111/1755-0998.12690

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities2017

    • Author(s)
      Sato Hirotoshi、Sogo Yuki、Doi Hideyuki、Yamanaka Hiroki
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 14860-14860

    • DOI

      10.1038/s41598-017-14978-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] eDNAの放出は成長段階によって変わるのか?~オオサンショウウオを例に~2020

    • Author(s)
      森本哲平, 田口勇輝, 源利文
    • Organizer
      日本生態学会第67回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 環境RNA分析を用いたコイの繁殖行動推定2020

    • Author(s)
      姜明揚, 山本義彦, 呉盧漢, 源利文
    • Organizer
      日本生態学会第67回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 琵琶湖産スジエビの移動行動の多型に関連した生態的・遺伝的な構造の解明2020

    • Author(s)
      ウ倩倩, 矢井田友暉, 沢田隼, 丸山敦, 高見泰興, 源利文
    • Organizer
      日本生態学会第67回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 環境DNAによる魚類繁殖期の推定2020

    • Author(s)
      呉盧漢, 姜明揚, 山本義彦, 稲川崇史, 沖津二朗, 源利文
    • Organizer
      日本生態学会第67回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Monitoring breeding behavior of Japanese giant salamander via eDNA analysis2019

    • Author(s)
      Toshifumi Minamoto, Teppei Morimoto, Yuki Taguchi, Ryohei Nakao
    • Organizer
      British Ecological Society Annual Meeting 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dead fish shed more intact cells into the environment and produce higher environmental DNA concentration in water than living fish2019

    • Author(s)
      Hiroki Yamanaka, Takaya Hirohara, Marshal Hoy, Dorothy Chase, Jeff Duda, Carl Ostberg
    • Organizer
      British Ecological Society Annual Meeting 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Current movement in and around environmental DNA analysis in Japan2019

    • Author(s)
      Hiroki Yamanaka
    • Organizer
      3rd Environmental DNA Technical Exchange Workshop (St. Petersburg)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 琵琶湖産スジエビの生活史の解明2019

    • Author(s)
      ウ倩倩, 源利文
    • Organizer
      第2回環境DNA学会神戸大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 大型脊椎動物を対象とした環境RNAの検出と展望について2019

    • Author(s)
      釣健司, 池田静也, 廣原嵩也, 島田康人, 源利文, 山中 裕樹
    • Organizer
      第2回環境DNA学会神戸大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 野外におけるコイの環境RNAの検出2019

    • Author(s)
      姜明揚, 前川和也, 中尾遼平, 源利文
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] オオサンショウウオの繁殖行動は水で検出可能か?~人工巣穴での環境DNA調査より~2019

    • Author(s)
      森本哲平, 田口勇輝, 源利文
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境DNA分析法を用いた琵琶湖におけるスジエビの動態の解明2019

    • Author(s)
      ウ倩倩, 河野健, 石川俊之, 坂田雅之, 中尾遼平, 平岩将良, 辻冴月, 山中裕樹, 源利文
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境RNA分析を用いた環境核酸の由来組織の推定2019

    • Author(s)
      釣健司, 池田静也, 廣原嵩也, 島田康人, 源利文, 山中裕樹
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境RNAと環境DNAによる魚類の検出感度の比較とその時間変化2019

    • Author(s)
      中道友規, 釣建司, 寺園裕一郎, 加茂耕太朗, 石原孝, 山中裕樹
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境DNA分析におけるPMA色素の有用性2019

    • Author(s)
      廣原嵩也, 釣健司, 宮川光一, 山中裕樹
    • Organizer
      第66回日本生態学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境DNA分析手法を用いたオオサンショウウオの繁殖期推定2018

    • Author(s)
      森本哲平, 中尾遼平, 源利文
    • Organizer
      第1回環境DNA学会東京大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Environmental DNA analysis for ecology and conservation2018

    • Author(s)
      Hiroki Yamanaka
    • Organizer
      6th Taiwan-Japan Ecology Workshop, Tainan
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 琵琶湖産スジエビの時空間分布および移動タイミングの推定2018

    • Author(s)
      ウ倩倩, 河野健, 石川俊之, 辻冴月, 山中裕樹, 源利文
    • Organizer
      第1回環境DNA学会東京大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境RNAを用いたコイの繁殖行動の検出2018

    • Author(s)
      前川和也、源利文、山本義彦
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 環境RNA分析による遺伝子発現解析にむけた基礎技術の検討2018

    • Author(s)
      池田静也、平尾陽平、多田眞証、佐藤博俊、源利文、山中裕樹
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 環境DNAで繁殖期や繁殖場所を特定する2018

    • Author(s)
      源利文
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 集約した環境DNAサンプルを利用した淡水魚類の環境DNAメタバーコーディング~その有用性と制約について~2018

    • Author(s)
      佐藤博俊、十河勇樹、土居秀幸、山中裕樹
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 河川およびため池における魚類相調査:環境DNAメタバーコーディングと直接捕獲の比較2018

    • Author(s)
      渡邊和希、山内寛、重吉実和、芦野洸介、辻冴月、本澤大生、池田静也、佐藤博俊、山中裕樹
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 農業水路網での魚類相調査における環境DNA分析の有用性2018

    • Author(s)
      丸山敦、高田恭輔、麻田弥希、渡邊和希、佐藤博俊、米倉竜次、山中裕樹
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 河川流量の変化が生物量と環境DNA濃度との関係に及ぼす影響:いつ水を汲むのが適切か?2018

    • Author(s)
      中道友規、櫻井翔、山中裕樹
    • Organizer
      第65回日本生態学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 水を調べれば生物がわかる~驚異の<環境DNA>2017

    • Author(s)
      源利文
    • Organizer
      読売テクノ・フォーラム第202回研究交流会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 水を汲むだけの生物調査:環境DNAを用いて水中生物の種類や量を把握する技術の開発2017

    • Author(s)
      源利文
    • Organizer
      近未来への招待状 ~ナイスステップな研究者2016からのメッセージ~
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Environmental DNA metabarcoding unveils spatiotemporal dynamics of fish community in the littoral zone of Lake Biwa, central Japan2017

    • Author(s)
      Hiroki Yamanaka, Hirotoshi Sato, Masaki Miya, Masamichi Hongo, Naoki Shibata, Kazuki Watanabe, Hideyuki Doi
    • Organizer
      Ecorogical Society of America Aunual Meeting 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, by combining eDNA and conventional surveys2017

    • Author(s)
      MINAMOTO Toshifumi、SAKATA K. Masayuki、MAKI Nobutaka、SUGIYAMA Hideki
    • Organizer
      Ecology Across Borders: Joint Annual Meeting 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Fish larvae inside? Indirect assessment of fish larvae presence in host mussels using environmental DNA analysis2017

    • Author(s)
      YAMANAKA Hiroki、YONEKURA Ryuji、KOMATSU Fumiya、KAKAMU Hiroto、TAKINO Fumiya、TADA Satoru、YAMAMOTO Yoshihiko、MINAMOTO Toshifumi
    • Organizer
      Ecology Across Borders: Joint Annual Meeting 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research

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Published: 2017-04-28   Modified: 2021-02-19  

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