Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

Till-Hendrik Macher; Robin Schütz; Jens Arle; Arne J. Beermann; Jan Koschorreck; Florian Leese

doi:10.3897/mbmg.5.66557

Till-Hendrik Macher, Jens Arle, Arne J. Beermann, Lina Frank, Kamil Hupało, Jan Koschorreck, Robin Schütz, Florian Leese (2024)
Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream. PeerJ 12: e18016.

DOI: 10.7717/peerj.18016

Kira‐Lee Courtaillac, Jannes Landschoff, Kelvin Hull, Sophie von der Heyden (2024)
The Effect of Spatio‐Temporal Sampling and Biological Replication on the Detection of Kelp Forest Fish Communities Using eDNA Metabarcoding. Environmental DNA 6: .

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Sophie Picq, Amanda N. Curtis, Andrew George, Eric R. Larson, Michelle E. Thompson, Philip W. Willink, Caleb D. McMahan, Lesley S. de Souza (2024)
Environmental DNA metabarcoding for whole community inventories of vertebrates in rivers of the midwestern United States. Journal of Freshwater Ecology 39: .

DOI: 10.1080/02705060.2024.2382454

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

Mandy Sander, Arne J. Beermann, Dominik Buchner, Iris Madge Pimentel, James S. Sinclair, Martina Weiss, Peter Haase, Florian Leese (2024)
Environmental DNA time series analysis of a temperate stream reveals distinct seasonal community and functional shifts. River Research and Applications 40: 850.

DOI: 10.1002/rra.4265

Josh Smith, Bruno David, Andy Hicks, Shaun Wilkinson, Nicolas Ling, Daniel Fake, Alastair Suren, Amy Gault (2024)
Optimizing eDNA Replication for Standardized Application in Lotic Systems in Aotearoa, New Zealand. Environmental DNA 6: .

DOI: 10.1002/edn3.70017

Lynsey R. Harper, Matthew L. Niemiller, Joseph B. Benito, Lauren E. Paddock, E. Knittle, Brenda Molano‐Flores, Mark A. Davis (2023)
BeeDNA: Microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities. Environmental DNA 5: 191.

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Starsha Bird, Paul Dutton, Shaun Wilkinson, Josh Smith, Ian Duggan, Angela McGaughran (2024)
Developing an eDNA approach for wetland biomonitoring: Insights on technical and conventional approaches. Environmental DNA 6: .

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Flurin Leugger, Michel Schmidlin, Martina Lüthi, Zacharias Kontarakis, Loïc Pellissier (2024)
Scanning amplicons with CRISPR‐Dx detects endangered amphibians in environmental DNA. Molecular Ecology Resources 24: .

DOI: 10.1111/1755-0998.14009

Till-Hendrik Macher, Robin Schütz, Atakan Yildiz, Arne J. Beermann, Florian Leese (2023)
Evaluating five primer pairs for environmental DNA metabarcoding of Central European fish species based on mock communities. Metabarcoding and Metagenomics 7: .

DOI: 10.3897/mbmg.7.103856

Yujin Kang, Seungwoo Han, Youngkeun Song (2024)
Optimising eDNA analysis for urban otter monitoring: seasonal patterns, detection strategies and prey availability. Metabarcoding and Metagenomics 8: .

DOI: 10.3897/mbmg.8.115512

Armando Espinosa Prieto, Jean‐Nicolas Beisel, Pieternel Verschuren, Laurent Hardion (2023)
Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding. Environmental DNA 5: 648.

DOI: 10.1002/edn3.407

Kamil Hupało, Saskia Schmidt, Till-Hendrik Macher, Martina Weiss, Florian Leese (2022)
Fresh insights into Mediterranean biodiversity: environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily. Hydrobiologia 849: 155.

DOI: 10.1007/s10750-021-04718-3

Shan Zhang, Jindong Zhao, Meng Yao (2023)
Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding. Journal of Environmental Management 340: 117971.

DOI: 10.1016/j.jenvman.2023.117971

Naoki Katayama, Satoshi Yamamoto, Yuki G. Baba, Kenji Ito, Junsuke Yamasako (2024)
Complementary role of environmental DNA for line-transect bird surveys: A field test in a Japanese rice landscape. Ecological Indicators 166: 112442.

DOI: 10.1016/j.ecolind.2024.112442

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.

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Holly A. Broadhurst, Luke M. Gregory, Emma K. Bleakley, Joseph C. Perkins, Jenna V. Lavin, Polly Bolton, Samuel S. Browett, Claire V. Howe, Natalie Singleton, Darren Tansley, Naiara Guimarães Sales, Allan D. McDevitt (2021)
Mapping differences in mammalian distributions and diversity using environmental DNA from rivers. Science of The Total Environment 801: 149724.

DOI: 10.1016/j.scitotenv.2021.149724

Dawn R. URycki, Anish A. Kirtane, Rachel Aronoff, Colton C. Avila, Rosetta C. Blackman, Luca Carraro, Olivier Evrard, Stephen P. Good, Diana C. Hoyos J., Nieves López‐Rodríguez, Demetrio Mora, Yvonne Schadewell, Oliver S. Schilling, Natalie C. Ceperley (2024)
A new flow path: eDNA connecting hydrology and biology. WIREs Water 11: .

DOI: 10.1002/wat2.1749

Camila Duarte Ritter, Giorgi Dal Pont, Paula Valeska Stica, Aline Horodesky, Nathieli Cozer, Otto Samuel Mäder Netto, Caroline Henn, Antonio Ostrensky, Marcio R. Pie (2022)
Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch. Environmental Advances 7: 100169.

DOI: 10.1016/j.envadv.2022.100169

Lorenzo Ballini, Giorgia Staffoni, Davide Nespoli, Dario Ottonello, Alessandro Candiotto, Simone Forte, Paolo Vezza, Alessio Iannucci, Sara Fratini (2024)
Environmental DNA metabarcoding as an efficient tool to monitor freshwater systems in northwestern Italy. Hydrobiologia : .

DOI: 10.1007/s10750-024-05723-y

Rebecca K. Loh, Sujatha N. Kutty, Darren C. J. Yeo, Rudolf Meier (2023)
Toward eDNA‐based bioassessment of freshwater reservoirs with small volumes of water: Robust molecular protocols. Environmental DNA 5: 264.

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Katy E. Klymus, Jacoby D. Baker, Cathryn L. Abbott, Rachel J. Brown, Joseph M. Craine, Zachary Gold, Margaret E. Hunter, Mark D. Johnson, Devin N. Jones, Michelle J. Jungbluth, Sean P. Jungbluth, Yer Lor, Aaron P. Maloy, Christopher M. Merkes, Rachel Noble, Nastassia V. Patin, Adam J. Sepulveda, Stephen F. Spear, Joshua A. Steele, Miwa Takahashi, Alison W. Watts, Susanna Theroux (2024)
The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. Metabarcoding and Metagenomics 8: .

DOI: 10.3897/mbmg.8.128689

Florian Altermatt, Luca Carraro, Manuel Antonetti, Camille Albouy, Yan Zhang, Arnaud Lyet, Xiaowei Zhang, Loïc Pellissier (2023)
Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs. Environmental DNA 5: 671.

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Saima Naz, Ahmad Manan Mustafa Chatha, Rifat Ullah Khan (2023)
Pragmatic applications of DNA barcoding markers in identification of fish species – A review. Annals of Animal Science 23: 363.

DOI: 10.2478/aoas-2022-0073

S. Elizabeth Alter, Jairo Arroyave (2022)
Environmental DNA metabarcoding is a promising method for assaying fish diversity in cenotes of the Yucatán Peninsula, Mexico. Metabarcoding and Metagenomics 6: .

DOI: 10.3897/mbmg.6.89857