Flow cytometry has potential as a rapid assessment technique to evaluate phytoplankton biomass and species composition. It facilitates for multi-parameter analysis of individual cells on the basis of light scattering effects induced from cellular constituents, as well as auto-fluorescence. Fluorescence emission characteristics may be especially useful in classifying cyanobacteria as they contain phycoerythrin which emits light predominantly in the 550–600 nm waveband, chlorophyll-a (650–700 nm emission) and allophycocyanin (660 nm emission). The objective of our study was to assess the utility of flow cytometry for the rapid identification and sorting of freshwater algae and cyanobacteria species. Using a selection of laboratory-cultured freshwater algae and cyanobacteria species, this study demonstrated unique light scatter and fluorescent characteristics for each species examined, allowing for rapid species identification and sorting of mixed populations of laboratory cultures and samples from two lakes in the Rotorua region (New Zealand). Analysis of lake water samples collected over seven months demonstrated changes in abundance and community composition of phytoplankton in the two lakes and demonstrates that flow cytometry may be a useful technique for examining seasonal changes in phytoplankton composition.

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