Environmental Matrices Need Consideration: Insights From Water and Biofilm Environmental <scp>DNA</scp> for Multi‐Taxonomic Biomonitoring

ABSTRACT Environmental DNA (eDNA) is revolutionizing biodiversity monitoring, offering a unique approach to assess multi‐taxonomic diversity with various applications related to evaluation, protection, and restoration of aquatic ecosystems. However, there is still a lack of sufficient studies to assess the complementarity of various environmental matrices and their contribution to enhancing biodiversity detection. This study evaluates the impact of eDNA sampling in different matrices to measure biodiversity of different taxonomic groups. We set up a year‐long eDNA sampling of water and biofilm matrices in a large lake littoral zone (Lake Geneva), focusing on microalgae, benthic macroinvertebrates, and fish. We first assessed primer specificity, which was high for microalgae (23S) and fish (12S) but was lower for macroinvertebrates (COI). We then evaluated the complementarity of eDNA signals in water and biofilms. For microalgae, communities from biofilm and water were highly different: water eDNA almost exclusively detected planktonic taxa while biofilm eDNA detected predominantly benthic taxa. For macroinvertebrates, communities in water and biofilms were also different, and biofilm eDNA could detect mostly Chironomidae. Finally, for fish, eDNA of both matrices enabled us to detect similar communities even if a few rare species were detected only in water. In the framework of the assessment of ecosystem quality or restoration actions success, we recommend diversifying matrices to collect eDNA to capture a complete picture of microalgae and macroinvertebrate communities. For fish, it is possible to sample water or biofilms, keeping in mind that water has become a standard practice for fish eDNA sampling.