Abstract

Monitoring phytoplankton diversity is essential for the conservation of marine ecosystems and the protection of human health. This study compares light microscopy (LM) and DNA metabarcoding (MB) for analysing phytoplankton community at a long-term station in the Central Adriatic Sea, representing the first application of metabarcoding in this region. Sampling was conducted in June 2024 using Niskin bottles and a 53 µm plankton net. Four genetic markers (COI, 18S V4, 18S V9, rbcL) were applied to bulk plankton DNA to broaden taxonomic coverage and assess their detection performance relative to LM. Among the molecular markers, rbcL detected the highest taxonomic richness and was particularly effective for diatom species detection. In contrast, 18S V4 and 18S V9 captured a broader spectrum of phytoplankton diversity, especially outperforming LM and the other two molecular markers in detecting a previously unrecognized but ecologically important phytoflagellate group. Species-level resolution within the taxonomically challenging genera Chaetoceros and Pseudo-nitzschia was considerably improved with metabarcoding. However, several taxa observed by LM, including certain coccolithophores and thecate dinoflagellates, were not detected by any of the molecular markers. Overall, the results show that methodological choices strongly influence biodiversity estimates and highlight the value of a complementary integrative approach in assessing phytoplankton diversity.

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