Comparison of imaging flow cytometry and microscopy for freshwater algal bloom detection

Imaging flow cytometry (IFC) is an emerging tool that allows for rapid identification and enumeration of phytoplankton in freshwater systems. However, few studies have assessed the effects of preservation on IFC results or compared live IFC and microscopy results in freshwater systems. Understanding the effects of preservation and differences between IFC and microscopy will improve interpretation of these data and inform strategies to use IFC-based approaches in freshwater systems. Our study objectives were to compare IFC and phase contrast with epifluorescence microscopy as techniques for phytoplankton identification and enumeration, and the effects of sample preservation with an emphasis on taxa forming harmful cyanobacterial blooms (HCBs). During June through October 2020, samples were collected from 2 lakes in the Finger Lakes region of New York. Live and preserved samples were analyzed by laboratory-based IFC, and preserved samples were analyzed by microscopy. The IFC approach captured community dynamics while detecting potential cyanobacterial bloom-forming taxa earlier and at lower abundances than microscopy. Laboratory-based IFC allowed for an intermediate level of taxonomic information when compared to microscopy, gross techniques, such as extracted chlorophyll a or fluorescence sensors, and field-based operation of IFC approaches. The laboratory-based application of IFC in this study allowed receipt of results in 5 d or less, a substantial improvement over microscopy, which can be time-consuming to conduct. However, the laboratory-based IFC approach had some limitations. Imaging flow cytometry-estimated biovolume may be less accurate than microscopy for some taxa because of the algorithms used to calculate biovolume, particularly for chrysophytes and coccoid cyanobacteria. Colonial dissociation during preservation appeared to affect detection of Microcystis by IFC less than for other fragile bloom-forming taxa like chrysophytes. Our study results advance understanding of how IFC may translate to field-based approaches for early harmful algal bloom indicators in freshwater.