Biology subjects

Domaizon, I.

Publications and source records attributed to Domaizon, I..

4 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↗

bioRxiv2024

An annotated reference library for supporting DNA metabarcoding analysis of aquatic macroinvertebrates in French freshwater environments

Freshwater ecosystems are increasingly threatened by human activities, leading to biodiversity loss and ecosystem degradation. Effective biodiversity monitoring, particularly through the use of aquatic macroinvertebrates as bioindicators, is crucial for assessing ecological health. While traditional morphological methods face limitations, DNA metabarcoding offers higher accuracy and efficiency in species identification using environmental DNA. However, the success of metabarcoding is contingent on the quality of reference libraries, which are often incomplete or biased. This study aimed to construct a comprehensive COI-based DNA barcode library for freshwater macroinvertebrates in France, specifically targeting short gene regions amplified with fwhF2/fwhR2N primers, suitable for degraded DNA. A list of species occurring in French freshwater ecosystems was established from official national checklists and Alpine lake surveys. The resulting library was analyzed for taxonomic completeness, barcode coverage and genetic diversity. The checklist consisted of 2,841 species across 10 phyla, for which 56% had at least one COI-5P sequences available in the Barcode of Life Data System (BOLD). Alignment challenges with the primers were identified for certain taxa, particularly among Coleoptera, Diptera, and Malacostraca. The genetic diversity approached by the number of haplotypes per species highlighted that most of the species have limited diversity, with only 3 species having more than 100 haplotypes. Finally, this study showed that a total of 57 haplotypes were shared among 116 distinct species. This work emphasized the need for expanded sequencing efforts to improve barcode coverage and highlighted the pitfalls associated with the use of these primers for further biodiversity assessment of macroinvertebrates with degraded DNA.

ecology↗

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↗