Environmental DNA as a complementary tool for monitoring fish assemblages in coastal lagoons: Insights for...

For their scarcity, invasive species in early invasion stages and endangered species are often difficult to detect compromising both conservation and ecosystem protection. Here environmental DNA (eDNA) was compared with beach seining for monitoring fish diversity in the protected Natural Park Ria Formosa lagoon (Portugal). Surface water for eDNA extraction was collected before sampling a mean of 1400m² from ten diverse shallow water habitats with a 25 m beach seine. Fragments of the 12S rRNA and COI mitochondrial genes were PCR-amplified and taxonomy was assigned to amplicon sequence variants. Sampling with the beach seine resulted in the identification of 33 species and 4 genera while 28 species were identified based on eDNA, with 18 taxa in common. Greater taxonomic resolution at a species level was possible with eDNA. While the majority of species detected with both methods were of least concern according to IUCN criteria, eDNA detected one invasive (the weakfish Cynoscion regalis with 12S marker) and two critically endangered species (the ray Aetomylaeus bovinus with 12S and the eel Anguilla anguilla with COI marker), none of which were caught by beach seining. C. regalis is a threat in Portuguese waters and should be surveyed in Ria Formosa. The results highlight the usefulness of eDNA as a cost-effective complementary method to traditional monitoring, especially for rare species. Based on these results, we recommend the use of eDNA with multiple markers in surface and bottom water samples in long-term monitoring programmes, to enhance the detection of rare, elusive species in coastal lagoons.