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

Abstract

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.

Temperature moderates eDNA–biomass relationships in northern pike

“…The spatial distribution of eDNA has been shown to be patchy and vary seasonally in both marine and freshwater environments (Hervé et al, 2022; Littlefair et al, 2021). However, the degree to which concentrations vary mainly depends on the spatial distribution of the target species but also hydrographic and environmental conditions.…”

“…However, the degree to which concentrations vary mainly depends on the spatial distribution of the target species but also hydrographic and environmental conditions. For example, in larger lakes and marine systems, it is common to find eDNA to be vertically stratified by thermoclines that form during periods of limited vertical mixing, effectively concentrating eDNA released from cold water species below the thermocline (Hervé et al, 2022, Littlefair et al, 2021). During our survey, the bays were thoroughly mixed which likely smoothed out any spatial differences (Table S1).…”

Temperature moderates eDNA-biomass relationships in northern pike

“…The spatial distribution of eDNA has been shown to be patchy and vary seasonally in both marine and freshwater environments (Littlefair et al 2021, Hervé et al 2022). However, the degree to which concentrations vary mainly depends on the spatial distribution of the target species but also hydrographic and environmental conditions.…”

“…However, the degree to which concentrations vary mainly depends on the spatial distribution of the target species but also hydrographic and environmental conditions. For example, in larger lakes and marine systems it is common to find eDNA to be vertically stratified by thermoclines that form during periods of limited vertical mixing, effectively concentrating eDNA released from cold water species below the thermocline (Littlefair et al 2021, Hervé et al 2022). During our survey, the bays were thoroughly mixed which likely smoothed out any spatial differences (Table S 1).…”

Fish Diversity Monitoring Using Environmental DNA Techniques in the Clarion–Clipperton Zone of the Pacific Ocean

“…eDNA-based methods detect the genetic material of target species in the aquatic environment, and have rapidly emerged as an effective tool to improve aquatic biodiversity monitoring [22,23]. eDNA refers to genetic material extracted from environmental samples (such as water, soil, or sediment) and is derived from mitochondrial or nuclear DNA [24,25]. Sources for eDNA include secretions, feces, urine, tissue, mucus, eggs, and sperm [26][27][28][29].…”