Environmental DNA has gained popularity in the last decades due to its non-invasive analysis options and efficacy on species detection. In addition, bulk DNA analyses have shown robust and reliable results for monitoring the aquatic environment. But, there is still a challenge posed by incomplete reference libraries which impedes correct identification of species missing from the database.
Currently, there are numerous independently managed DNA barcode reference libraries hosted by various institutions in different countries. They are either of general purpose (e.g. EMBL-EBI, NCBI) or focused on specific genetic markers (e.g. Barcode of Life Datasystems (BOLD) database), or on particular taxonomic groups (e.g. Protist Ribosomal Reference (PR2) database). Similarly, there is a high number of projects and initiatives, both formal and informal, funded regionally or at a national scale in various countries with the aim of generating reference sequences (e.g. GBOL, NorBOL). So far, there is no comprehensive overview of which taxonomic groups, geographic areas, markers and sampling procedures are covered across these projects and how much they overlap.
eDNAqua-Plan envisions the creation of a digital ecosystem by linking reference sequence libraries and DNA repositories available for Europe. As a prerequisite, an overview over existing resources including projects, platforms, and initiatives needs to be compiled. In a second step, work Package 4 pursues the goal to provide operational input and testing frameworks for using barcode reference libraries to its full potential. This involves leveraging a diverse array of DNA and eDNA-based marine and freshwater monitoring projects across Europe to gather information on current practices related to data collection, treatment and storage.
eDNAqua-Plan has set as a Milestone, under the responsibility of Work Package 4, the selection of key datasets with their relevant metadata. In total, 19 datasets from eight institutes (EV ILVO, INRAE, WUR, UVEG, UDE, UNESCO, UMinho, BIOPOLIS) are available for testing and optimizing the digital ecosystem. These datasets gather a wide range of organisms that are used in monitoring programs and environmental impact assessments (bacteria, phytobenthos, macrozoobenthos and fish). The datasets cover oceans, seas, wetlands and riverine systems and different molecular methods and data (metabarcoding, metagenomics) and sequencing platforms (short vs. long read platforms). The use cases ensure that the digital ecosystem will befit for DNA and eDNA-based aquatic research.