Flow cytometry (FCM) is a promising tool in the field of aquatic phytoplankton
ecology because it allows for multi-parameter assessment of the physiological state of individual cells in
an algal population. It can help to elucidate major questions such as phytoplankton taxa identification,
the evaluation of cell quantity and viability, and the measuring of phytoplankton and general microbial
metabolic activities. Traditionally, microalgal characterization is performed by microscopic analysis using
UV-excited nuclear dyes (e.g. Hoechst and DAPI) or dyes that are excited in the blue-green part of the
spectrum such as propidium iodide and eosin. The development of multi-laser cytometric systems has
widened the possibilities for multi-parametric analysis and cell sorting of phytoplankton populations.
Notwithstanding, significant algae autofluorescence originating from different types of chlorophyll and
accessory pigments may overlap with propidium iodide and/or eosin staining and affect the resolution
of algae clusters and cell sorting
