Abstract
Estuaries are ecologically vital yet highly impacted ecosystems that serve as transitional zones between land and sea. Monitoring their biodiversity is essential but challenging due to their dynamic nature and the transient presence of many species. Traditionally, actinopterygian monitoring in these systems still relies on conventional and intrusive methods such as gill nets and trawls. Environmental DNA (eDNA) metabarcoding offers a non-invasive, multi-taxa alternative that can complement these traditional approaches. Here, we applied an eDNA-based metabarcoding approach to characterize vertebrate diversity in the Rance Estuary, located in the Brittany Region of France. Water samples were collected from five stations spanning marine to freshwater environments. Special attention was given to two stations located upstream and downstream of the tidal power plant (TPP) dam to assess its potential impact on ecological continuity. We detected a total of 124 distinct vertebrate MOTUs, comprising actinopterygians, birds, mammals, and amphibians. Taxonomic composition followed the estuarine gradient, with Jaccard dissimilarity increasing with distance from the sea and largely driven by species turnover. While taxonomic and phylogenetic diversity remained relatively stable across the vertebrate community, functional diversity revealed an increasing terrestrial influence. For actinopterygians, taxonomic diversity decreased upstream, whereas phylogenetic and functional diversity indicated fine-scale structuring, even among nearby stations. This approach enabled the development of biodiversity metrics and facilitated comparisons with previous actinopterygian monitoring surveys in the same area based on conventional methods (scientific fishing using nets and dredges). Our results emphasize the potential of eDNA for holistic estuarine biomonitoring and establish a valuable baseline for future non-invasive assessments.