eDNAqua-Plan Milestone 4: Gap analysis complete

This report evaluates current practices, challenges, and gaps in the reference libraries and repositories for environmental DNA (eDNA) in monitoring aquatic biodiversity, with a particular focus on Europe. The study finds that COX1, 16S, ITS, and 18S are the most common molecular markers in reference libraries, which mainly store data in public databases like NCBI GenBank, BOLD, and SILVA. However, metadata quality varies significantly, and metadata standards are frequently overlooked. The inventory for eDNA repositories, compiled through extensive manual review, questionnaires, and automated paper mining, highlights 55 repositories but finds only 20% of these are highly relevant for broader use. Most repositories are regularly updated, though only a fraction provide annual updates or API support. Inconsistent metadata standards, incomplete taxonomic confidence indicators, and a lack of workflow details limit interoperability and accessibility. The report concludes that progress is needed in metadata standardization, consistent taxonomic curation, and increased interoperability across repositories. Additionally, standardized workflows are critical to make eDNA data Findable, Accessible, Interoperable, and Reusable (FAIR). The report suggests encouraging open access, mandating eDNA data submission to repositories, and developing incentives for comprehensive data documentation to enhance data quality and usability across Europe’s aquatic ecosystems.