Journal Article

Spatio-temporal variability of eDNA signal and its implication for fish monitoring in lakes

Valentini, Alice, Hervé, Alix, Domaizon, Isabelle, Jean, Pauline, Vautier, Marine, Raymond, Jean-Claude, SPYGEN [Le Bourget-du-Lac], OFB Direction de la recherche et de l’appui scientifique (OFB - DRAS) ; Office français de la biodiversité (OFB), Dejean, Tony, Baudoin, Jean-Marc, Office français de la biodiversité (OFB), RiverLy - Fonctionnement des hydrosystèmes (RiverLy) ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peroux, Tiphaine, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER) ; Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL) ; Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Observatoire des Sciences de l'Univers de Grenoble (Fédération OSUG), Log

2022

Overview

Environmental DNA (eDNA) metabarcoding is revolutionizing the monitoring of aquatic biodiversity. The use of eDNA has the potential to enable non-invasive, cost-effective, time-efficient and high-sensitivity monitoring of fish assemblages. Although the capacity of eDNA metabarcoding to describe fish assemblages is recognised, research efforts are still needed to better assess the spatial and temporal variability of the eDNA signal and to ultimately design an optimal sampling strategy for eDNA monitoring. In this context, we sampled three different lakes (a dam reservoir, a shallow eutrophic lake and a deep oligotrophic lake) every 6 weeks for 1 year. We performed four types of sampling for each lake (integrative sampling of sub-surface water along transects on the left shore, the right shore and above the deepest zone, and point sampling in deeper layers near the lake bottom) to explore the spatial variability of the eDNA signal at the lake scale over a period of 1 year. A metabarcoding approach was applied to analyse the 92 eDNA samples in order to obtain fish species inventories which were compared with traditional fish monitoring methods (standardized gillnet samplings). Several species known to be present in these lakes were only detected by eDNA, confirming the higher sensitivity of this technique in comparison with gillnetting. The eDNA signal varied spatially, with shoreline samples being richer in species than the other samples. Furthermore, deep-water samplings appeared to be non-relevant for regularly mixed lakes, where the eDNA signal was homogeneously distributed. These results also demonstrate a clear temporal variability of the eDNA signal that seems to be related to species phenology, with most of the species detected in spring during the spawning period on shores, but also a peak of detection in winter for salmonid and coregonid species during their reproduction period. These results contribute to our understanding of the spatio-temporal distribution of eDNA in lakes and allow us to provide methodological recommendations regarding where and when to sample eDNA for fish monitoring in lakes.

• Publisher: CCSD,Public Library of Science,Public Library of Science (PLoS)
• Subject: [SDE.BE] Environmental Sciences/Biodiversity and Ecology / ADN électronique / Altitude / Analysis / Animals / Aquatic ecosystems / Biodiversity / Biodiversity and Ecology / Biodiversité aquatique / Biology and Life Sciences / Cost analysis / Dams / Deep water / Deoxyribonucleic acid / DNA / DNA barcoding / DNA Barcoding, Taxonomic / DNA Barcoding, Taxonomic - methods / DNA, Environmental / DNA, Environmental - genetics / Earth Sciences / Ecology and Environmental Sciences / Environmental DNA / Environmental Monitoring / Environmental Monitoring - methods / Environmental policy / Environmental Sciences / Eutrophic environments / Eutrophic lakes / Eutrophic reservoirs / Eutrophication / Fish / Fishes / Fishes - genetics / Fishing nets / Genetic aspects / Inventaire / Lac / Lake bottom / Lakes / Medicine / Methods / Monitoring / Monitoring methods / Oligotrophic lakes / Q / R / Reproduction (biology) / Research and analysis methods / Research Article / Sampling / Science / Sensitivity / Shorelines / Shores / Spatial distribution / Spatial variability / Spawning / Species / Subsurface water / Surface water / Taxonomy / Temporal distribution / Temporal variability / Time / Variability / Variabilité spatiale / Water / Water supply
• ISBN: 0009441322000