Multi-marker eDNA metabarcoding reveals significant eukaryotic biodiversity gaps in the Gulf of Gdańsk, Southeastern Baltic Sea

As climate change and human pressures intensify, advancing our understanding of biodiversity and ecological shifts in vulnerable regions, such as the Baltic Sea, is becoming increasingly important. In this study, we analyzed the diversity of microeukaryotes in the Gulf of Gdańsk, the southern Baltic Sea, using environmental DNA ( e DNA) collected from the water column and surface sediment samples. Three primer sets were used, including two targeting universal eukaryotic regions (V4 and V9) and one specific to foraminifera (37F) of the 18S rDNA. The results showed that eukaryotic community composition varied depending on the type of samples and the time of sampling. We observed an increase in alpha diversity from the surface to the sediments, along with dynamic patterns in eukaryotic comunities in water samples. Numerous amplicon sequence variants (ASVs) could not be classified in any eukaryotic group at 90% similarity. Moreover, a significant proportion of ASVs could not be assigned to the genus or species level within the groups such as Cercozoa, parasitic Perkinsea, nematodes, fungi, and benthic foraminifera. Our study highlights the importance of this cryptic diversity and demonstrates the usefulness of metabarcoding as a tool for expanding our understanding of eukaryotic communities in this brackish environment.