Environmental DNA (eDNA) based methods are proving to be a promising tool for freshwater fish biodiversity
assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers
and lakes where current fish monitoring techniques have known shortcomings. 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. 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 specifically designed to measure freshwater fish
biodiversity in Alpine lakes and rivers has been extensively evaluated by using mock samples within an
intercalibration test. This eDNA method was validated and 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.
More in detail, this metabarcoding approach, based on HTS sequencing of a section of the 12S rRNA gene,
was used 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 in different
ecosystems of the Alpine area confirming the applicability of eDNA metabarcoding analyses for the
biomonitoring of fish inhabiting Alpine and perialpine lakes and rivers
