Freshwater fish biomonitoring in the Alpine area using eDNA metabarcoding

Many freshwater fish are experiencing critical population declines with risk of local or global extinction because of intense anthropogenic pressure and this can have serious consequences on freshwater ecosystem functioning and diversity. Current fish monitoring techniques for large rivers and lakes, however, have known shortcomings. Within the Water Framework Directive (WFD, 2000/60/EC) environmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity assessment. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. An eDNA metabarcoding approach has been evaluated by using mock samples within an intercalibration test, and has been used to study fish biodiversity of eight lakes and six rivers of the Alpine region including four EC countries (Austria, France, Italy, Slovenia) and Switzerland. This approach, based on HTS sequencing of a section of the mitochondrial 12S rRNA, allowed to assess freshwater fish biodiversity and their distribution in the different habitats. These data represent the first attempt to provide a comprehensive description of freshwater fish diversity confirming the applicability of eDNA metabarcoding analyses for fish biomonitoring in Alpine and perialpine lakes and rivers.