Environmental DNA to Enhance Fish Biodiversity Assessment.

Fish community biodiversity is gravely threatened by overfishing, habitat destruction, and climate change. These pressures impact fish stocks, which are economically, culturally, and ecologically essential. To ensure the conservation of fish communities, it is crucial to collect accurate data through regular monitoring programs. Currently, fish assemblages is primarily assessed through conventional methods such as underwater visual censuses (UVC), underwater video, and experimental fishing. UVC, which involves counting fish during dives, is the most commonly used method, yet it has limitations related to visibility, depth, and the detection of cryptic or pelagic species and requires taxonomic expertise.

Metabarcoding of environmental DNA (eDNA), derived from DNA fragments released by fish into the environment, emerges as a promising complementary method. By analyzing water samples, it is possible to identify present species without direct observation. Our recent study conducted in protected Mediterranean marine areas showed that eDNA surpassed UVC in detection capabilities, allowing for the identification of rare species often invisible through traditional methods (https://doi.org/10.1016/j.scitotenv.2024.177250). Furthermore, eDNA is not limited by depth or visibility, which facilitates its use in diverse conditions.

The assessment of fish biodiversity traditionally relies on taxonomic diversity (TD), which quantifies species and their abundance. However, functional diversity (FD), which measures the ecological roles of species, is increasingly considered a more relevant indicator for assessing the impact of anthropogenic disturbances. eDNA not only allows for species identification but also helps deduce their functional characteristics, such as dietary habits and social behavior. This information is valuable in understanding the impact of environmental changes on marine ecosystem functioning.

Nevertheless, eDNA presents certain limitations: it does not yet permit precise estimation of fish biomass or population density, and the transport of DNA molecules by currents can complicate the accurate identification of species' locations. UVC remains more reliable for these estimations. Additionally, some species detected by UVC evade eDNA detection due to the absence of their sequences in genetic databases.

Combining UVC and eDNA would provide a more comprehensive view of fish biodiversity. Further research is needed to optimize this mixed approach, which represents an opportunity to enhance marine ecosystem management. eDNA could also facilitate the early detection of invasive species coming from the Red Sea such as the lionfish, as well as the location of rare or endangered species like the angel shark, thereby supporting conservation efforts.

In conclusion, eDNA is an innovative method that, when combined with traditional techniques, could significantly enrich knowledge and support the conservation of marine ecosystems.