Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Masayuki Ushio; Hiroaki Murakami; Reiji Masuda; Tetsuya Sado; Masaki Miya; Sho Sakurai; Hiroki Yamanaka; Toshifumi Minamoto; Michio Kondoh

doi:10.3897/mbmg.2.23297

Joshua H. Kestel, David L. Field, Philip W. Bateman, Nicole E. White, Morten E. Allentoft, Anna J.M. Hopkins, Mark Gibberd, Paul Nevill (2022)
Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. Science of The Total Environment 847: 157556.

DOI: 10.1016/j.scitotenv.2022.157556

Samuel Thompson, Simon Jarman, Kingsley Griffin, Matthew Heydenrych, Julian Partridge, Tim Langlois (2025)
In Vitro Passive eDNA Sampling Provides a Cost‐Effective Alternative for Large Scale Sample Collection. Environmental DNA 7: .

DOI: 10.1002/edn3.70101

Lynsey R. Harper, Andrew S. Buxton, Helen C. Rees, Kat Bruce, Rein Brys, David Halfmaerten, Daniel S. Read, Hayley V. Watson, Carl D. Sayer, Eleanor P. Jones, Victoria Priestley, Elvira Mächler, Cesc Múrria, Sandra Garcés-Pastor, Cecilia Medupin, Katherine Burgess, Gillian Benson, Neil Boonham, Richard A. Griffiths, Lori Lawson Handley, Bernd Hänfling (2019)
Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia 826: 25.

DOI: 10.1007/s10750-018-3750-5

Satoshi Yamagishi, Yasuhide Nakamura, Koji Seto, Takuto Ando, Kota Katsuki, Teruhiko Takahara (2025)
Reconstruction of paleo-environments by two aquatic plants: eDNA analysis in lake sediment cores. Limnology 26: 417.

DOI: 10.1007/s10201-025-00782-z

Masayuki Ushio, Testuya Sado, Takehiko Fukuchi, Sachia Sasano, Reiji Masuda, Yutaka Osada, Masaki Miya (2023)
Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities. eLife 12: .

DOI: 10.7554/eLife.85795.3

Peiyuan Ye, Jinping Cheng, Linus Shing Him Lo, Jingyu Liu, Chao Li, Kelvin Jun Yin So, Fei Xia, Meng Yan, Junjie Wang, Clara U, Jian-Wen Qiu, Wenlong Cai, Kenneth Mei Yee Leung (2025)
Environmental DNA/RNA metabarcoding for noninvasive and comprehensive monitoring and assessment of marine fishes. Marine Pollution Bulletin 211: 117422.

DOI: 10.1016/j.marpolbul.2024.117422

Takeshi Ito, Tetsu Yatsuyanagi, Tomohiro Yokobe, Misaki Shiomi, Reiji Masuda, Qing Wang (2025)
Seasonal changes in the structure of river fish communities in temperate Japan depicted using quantitative eDNA metabarcoding. PLOS One 20: e0328280.

DOI: 10.1371/journal.pone.0328280

Megan R. Shaffer, Elizabeth Andruszkiewicz Allan, Amy M. Van Cise, Kim M. Parsons, Andrew Olaf Shelton, Ryan P. Kelly (2025)
Observation Bias in Metabarcoding. Molecular Ecology Resources : .

DOI: 10.1111/1755-0998.14119

David Wari, Yoshinobu Kusumoto, Toshio Kitamura (2025)
Sampling and metabarcoding of arthropod environmental DNA traces from flowers. MethodsX 14: 103329.

DOI: 10.1016/j.mex.2025.103329

Michihito TAKIYAMA, Seiji MIYAZONO, Ryohei NAKAO, Ryutei INUI, Yoshihisa AKAMATSU (2025)
ESTIMATION OF BASIN-WIDE FISH HABITAT POTENTIAL USING ENVIRONMENTAL DNA. Japanese Journal of JSCE 81: n/a.

DOI: 10.2208/jscejj.24-16123

Huihui Chang, Tao Ye, Zhaohui Xie, Xinhu Liu (2025)
Application of Environmental DNA in Aquatic Ecosystem Monitoring: Opportunities, Challenges and Prospects. Water 17: 661.

DOI: 10.3390/w17050661

Dongyi WU, Pingshin LEE, Hongman CHEN, Fang YAN, Jiayue HUANG, Yanhong HE, Ruiyao WU, Zhiyong YUAN (2025)
Validation and development of eDNA metabarcoding primers for comprehensive assessment of Chinese amphibians. Integrative Zoology 20: 504.

DOI: 10.1111/1749-4877.12832

Till-Hendrik Macher, Arne J. Beermann, Jens Arle, Julia Foerster, Matthias Greyer, Demetrio Mora, Jan Koschorreck, Peter Rolauffs, Anne Rother, Susanne Schüler, Jonas Zimmermann, Daniel Hering, Florian Leese (2025)
Fit for purpose? Evaluating benthic invertebrate DNA metabarcoding for ecological status class assessment in streams under the Water Framework Directive. Water Research 272: 122987.

DOI: 10.1016/j.watres.2024.122987

Seiji MIYAZONO, Michihito TAKIYAMA, Ryohei NAKAO, Yoshihisa AKAMATSU (2025)
BASIN-WIDE RIVER ENVIRONMENTAL EVALUATION BASED ON ENVIRONMENTAL DNA AND STABLE ISOTOPE. Japanese Journal of JSCE 81: n/a.

DOI: 10.2208/jscejj.24-16122

Hiroshi Funaki, Chetan Chandrakant Gaonkar, Tomohiro Nishimura, Kouki Tanaka, Kaito Kamimura, Tatsuya Kaji, Keizo Nagasaki, Masao Adachi (2025)
Vertical distribution of harmful algae in the sediment of Uranouchi Inlet by metabarcoding. Frontiers in Protistology 3: .

DOI: 10.3389/frpro.2025.1612811

Masayuki Ushio, Hiroki Saito, Motoaki Tojo, Atsushi J Nagano (2023)
An ecological network approach for detecting and validating influential organisms for rice growth. eLife 12: .

DOI: 10.7554/eLife.87202

Lynsey R. Harper, Lori Lawson Handley, Christoph Hahn, Neil Boonham, Helen C. Rees, Kevin C. Gough, Erin Lewis, Ian P. Adams, Peter Brotherton, Susanna Phillips, Bernd Hänfling (2018)
Needle in a haystack? A comparison ofeDNAmetabarcoding and targetedqPCRfor detection of the great crested newt (Triturus cristatus). Ecology and Evolution 8: 6330.

DOI: 10.1002/ece3.4013

Masayuki Ushio, Hiroki Saito, Motoaki Tojo, Atsushi J Nagano (2023)
An ecological network approach for detecting and validating influential organisms for rice growth. eLife 12: .

DOI: 10.7554/eLife.87202.3

Masayuki Ushio, Testuya Sado, Takehiko Fukuchi, Sachia Sasano, Reiji Masuda, Yutaka Osada, Masaki Miya (2023)
Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities. eLife 12: .

DOI: 10.7554/eLife.85795

Jeanine Brantschen, Florian Altermatt (2024)
Contrasting strengths of eDNA and electrofishing compared to historic records for assessing fish community diversity and composition. Canadian Journal of Fisheries and Aquatic Sciences 81: 178.

DOI: 10.1139/cjfas-2023-0053

Kamil Hupało, Isabel Blasco-Costa, Alejandro Trujillo-González, Florian Leese (2025)
Aquatic Parasitology: Ecological and Environmental Concepts and Implications of Marine and Freshwater Parasites. Chapter 14: 361.

DOI: 10.1007/978-3-031-83903-0_14