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

There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish pop-ulations' dynamics. When monitored in lakes, fish spawning is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs. Over the last decade, envi-ronmental DNA (eDNA) based methods have been widely developed and now offer a non-invasive alternative method to these traditional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offers 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 approach to monitor the spawning activity in a lentic environment for two non-migratory fish species, European perch and whitefish. The 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 effectiveness of weekly eDNA sampling coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the target species. In addition, we highlight that the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) helps to clearly discriminate the eDNA signal associated to the spawning activity. The filtration of 2 L of subsurface water was shown to be effective for the monitoring of spawning activity; however, using discrete sampling strategy we observed a spatial variability in the eDNA signal. For future implementation, we recommend (i) using an integrative sampling strategy to smooth the local variability of the eDNA signal, and (ii) to cover a sampling period long enough to clearly distinguish the spawning signal from the basal signal of the target species. These results show that we reached an operational level to use these non-invasive eDNA approaches to monitor the spawning periods of these two fish species in large lakes.

Automated summary

This study developed a quantitative environmental DNA (eDNA) approach to monitor the spawning activity of European perch and whitefish in Lake Geneva. The results showed that the weekly sampling coupled with droplet digital PCR (ddPCR) was effective in identifying the timing and peak of spawning activity. It was also emphasized that the use of a control species helped to discriminate the eDNA signal associated with spawning. Recommendations were made for future implementation, including an integrative sampling strategy and a longer sampling period.