Environmental DNA and oyster reef restoration: establishment of a bottom-water baseline at selected Adriatic sites

Marine biodiversity monitoring is a key challenge in evolutionary and conservation biology, particularly in coastal ecosystems where environmental changes and anthropogenic pressures can alter community composition. Oysters are ecosystem engineers, and oyster reefs were once an important global feature of the coastline, creating biogenic habitat, but are now declining. In this study, environmental DNA (eDNA) metabarcoding was applied to assess marine biodiversity across three coastal locations in the Adriatic Sea (Lignano, Chioggia, and Casteldimezzo). Each location was subdivided into two different areas: an "inside" and an "outside" area, depending on whether they will or will not be affected by the oyster restoration activities. Three sampling sites were defined within each area, to obtain a comprehensive picture of biodiversity before the restoration activities. Five replicates of seawater samples were collected at each site using CTD-rosette equipped with Niskin bottles. The samples were filtered and eDNA was extracted and amplified using three primer sets targeting different taxonomic groups, and the resulting libraries were then sequenced using a high-throughput approach. This work provides an overview of coastal biodiversity in the Northern Adriatic Sea, representing a baseline for future assessments after the planned restoration of oyster communities at these sites, offering valuable reference data for evaluating post-restoration ecological changes.