Comparative analysis of phytoplankton diversity using microscopy and metabarcoding: insights from an eLTER station in the Northern Adriatic Sea

The monitoring of phytoplankton is crucial to highlight changes in the marine ecosystems. In the present study, the phytoplankton community of an eLTER station in the Northern Adriatic Sea was analysed combining two approaches, i.e. microscopy and eDNA metabarcoding (targeting V4 and V9 regions of the 18S rRNA gene, and using PR2 and SILVA as reference databases), to highlight the strengths and weaknesses of these two methods. Metabarcoding revealed a so far unknown phytoplankton diversity (99 genera and 151 species), while microscopy detected 14 genera and 44 species not revealed by metabarcoding. Only a small percentage of genera and species were shared by the two methods (microscopy and metabarcoding), 18S regions (V4 and V9) and reference databases (PR2 and SILVA). Metabarcoding showed a community characterized by a higher number of phytoflagellate and dinoflagellate genera and species, in comparison with microscopy where diatom and dinoflagellate taxa were the most represented. Moreover, metabarcoding failed to reveal almost all the coccolithophores. The results confirmed metabarcoding as a powerful tool, but it should still be combined with microscopy to have a more detailed information on the community and to counteract the drawbacks of metabarcoding, such as gaps in the reference databases.