Phytoplankton pigments and epifluorescence microscopy as tools for ecological status assessment in coastal and estuarine waters, within the Water Framework Directive.

Inverted microscopy is widespread employed for the analysis of phytoplankton composition within water quality monitoring networks. However, the analysis at the lowest taxonomical level is not always required for ecological status assessment. In addition, inverted microscopy can underestimate the small phytoplankton, and not always distinguish photoautotrophic from heterotrophic cells. In this study, as alternative tools, epifluorescence microscopy and High Performance Liquid Chromatography (HPLC) were employed to characterize phytoplankton communities within waters of different trophic condition. Epifluorescence microscopy confirmed its effectiveness to count the small phytoplankton. Furthermore, significant correlations between nutrients of anthropogenic origin and nanoplankton abundances were found. However, this technique resulted very time-consuming. HPLC together with the CHEMTAX program was more appropriate than inverted microscopy, in terms of cost-effectiveness. Also, the main variability patterns observed in the phytoplankton community structure by HPLC coincided with previous findings in the study area. Nevertheless, a rapid screening at the inverted microscope is recommended.