Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Jonas Bylemans; Dianne M. Gleeson; Mark Lintermans; Christopher M. Hardy; Matthew Beitzel; Dean M. Gilligan; Elise M. Furlan

doi:10.3897/mbmg.2.30457

Nathan P. Griffiths, Jonathan D. Bolland, Rosalind M. Wright, Leona A. Murphy, Robert K. Donnelly, Hayley V. Watson, Bernd Hänfling (2020)
Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments. Journal of Fish Biology 97: 1375.

DOI: 10.1111/jfb.14497

Opale Coutant, Cécile Richard‐Hansen, Benoit de Thoisy, Jean‐Baptiste Decotte, Alice Valentini, Tony Dejean, Régis Vigouroux, Jérôme Murienne, Sébastien Brosse (2021)
Amazonian mammal monitoring using aquatic environmental DNA. Molecular Ecology Resources 21: 1875.

DOI: 10.1111/1755-0998.13393

Amin Golpour, Marek Šmejkal, Martin Čech, Rômulo A. dos Santos, Allan T. Souza, Tomáš Jůza, Carlos Martínez, Daniel Bartoň, Mojmír Vašek, Vladislav Draštík, Tomáš Kolařík, Luboš Kočvara, Milan Říha, Jiří Peterka, Petr Blabolil (2022)
Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs. Frontiers in Ecology and Evolution 10: .

DOI: 10.3389/fevo.2022.913279

Hideyuki Doi, Ryutei Inui, Shunsuke Matsuoka, Yoshihisa Akamatsu, Masuji Goto, Takanori Kono (2021)
Estimation of biodiversity metrics by environmental DNA metabarcoding compared with visual and capture surveys of river fish communities. Freshwater Biology 66: 1257.

DOI: 10.1111/fwb.13714

Elvira Mächler, Chelsea J. Little, Remo Wüthrich, Roman Alther, Emanuel A. Fronhofer, Isabelle Gounand, Eric Harvey, Samuel Hürlemann, Jean‐Claude Walser, Florian Altermatt (2019)
Assessing different components of diversity across a river network using eDNA. Environmental DNA 1: 290.

DOI: 10.1002/edn3.33

Eric Capo, Göran Spong, Sven Norman, Helena Königsson, Pia Bartels, Pär Byström, Arnar Palsson (2019)
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. PLOS ONE 14: e0226638.

DOI: 10.1371/journal.pone.0226638

Bruno O. David, Daniel R. Fake, Andy S. Hicks, Shaun P. Wilkinson, Michael Bunce, Josh S. Smith, David W. West, Katie E. Collins, Dianne M. Gleeson (2021)
Sucked in by eDNA – a promising tool for complementing riverine assessment of freshwater fish communities in Aotearoa New Zealand. New Zealand Journal of Zoology 48: 217.

DOI: 10.1080/03014223.2021.1905672

Luca Carraro, Julian B. Stauffer, Florian Altermatt (2021)
How to design optimal eDNA sampling strategies for biomonitoring in river networks. Environmental DNA 3: 157.

DOI: 10.1002/edn3.137

Tatsuya Kawakami, Aya Yamazaki, Maki Asami, Yuko Goto, Hiroki Yamanaka, Susumu Hyodo, Hiromichi Ueno, Akihide Kasai (2023)
Evaluating the sampling effort for the metabarcoding‐based detection of fish environmental DNA in the open ocean. Ecology and Evolution 13: .

DOI: 10.1002/ece3.9921

Masaki Miya, Ryo O. Gotoh, Tetsuya Sado (2020)
MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples. Fisheries Science 86: 939.

DOI: 10.1007/s12562-020-01461-x

Eric Capo, Charline Giguet-Covex, Alexandra Rouillard, Kevin Nota, Peter D. Heintzman, Aurèle Vuillemin, Daniel Ariztegui, Fabien Arnaud, Simon Belle, Stefan Bertilsson, Christian Bigler, Richard Bindler, Antony G. Brown, Charlotte L. Clarke, Sarah E. Crump, Didier Debroas, Göran Englund, Gentile Francesco Ficetola, Rebecca E. Garner, Joanna Gauthier, Irene Gregory-Eaves, Liv Heinecke, Ulrike Herzschuh, Anan Ibrahim, Veljo Kisand, Kurt H. Kjær, Youri Lammers, Joanne Littlefair, Erwan Messager, Marie-Eve Monchamp, Fredrik Olajos, William Orsi, Mikkel W. Pedersen, Dilli P. Rijal, Johan Rydberg, Trisha Spanbauer, Kathleen R. Stoof-Leichsenring, Pierre Taberlet, Liisi Talas, Camille Thomas, David A. Walsh, Yucheng Wang, Eske Willerslev, Anne van Woerkom, Heike H. Zimmermann, Marco J. L. Coolen, Laura S. Epp, Isabelle Domaizon, Inger G. Alsos, Laura Parducci (2021)
Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary 4: 6.

DOI: 10.3390/quat4010006

Ashish Sahu, Neelesh Kumar, Chandra Pal Singh, Mahender Singh (2023)
Environmental DNA (eDNA): Powerful technique for biodiversity conservation. Journal for Nature Conservation 71: 126325.

DOI: 10.1016/j.jnc.2022.126325

Opale Coutant, Isabel Cantera, Kévin Cilleros, Tony Dejean, Alice Valentini, Jérôme Murienne, Sébastien Brosse (2021)
Detecting fish assemblages with environmental DNA: Does protocol matter? Testing eDNA metabarcoding method robustness. Environmental DNA 3: 619.

DOI: 10.1002/edn3.158

Peiwen Jiang, Shuai Zhang, Shannan Xu, Pengli Xiong, Yiting Cao, Zuozhi Chen, Min Li (2023)
Comparison of environmental DNA metabarcoding and bottom trawling for detecting seasonal fish communities and habitat preference in a highly disturbed estuary. Ecological Indicators 146: 109754.

DOI: 10.1016/j.ecolind.2022.109754

Georgia M. Nester, Maarten De Brauwer, Adam Koziol, Katrina M. West, Joseph D. DiBattista, Nicole E. White, Matthew Power, Matthew J. Heydenrych, Euan Harvey, Michael Bunce (2020)
Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA 2: 614.

DOI: 10.1002/edn3.93

Toshifumi Minamoto, Masaki Miya, Tetsuya Sado, Satoquo Seino, Hideyuki Doi, Michio Kondoh, Keigo Nakamura, Teruhiko Takahara, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Wataru Iwasaki, Akihide Kasai, Reiji Masuda, Kimiko Uchii (2021)
An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols. Environmental DNA 3: 8.

DOI: 10.1002/edn3.121

Eric Capo, Göran Spong, Helena Königsson, Pär Byström (2020)
Effects of filtration methods and water volume on the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) eDNA concentrations via droplet digital PCR. Environmental DNA 2: 152.

DOI: 10.1002/edn3.52

Charlotte Van Driessche, Teun Everts, Sabrina Neyrinck, Rein Brys (2023)
Experimental assessment of downstream environmental DNA patterns under variable fish biomass and river discharge rates. Environmental DNA 5: 102.

DOI: 10.1002/edn3.361

Miwa Takahashi, Mattia Saccò, Joshua H. Kestel, Georgia Nester, Matthew A. Campbell, Mieke van der Heyde, Matthew J. Heydenrych, David J. Juszkiewicz, Paul Nevill, Kathryn L. Dawkins, Cindy Bessey, Kristen Fernandes, Haylea Miller, Matthew Power, Mahsa Mousavi-Derazmahalleh, Joshua P. Newton, Nicole E. White, Zoe T. Richards, Morten E. Allentoft (2023)
Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. Science of The Total Environment 873: 162322.

DOI: 10.1016/j.scitotenv.2023.162322

Shin‐ichiro Oka, Hideyuki Doi, Kei Miyamoto, Nozomi Hanahara, Tetsuya Sado, Masaki Miya (2021)
Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation. Environmental DNA 3: 55.

DOI: 10.1002/edn3.132

Erik García‐Machado, Eric Normandeau, Guillaume Côté, Louis Bernatchez (2023)
How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes. Environmental DNA : .

DOI: 10.1002/edn3.444

François Keck, Rosetta C. Blackman, Raphael Bossart, Jeanine Brantschen, Marjorie Couton, Samuel Hürlemann, Dominik Kirschner, Nadine Locher, Heng Zhang, Florian Altermatt (2022)
Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Molecular Ecology 31: 1820.

DOI: 10.1111/mec.16364

Jack Rojahn, Dianne M. Gleeson, Elise Furlan, Tim Haeusler, Jonas Bylemans (2021)
Improving the detection of rare native fish species in environmental DNA metabarcoding surveys. Aquatic Conservation: Marine and Freshwater Ecosystems 31: 990.

DOI: 10.1002/aqc.3514

Huiguo Yan, Sibao Chen, Xia Liu, Zhenhao Cheng, Bjorn Victor Schmidt, Wenping He, Fei Cheng, Songguang Xie (2023)
Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China. Animals 13: 1614.

DOI: 10.3390/ani13101614

Hideyuki Doi, Shunsuke Matsuoka, Shin‐ichiro S. Matsuzaki, Mariko Nagano, Hirotoshi Sato, Hiroki Yamanaka, Saeko Matsuhashi, Satoshi Yamamoto, Toshifumi Minamoto, Hitoshi Araki, Kousuke Ikeda, Atsuko Kato, Kouichi Kumei, Nobutaka Maki, Takashi Mitsuzuka, Teruhiko Takahara, Kimihito Toki, Natsuki Ueda, Takeshi Watanabe, Kanji Yamazoe, Masaki Miya (2023)
Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities. Freshwater Biology 68: 1346.

DOI: 10.1111/fwb.14107

Masayuki K. Sakata, Takeshi Watanabe, Nobutaka Maki, Kousuke Ikeda, Toshihiro Kosuge, Hiroaki Okada, Hiroki Yamanaka, Tetsuya Sado, Masaki Miya, Toshifumi Minamoto (2021)
Determining an effective sampling method for eDNA metabarcoding: a case study for fish biodiversity monitoring in a small, natural river. Limnology 22: 221.

DOI: 10.1007/s10201-020-00645-9

Erik García‐Machado, Martin Laporte, Eric Normandeau, Cecilia Hernández, Guillaume Côté, Yves Paradis, Marc Mingelbier, Louis Bernatchez (2022)
Fish community shifts along a strong fluvial environmental gradient revealed by eDNA metabarcoding. Environmental DNA 4: 117.

DOI: 10.1002/edn3.221

Charlotte Van Driessche, Teun Everts, Sabrina Neyrinck, David Halfmaerten, Annelies Haegeman, Tom Ruttink, Dries Bonte, Rein Brys (2023)
Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information. Environmental Research 228: 115857.

DOI: 10.1016/j.envres.2023.115857

Masaki Miya (2022)
Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities. Annual Review of Marine Science 14: 161.

DOI: 10.1146/annurev-marine-041421-082251

Matthew R. Snyder, Carol A. Stepien (2020)
Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River. Metabarcoding and Metagenomics 4: .

DOI: 10.3897/mbmg.4.53455

Rein Brys, Annelies Haegeman, David Halfmaerten, Sabrina Neyrinck, Ariane Staelens, Johan Auwerx, Tom Ruttink (2021)
Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA. Molecular Ecology 30: 3097.

DOI: 10.1111/mec.15742

Alessia Bani, Maarten De Brauwer, Simon Creer, Alex J. Dumbrell, Gino Limmon, Jamaluddin Jompa, Sophie von der Heyden, Maria Beger (2020)
Tropical Ecosystems in the 21st Century. : 375.

DOI: 10.1016/bs.aecr.2020.01.011