Biodiversity assessment of coastal lagoon through eDNA metabarcoding

Mediterranean coastal lagoons are environmentally important ecosystems whose conservation has been challenged due to anthropogenic impacts that promoted the expansion of non-indigenous and, sometimes, invasive species. Therefore, it is crucial to inventory biodiversity in these areas for the development of strategies of conservation and management. Classic methods used for biodiversity surveys and detection of non-native species may be unsuccessful for the detection and identification of species in early development stages, cryptic, microscopic, elusive and new coming species at low population density. The development of metabarcoding techniques in the last decade offers new opportunities for reliable biodiversity surveillance and facilitates early detection of nuisance species. The objective of this study was to analyse the species occurring in the protected coastal lagoon Canet-Saint Nazaire where environmental DNA (eDNA) were extracted from water samples, employing molecular and bioinformatic tools. Three replicates were taken in the proximity of the canal that connect the lagoon with the open sea. 27 OTUs were identified, corresponding 10 of them to Class Dinophyceae and other 17 correspond to Class Hexanuplia, Polychaeta, Bacillariophyceae and Eurotatoria. Results revealed the occurrence of several invasive species (Polydora cornuta and Acartia tonsa), organisms typical of polluted areas (Polydora cornuta and Capitella capitata), and algae that produce Harmful Algal Blooms (HABs), altogether proving the poor conservation status of the lagoon despite being under protection. The combined results demonstrate the importance of eDNA as an ecological warning system and suggest the need for detailed inventories in this lagoon.