The protection, preservation and restoration of aquatic ecosystems and their functions is of global importance. In order to assess the ecological status of a given water body, aquatic biodiversity data can be collected and compared to a reference water body. The quantified mismatch thus obtained determines the extent of potential management actions. On a European level, standard bioassessments are e.g. implemented in the Marine Strategy Framework Directive (2008/56/EC) or Water Framework Directive (2000/60/EC). Thereby, bioassessments are often inferred based on a few morpho-species, but typically higher-order taxa (genus, family). Misidentifications are a common concern in these assessments. In the past decade, molecular data has proven a) to provide a higher resolution (i.e. detectability of taxa and genetic diversity), and b) to allow for the identification of cryptic or unidentifiable organisms (e.g. non-diagnostic genders or juvenile stages). Hence, the implementation of molecular (i.e. DNA barcoding) or ecogenomic data (i.e. DNA metabarcoding) into routine bioassessment strategies seems promising. However, such a wide-ranging implementation faces several critical conceptual challenges. Species identification is only possible if a validated DNA barcode reference library for target taxa exists. Field, lab and analytical protocols should be standardised and manifested in Standard Operational Procedures (SOPs), thus allowing reproducibility and comparability. Also, High-Performance-Computing (HPC) and innovative data storage concepts have to be developed as to deal with the terabytes of ecogenomic biodiversity datasets. Finally, good-practice SOPs have to be legally implemented. As of October 2016, the Co-Operation in Science and Technology (COST) program of the European Commission supports the COST Action CA15219 ('DNAqua-Net'), comprising of five working groups (WGs): 'WG1: DNA Barcode References'; 'WG2: Biotic Indices & Metrics'; 'WG3: Lab & Field Protocols'; 'WG4: Data Analysis & Storage' and 'WG5: Implementation Strategies & Legal Issues'. DNAqua-Net will explicitly target the aforementioned challenges and deliver innovative, good-practice SOPs for a standardised aquatic bioassessment strategy in Europe – and beyond.
