Biology subjects

Vautier, M.

Publications and source records attributed to Vautier, M..

3 recordsLinked to original sources

bioRxiv2025

Advancing eDNA methods for monitoring the reproduction of quagga and zebra mussels in lakes

This study demonstrates the applicability of environmental DNA (eDNA) methods to monitor the reproductive periods of two invasive freshwater mussels, Dreissena polymorpha (zebra mussel) and Dreissena rostriformis bugensis (quagga mussel), addressing the need for improved detection and monitoring techniques for these ecosystem-altering species. New primers and probes for multiplex droplet digital PCR (ddPCR) were developed to enable the discrimination between zebra and quagga mussels, whose veliger larvae are morphologically indistinguishable. Three eDNA sampling methods were compared: integrated water samples (0-50 m depth), sub-surface water samples, and plankton bulk samples. These methods were applied in four deep peri-alpine lakes and the results obtained with eDNA were compared to traditional veliger microscopic counts. The values obtained with the three eDNA approaches are positively corelated with visual counting of veliger larvae, but integrated water and plankton bulk eDNA samplings were found to be more effective in quantifying dreissenid veliger larvae and estimating reproductive periods than sub-surface water eDNA. The bulk-based approach is robust for qualitative presence/absence veliger larvae information, with a positive eDNA signal only when larvae are observed; it is the only eDNA method that successfully detected zebra signals in Lake Geneva. However, an overestimation of winter reproduction signal was observed for one lake with this method. The water-integrated approach captures well the quantitative dynamics of counted veliger larvae, but with the presence of false positives reproductive signal (mussel eDNA signal when no larvae are observed). The eDNA approaches tested here have enabled the characterisation of the reproductive dynamics of each of the two species in the studied lakes, highlighting the fact that quagga can reproduce throughout the year in peri-alpine lakes where it is dominant, whereas in lakes dominated by zebra, the reproduction period is limited to the warm season. The study also provides the first clue of quagga mussel presence in Lakes Annecy and Aiguebelette. Although further methodological refinements are suggested for the eDNA approaches evaluated in this study, those approaches are nonetheless already applicable and can contribute to a better understanding of these invasive species ecology in lakes.

ecology↗

bioRxiv2025

Environmental DNA (eDNA) sampling strategies influence estimates of freshwater fish eDNA concentrations.

Quantifying in-situ environmental DNA (eDNA) concentrations is increasingly used to infer fish abundance and biomass in freshwater ecosystems. While various sampling strategies (i.e. the combination of sample collection, eDNA preservation and extraction protocols) have been proposed to collect eDNA, little efforts have been undertaken to evaluate how these different strategies affect taxon-specific eDNA recovery and the subsequent estimates of in-situ eDNA concentrations. In this study, we compared a point (i.e. eDNA collection from relatively small and spatially separated water samples filtered using low capacity filter units) and a spatially integrated sampling strategy (i.e. eDNA collected from spatially integrated larger water volumes filtered using high capacity filter units) in two natural lakes. Through quantitative analyses of total DNA, total fish eDNA and species-specific eDNA, we assessed the performance of both strategies to infer in-situ eDNA concentrations. Our results showed that the integrated strategy led to a reduced recovery of fish eDNA and a subsequent underestimation of in-situ eDNA concentrations compared to the point sampling strategy. While the exact mechanisms underlying this pattern require further investigation, our findings highlight the importance of carefully selecting sampling strategies according to study objectives.

genetics↗

bioRxiv2022

A quantitative eDNA-based method 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 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.

ecology↗