Evaluating Different Natural Phytoplankton Communities: a Comparison Between Flow Cytometry and Microscopy

Flow cytometry (FCM) is becoming a popular method in phytoplankton analysis. The ability to identify species populations and the accuracy of cell counts are determining factors that make this technique attractive in research and monitoring. In addition, the analysis speed prompts for sampling in high spatial and/or temporal resolution. On the other hand, inverted microscopy remains the gold standard in analysis of coastal phytoplankton providing detailed insights on community taxonomical composition and structure. We compared quantification conducted by a CYTOBOUY scanning flowcytometer and inverted microscopy on natural phytoplankton communities from a temperate estuary (Roskilde Fjord, Denmark). Both methods reveal expressively the differences in the spring and autumn blooms among the inner and outer basins the latter manifested by higher diversity and higher contribution of larger organisms. Functional traits can be obtained from “finger printing” silico imaging of cell populations derived from optical properties FCM, but to apply full taxonomical resolution, it is necessary to combine FCM and inverted microscopy, to create a solid local phytoplankton data basis. Our work shows that the results from such different techniques are comparable and that the FCM fingerprinting can increase the resolution for characterizing the phytoplankton community in time and space.