Monitoring and methods for estimating the biodiversity of a watercourse in an alpine ecosystem by metabarcoding analyses

Alpine ecosystems, like many other environments, are impacted by climate change. These alpine areas are characterized by significant biodiversity, which is highly vulnerable to climatic changes. To preserve these fragile habitats, it is essential to characterize and monitor their diversity. To this end, we aimed to identify plant and mammal species present in a watershed in Savoie, in the French Alps, using eDNA and metabarcoding. In order to verify the completeness of our inventory, we compared our results with those of the organization responsible for cataloguing fauna and flora (CREA). The protocol was also tested with and without human blocking primers to determine whether this improved the results. Our findings show that, for plants, eDNA approaches and traditional inventories conducted by CREA are complementary, as they identify different species. However, for mammals, CREA was more effective in identifying the species present. The use of human blocking primers proved beneficial for sediment samples, reducing human contamination, but had no significant impact on water samples. Estimates of richness and species composition revealed a differentiation between samples collected at high altitudes and those from lower elevations. Taxonomic assignments further highlighted the superior resolution of the water matrix for both plants and mammals, although sediments provided complementary information by detecting unique taxa.