An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

William Bernard Perry (), Mathew Seymour (), Luisa Orsini, Ifan Bryn Jâms, Nigel Milner, François Edwards, Rachel Harvey, Mark Bruyn, Iliana Bista, Kerry Walsh, Bridget Emmett, Rosetta Blackman, Florian Altermatt, Lori Lawson Handley, Elvira Mächler, Kristy Deiner, Holly M. Bik, Gary Carvalho, John Colbourne, Bernard Jack Cosby, Isabelle Durance and Simon Creer ()
Additional contact information
William Bernard Perry: Bangor University
Mathew Seymour: The University of Hong Kong
Luisa Orsini: University of Birmingham
Ifan Bryn Jâms: Cardiff University
Nigel Milner: Bangor University
François Edwards: A17 Embankment Business Park, Heaton Mersey
Rachel Harvey: Environment Centre Wales
Mark Bruyn: School of Environment and Science
Iliana Bista: LOEWE Centre for Translational Biodiversity Genomics
Kerry Walsh: Horizon House
Bridget Emmett: Environment Centre Wales
Rosetta Blackman: Eawag: Swiss Federal Institute of Aquatic Science and Technology
Florian Altermatt: Eawag: Swiss Federal Institute of Aquatic Science and Technology
Lori Lawson Handley: University of Hull (UoH)
Elvira Mächler: Eawag: Swiss Federal Institute of Aquatic Science and Technology
Kristy Deiner: ETH Zurich
Holly M. Bik: University of Georgia
Gary Carvalho: Bangor University
John Colbourne: University of Birmingham
Bernard Jack Cosby: Environment Centre Wales
Isabelle Durance: Cardiff University
Simon Creer: Bangor University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20–35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Date: 2024
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DOI: 10.1038/s41467-024-48640-3

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