A comparison of FlowCam and microscopy methods for phytoplankton community assessment in Lake Champlain

FlowCam is a particle analysis system, and its relatively recent application to phytoplankton permits rapid identification and biovolume measurements through automated imaging and analysis. However, direct comparisons of estimates from FlowCam and standard microscopy methods using diverse phytoplankton assemblages have been limited. We processed over 100 samples collected bi-weekly from heterogeneous regions of Lake Champlain from May to October 2015. Habitats ranged from shallow, eutrophic bays to the deep, mesotrophic main lake, and the phytoplankton assemblages included cyanobacteria, chlorophytes, diatoms, chrysophytes, dinoflagellates, and cryptophytes. We measured cell densities and dimensions with both an inverted microscope and a FlowCam, and compared taxa biovolumes and community metrics such as genera richness and diversity. FlowCam calculates higher biovolume estimates than microscopy, however, it is possible to calculate a conversion factors between the two methods to better synchronize results. Results from this study inform the use of FlowCam for diverse phytoplankton communities in other freshwater systems.