Environmental DNA metabarcoding captures plankton diversity in the southern North Sea

Abstract DNA metabarcoding is increasingly used to monitor marine plankton communities. Here, we investigated the taxonomic diversity and community structure of eukaryotic plankton, including well-studied phytoplankton and mesozooplankton, as well as lesser-known taxa in the Belgian part of the North Sea. We used an integrative morphological and molecular approach, combining environmental DNA (eDNA) metabarcoding with imaging of plankton samples, collected using plankton nets and analyzed via either FlowCAM or ZooScan. Water samples were collected over one year and analyzed based on a 650 bp fragment of the 18S rRNA V4–V5 region using Oxford Nanopore sequencing. Across 77 samples, we examined community composition and diversity metrics at the phylum level and compared molecular results (after normalization of read numbers) with morphological assessments. Diversity indices were positively correlated with nutrient concentrations and turbidity, but negatively with water temperature. No correlation was found between microalgal cell density and taxon richness, although cell density correlated negatively with diversity indices incorporating evenness. Metabarcoding identified 25 phyla not detected morphologically, including four fungal phyla, picozoans, and loukozoans. Significant correlations were observed between eDNA-derived abundances (based on both rarefied read counts and the eDNA index) and morphological densities for the dominant phyla (Arthropoda and Myzozoa), whereas no such relationships were found for less abundant taxa. However, discrepancies remained between relative abundances derived from morphology and DNA reads, reflecting differences in taxonomic resolution and detection biases. Overall, eDNA metabarcoding provided broader taxonomic coverage, while morphological methods offered finer taxonomic resolution of a limited selection of taxa.