A quantitative eDNA-based method to monitor fish spawning in lakes: application to European perch and whitefish

Abstract

There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish populations dynamics. When monitored in lakes, the spawning of fish is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs. Over the last decade, environmental DNA (eDNA) based methods have been widely developed for the detection of aquatic species, offering a non-invasive alternative method to conventional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offer the possibility to quantify an absolute eDNA signal in a very sensitive way and at a low cost. Here, we developed and implemented a quantitative eDNA method to monitor the spawning activity of two fish species, European perch and whitefish. ddPCR protocols were formalized based on existing and newly designed COI primers, and were applied during four spawning periods in lake Geneva. The results demonstrate the efficiency of eDNA coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the targeted species. In addition, the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) was shown to be relevant to clearly discriminate fluctuations of the eDNA signal associated to the spawning activity from the baseline eDNA signal. For future implementation, we recommend using an integrative sampling strategy (e.g., pooled samples for a give station) to smooth the local variability of the eDNA signal. These results show that we reached an operational level to use these non-invasive eDNA methods to monitor the spawning periods of these two fish species in large lakes.

An integrative approach to assess the impact of disturbance on native fish in lakes

“…Vautier et al . (2023) also used eDNA to monitor the spawning activity of European perch ( Perca fluviatilis ) and whitefish ( Coregonus lavaretus ) in Lake Geneva, correlating fluctuations in eDNA signal with spawning periods.…”

“…More recently, studies have positively related eDNA concentrations in water samples to abundance and biomass estimates of fish populations in lakes (Spear et al, 2021;Rourke et al, 2022). Vautier et al (2023) also used eDNA to monitor the spawning activity of European perch (Perca fluviatilis) and whitefish (Coregonus lavaretus) in Lake Geneva, correlating fluctuations in eDNA signal with spawning periods.…”

Quantifying invasion dynamics: qPCR vs. ddPCR in monitoring the alien invasive red-blood mysid Hemimysis anomala and its interaction with perch in Lake Geneva

“…All available sequences were obtained regardless of geographical location in order to avoid intraspecies variation. Primer design and in silico validation was performed as provided by Vautier et al (2023). The primer set selected for H. anomala were : H anomala COI-5P F (5'-AATTGGGT-CAGCCCGGTAGG -3'), H anomala COI-5P R (5'-TAACCAGTTGCCGAAACCACC -3') and H anomala COI-5P P (5'-ACAAACGCATGCGCTGTCACAATCACG -3') (Table 1).…”

“…To determine the LOD and LOQ values, we prepared a dilution series of DNA extracted from tissue sample of H. anomala . A 1:5 serial dilutions was conducted to obtain eight dilution points ranging from 1000 pg μL -1 to 0.0124 pg μL -1 as in Vautier et al (2023). This series was then analyzed by ddPCR in 5 replicates for each dilution, using 5 μL of DNA template per 22 μL ddPCR reaction.…”

Reconstructing the response of native fish in lakes to historical anthropogenic disturbances

“…More recently, studies have positively related eDNA concentrations in water samples to abundance and biomass estimates of fish populations in lakes (Rourke et al, 2022;Spear et al, 2021). Vautier et al (2023) also used eDNA to monitor the spawning activity of European perch (Perca fluviatilis) and whitefish (Coregonus lavaretus) in Lake Geneva, correlating fluctuations in eDNA signal with spawning periods.…”