Environmental DNA metabarcoding as an efficient tool to monitor freshwater systems in northwestern Italy

Freshwater ecosystems are experiencing one of the highest rates of biodiversity decline among extant ecosystems. To inform effective conservation actions, it is imperative to develop reliable monitoring techniques to assess the species richness of freshwater communities. In this study, we applied for the first time an eDNA metabarcoding assay on six watercourses in Liguria, northwestern Italy. Our first aim was to validate this method as a reliable monitoring tool for Ligurian fish communities. To reach this goal, we compared the results of the eDNA-based sampling with those obtained from two electrofishing campaigns carried out during the same season. The eDNA-based approach yielded congruent results with electrofishing data and showed a slightly higher resolution since it was able to detect two threatened species that were not detected by traditional monitoring. Just one species that eluded eDNA detection was electrofished instead. Thanks to a multi-marker metabarcoding approach, we were also able to detect other vertebrate species living in, or associated with, the sampled watercourses, such as aquatic birds and amphibians. Overall, our results confirmed that aquatic eDNA assay proves to be a valuable tool to monitor freshwater-related systems and to inform efficient management and protection schemes for such habitats.