Baseline survey of meiofaunal biodiversity in Baltic Sea using multi-marker metabarcoding

This study investigates meiofaunal community diversity in the Baltic Sea with a focus on differences between marine protected areas (MPAs) and adjacent reference sites (REFs). Samples were collected in the Fehmarn Belt and Oderbank regions as part of the MGF Ostsee project, prior to the exclusion of bottom-trawling activities. Whole-community metabarcoding was performed using two genetic markers, mitochondrial COI and nuclear 18S rRNA, complemented by morphological identification of harpacticoid copepods. The combined dataset provides one of the first integrated assessments of meiofaunal biodiversity in Baltic Sea MPAs and REFs, offering a valuable baseline of community composition under current conditions. Results demonstrate marker complementarity, regional differences in assemblages, and method-specific taxonomic coverage, supporting the utility of multi-marker metabarcoding together with classical taxonomy for long-term biodiversity monitoring and management.