Proposal for a federated landscape of curated reference libraries for enhancing aquatic (e)DNA biomonitoring in Europe

DNA and environmental DNA (eDNA) metabarcoding are transforming aquatic biodiversity monitoring in Europe. Still, the reliability of taxonomic assignments depends critically on the quality, completeness, and interoperability of the underlying DNA reference libraries. Here, we combine a landscape assessment of the current state of DNA reference libraries for aquatic organisms in Europe with a set of recommendations for a federated system of taxonomically curated reference libraries, following community consultation. We surveyed 26 major reference libraries across 40 attributes spanning taxonomic scope, metadata provision, curation practice, and technical accessibility, and complemented this with a questionnaire completed by 33 institutions actively generating new reference sequence data. Our assessment revealed a markedly heterogeneous landscape: databases vary widely in taxonomic and geographic coverage, molecular markers, and update frequency; most lack programmatic (API) access; and curation practice ranges from minimal taxonomic annotation to full phylogenetically-informed validation along with review of bibliographic references, with no collectively agreed minimum standard applied across databases or declared by data contributors. Building on these findings and on extensive stakeholder consultation within the eDNAqua-Plan project, we propose a federated system resting on three pillars: a minimum set of essential, interoperable metadata; standardised curation workflows culminating in a transparent, traceability-based quality ranking; and technical interoperability grounded in existing (meta)data standards (e.g., GSC MIxS, Darwin Core). We outline two feasible data-architecture options for implementation, together with a phased roadmap addressing governance and long-term sustainability. These recommendations aim to strengthen the reliability, reproducibility, and interoperability of eDNA-based aquatic biomonitoring across Europe and beyond.