MSFD and impact monitoring with eDNA: Insights from case studies in the Belgian Part of the North Sea (BPNS) and Avlekete Beach, Benin

With increasing anthropogenic impacts and changing climate conditions, monitoring biodiversity in marine ecosystems has become critically important. Stakeholders have gained interest in eDNA monitoring as a cost-effective and non-invasive method, but a standardized framework for reporting and storing eDNA results is currently lacking. Furthermore, the reliability of eDNA monitoring is highly dependent on the comprehensiveness of the reference database. We demonstrate this with eDNA data from two use cases. The BPNS is characterized by international shipping routes, wind farms, fisheries, aquaculture, sand extraction, dredging, and military activities. Monitoring fish and benthic communities in this region is in alignment with the Marine Strategy Framework Directive (MSFD, 2008/56/EC) requirements, and currently only involves morphological datasets. A detailed morphological archive of the area's fish species led to an extensive barcode reference database. Building on this, we reconstructed the spatial patterns of fish with eDNA, demonstrating a strong alignment with the long-term trawl monitoring data. This opens up the debate on how to use eDNA for MSFD reporting. The second case study, in collaboration between the dredging company Jan De Nul and ILVO, used eDNA to study the impact of a submerged breakwater parallel to the shore - constructed to prevent beach erosion and to create a safe swimming area - on fish communities of the coastal town of Avlékété, Benin. Fish diversity data were collected through examining fishing nets of local fishermen. We developed a custom 12S reference database using local fish fin clips and available reference sequences from NCBI. Among the 50 species detected morphologically, 28 species were not detected with eDNA. Of these, only nine had available 12S reference sequences. Taxonomic identification revealed many Pacific species assignments, likely indicating the presence of species in the area sharing identical sequences with their non-native relatives. Despite a reasonably good fish inventory in the Gulf of Guinea, the barcode database remains insufficient for fully representing marine fish diversity of the area with eDNA. These comparative studies underscore the importance of consistent barcoding efforts for developing cost-effective monitoring programs.