Eelgrass (Zostera marina) meadows are highly biodiverse coastal ecosystems providing various provisioning and regulating ecosystem services. Widespread decline of eelgrass coverage in the Baltic Sea has necessitated restoration initiatives, requiring reliable biodiversity monitoring to assess their effectiveness. Traditional morphological assessments are labour-intensive, costly, and limited in taxonomic resolution, constraining scalability and consistency. Environmental DNA (eDNA) metabarcoding offers a promising alternative, providing non-invasive, cost-effective, comprehensive biodiversity estimates across taxa. However, its application to eelgrass restoration monitoring has not yet been investigated.
This study presents the first comparison of morphology-based and eDNA-based community assessments across three restoration sites in the western Baltic Sea. eDNA metabarcoding targeted the mitochondrial cytochrome oxidase I gene (COI) and nuclear 18S rRNA V1–V2 region, while morphological identification examined infauna and epifauna. eDNA-based approaches detected 111 species across 120 genera and 13 phyla, substantially exceeding morphological detection of 20 species across 38 genera and 5 phyla. Beyond significant richness differences, the approaches revealed markedly distinct community compositions with minimal taxonomic overlap. The absence of some common eelgrass- associated taxa in eDNA datasets and the lack of abundance data from eDNA indicate these approaches are complementary rather than interchangeable, each illuminating different ecological dimensions. These findings demonstrate that integrating eDNA metabarcoding with morphological assessment offers valuable insights for comprehensive biodiversity monitoring in eelgrass restoration programs, enabling more robust evaluation of restoration success.