Phytoplankton Diversity in the Northern Adriatic Sea: Insights and Inconsistencies from Microscopy and Metabarcoding

Phytoplankton is a key component of marine ecosystems and a sensitive indicator of environmental change. In this study, light microscopy (LM) and DNA metabarcoding (18S-V4, 18S-V9, and rbcL) were combined to assess differences in phytoplankton diversity and community structure across three LTER sites in the northern Adriatic Sea, and to evaluate the methodological effects on community assessment. A total of 329 genera and 527 species were recorded by integrating both the approaches. Metabarcoding (MB) revealed increased taxonomic richness than LM, particularly for dinoflagellates and small phytoflagellates, while LM was better for identifying the diatoms and coccolithophores. The rbcL marker improved the taxonomic resolution for the diatoms compared to the 18S regions. The proportion of species shared among the sites increased from 13% with LM to 33–42% with MB, suggesting that MB may effectively reduce the discrepancies observed when relying solely on LM. Cluster analysis performed on species-relative abundances grouped the samples by approaches rather than sites, showing that methodological variability exceeded the ecological differences. The relative abundance patterns differed between methods but became more comparable after applying correction factors based on the 18S rRNA gene copy numbers, particularly for the dinoflagellates. Overall, MB enhances biodiversity assessment and comparability among sites, while LM remains essential for morphological validation and for abundance assessment.