Long-term monitoring of coastal biodiversity in France using environmental DNA metabarcoding: the ‘Sentinel Marine Areas’ network

Coastal ecosystems are affected by numerous direct anthropogenic pressures (urbanization, fisheries, etc.) and global changes (climate change, biological invasions, etc.). Long-term monitoring of their biodiversity is crucial for (1) diagnosing disturbances as early as possible, (2) evaluating conservation (Marine Protected Areas) and restoration actions, and (3) better predicting the dynamics of their functioning. However, national and international programs are often limited in time (1-4 years) and offer few opportunities for standardized long-term monitoring in partnership with local stakeholders. To address this gap, French organizations, including the UMR Marbec and CEFE research labs, the Agence de l’Eau Rhône Méditerranée Corse, and the companies Spygen and EDF have collaborated to set up the ‘Sentinel Marine Areas’ network as part of the VigiLife international initiative. Since 2023, 13 Sentinel Marine Areas (SMA) distributed across the different maritime fronts of mainland France (Mediterranean, Atlantic, and English Channel) have been monitored annually using eDNA metabarcoding technology to identify the fish and crustacean species present. This non-destructive, highly efficient monitoring technology is ideal for assessing coastal biodiversity. Each SMA is centered on an area of interest (marine reserve, wind farm, thermal discharge from a nuclear power plant, artificial reef, entry point for non-native species), and several water filtrations are carried out by boat both inside and outside this area of interest. Each transect is conducted over 30 minutes during which 30L of seawater are collected and filtered 1m below the surface, sometimes complemented by filtration in the mesophotic zone (30-150m depth). Samples are then sent to the laboratory and processed using a standardized bioinformatic workflow to obtain a list of the species present. The objectives of this monitoring and research program are (i) to assess the influence of each area of interest on coastal biodiversity and its evolution over time, and (ii) to establish a network of sentinel sites to monitor the effects of climate change and the arrival of new species, as well as the effects of direct human pressures. During the first campaign in 2023, DNA copies of more than 140 fish species and 200 crustacean taxa were detected. These initial results have helped to update certain distribution ranges, with some species, such as the salema porgy Sarpa salpa, detected more than 500 km north of their former known northern limit. In connection with these northward shifts, we have also identified unprecedented species co-occurrences, the consequences of which on the functioning of coastal ecosystems are still unknown. The ‘Sentinel Marine Areas’ network is intended to become a permanent monitoring program, in particular by making local partners autonomous in carrying out the sampling, and to be extended to other areas of interest in France, including overseas, as well as to other territories abroad.