Complementary roles of eDNA metabarcoding and microscopy in plankton monitoring across seven habitats

Abstract Plankton biodiversity in aquatic ecosystems is currently investigated by labor-intensive and time-consuming microscope identification. Environmental DNA (eDNA) metabarcoding is emerging as a highly effective and objective tool for assessing biodiversity. In this study, we compared the effectiveness of eDNA metabarcoding with conventional microscope identification for monitoring plankton biodiversity in seven habitats. The eDNA metabarcoding identified a rich diversity of 190 families, 410 genera and 871 species within the planktonic community across seven habitats. In contrast, traditional microscope identification only identified 51 families, 75 genera and 96 species. In addition, primer choice influenced the detected plankton community diversity, with the V4 primers performing poorly for detecting Cladocera and Euglenophyta taxa and the V9 primers revealing more eukaryotic plankton species. Despite primer-specific differences in species detection, there was substantial overlap between the species detected by eDNA metabarcoding strategies and microscope identification. These results suggest that eDNA metabarcoding can be used as a complementary method alongside microscope identification rather than replacing them entirely.