Journal Article

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

Seymour, Mathew, Bik, Holly M., Deiner, Kristy, Durance, Isabelle, Cosby, Bernard Jack, Colbourne, John, Emmett, Bridget, Milner, Nigel, Harvey, Rachel, Walsh, Kerry, de Bruyn, Mark, Perry, William Bernard, Blackman, Rosetta, Altermatt, Florian, Lawson Handley, Lori, Mächler, Elvira, Jâms, Ifan Bryn, Carvalho, Gary, Orsini, Luisa, Creer, Simon, Bista, Iliana, Edwards, François

2024

Overview

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. Using intensive eDNA sampling in space and time across five rivers in Europe and North America, this study shows that eDNA gives relevant information on freshwater diversity and ecology across broad taxonomic groups, and with limited downstream transport. The findings demonstrate that eDNA is vital for freshwater biodiversity monitoring in a time of anthropogenic change.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 45/23 / 45/77 / 631/158/670 / 631/208/721 / 704/158/670 / Animals / Anthropogenic factors / Biodiversity / Community ecology / DNA barcoding / DNA Barcoding, Taxonomic - methods / DNA, Environmental - analysis / DNA, Environmental - genetics / Ecology / Ecosystem / Environmental changes / Environmental conditions / Environmental DNA / Environmental effects / Europe / Fishes - classification / Fishes - genetics / Freshwater ecology / Habitat utilization / Humanities and Social Sciences / Life history / Monitoring / multidisciplinary / North America / Rainfall / River flow / Rivers / Salmon / Sampling / Science / Science (multidisciplinary) / Seasons / Spatio-Temporal Analysis / Temporal resolution