eDNAqua-Plan Deliverable 13: Recommendations for implementing DNA-based methods into the Water Framework Directive and Marine Strategy Framework Directive

The eDNAquaPlan project develops a vision for a future digital ecosystem for DNA-based biodiversity data. In this report we provide input on specific requirements for integrating such a system with two key aquatic European directives - the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). Both directives are formal regulatory frameworks with strict requirements for ecological assessment targets and reporting. Therefore they require biomonitoring data that are transparent, comparable and reproducible across Member States (MSs) and over time. A central requirement shared by both directives is the use of valid and stable taxonomic references. Taxonomy used in assessments must be clearly defined, fixed for reporting cycles, and version-controlled rather than continuously changing, ensuring traceability and comparability of results over time. This is particularly relevant for eDNA-based monitoring systems, which rely on reference databases that are often dynamic. Ensuring transparent versioning and documentation of reference databases is therefore a key prerequisite for the use of DNA-based methods in regulatory monitoring. Our review identified that the integration of DNA-based monitoring into WFD and MSFD implementation must also address data interoperability and reporting compatibility. DNA-derived biodiversity data are typically described using internationally recognised metadata standards such as MIxS for sequence and sample metadata and Darwin Core (DwC) for biodiversity observations. However, policy reporting systems such as WISE and WISE-Marine currently use dedicated schemas and vocabularies developed for morphology-based monitoring. To ensure compatibility between molecular data and policy reporting, sustained semantic mappings between DwC/MIxS metadata terms and WFD/MSFD reporting vocabularies are required. Such mappings would allow DNA-based biodiversity datasets to be translated into policy-relevant reporting formats while maintaining traceability to the underlying sequence data and analytical workflows. Furthermore - and in line with eDNAquaPlan’s general recommendations, we highlight the need that DNA-based monitoring data are archived in international sequence repositories, particularly those of the International Nucleotide Sequence Database Collaboration (INSDC) such as the European Nucleotide Archive (ENA). Depositing sequence data together with relevant metadata ensures long-term accessibility, persistent identifiers and the possibility of re-analysis. Linking these repositories with biodiversity data infrastructures and policy reporting systems will significantly improve the findability, accessibility and comparability of monitoring data across MSs. Finally, the integration of DNA-based methods into WFD and MSFD monitoring requires the development of harmonised methodological guidance, standards and intercalibration procedures between traditional and molecular monitoring approaches to build a bridge between data continuity and innovation. While DNA-based methods already provide valuable complementary information for biodiversity assessments, some indicators required under current directives - such as abundance, biomass or age structure - cannot yet be fully derived from DNA data alone. In the short term, DNA-based approaches will therefore complement existing monitoring systems and help fill gaps in spatial and temporal coverage. Over time, the establishment of interoperable data infrastructures, harmonised standards and transparent data reporting will empower DNA-based biodiversity monitoring to become an integral component of European environmental monitoring frameworks. Further, these will maximise the reuse of biodiversity data generated through public monitoring programmes for all sectors, feeding more FAIR biodiversity data to European and global data infrastructures, including EMODnet (the European Marine Observation and Data Network) and enriching the biodiversity component of the EDITO infrastructure, underpinning the European Digital Twin Ocean. The principles discussed in this report are therefore also relevant for broader biodiversity monitoring frameworks, including the EU Biodiversity Strategy for 2030 and international agreements such as the Kunming–Montreal Global Biodiversity Framework.