Environmental DNA metabarcoding outperforms bottom trawling in detecting estuarine fish communities for ecological status assessment.
Supervisors: Naiara Rodriguez Ezpeleta, Oriol Canals (AZTI)
Current methods for monitoring fish diversity mostly rely on trawling surveys, which are invasive, costly, and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues, or mucus, is used to provide information about fish diversity in transitional waters of the Basque Country (Northern Spain) and carry out a fish-based ecological status assessment with an already known, highly validated biotic index. Further, the results of eDNA the assessment were compared to that obtained with traditionally used bottom trawling method. A total of 35 5 L-water samples were collected from 11 Basque estuaries during routine bottom trawling monitoring campaigns. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating 30.4 million quality-filtered reads. Most abundant species from eDNA samples (thinlip grey mullet and European pilchard) were different from those from bottom trawling (Pomatoschistus sp. and black goby), and eDNA metabarcoding detected more bony fish and elasmobranch species (142) than trawling (22 species, 1 genus and 1 family). Ecological status assessment inferred from eDNA data improved the status classification of samples and provided more information by detecting more species, suggesting that this improvement was due to the limitations inherent to bottom trawling method. The results presented in this work support eDNA metabarcoding for fish diversity monitoring in transitional waters in the context of regulations such as the Water Framework Directive or the Marine Strategy Framework Directive.