Automated in situ imaging flow cytometry in long-term phytoplankton monitoring

Phytoplankton, as a primary producer and first level of food webs, is an important component of all aquatic ecosystems. Phytoplankton communities are very dynamic having fast turnover rates, from half a day to a few days, which makes monitoring of the phytoplankton communities challenging. Classically phytoplankton communities are followed with manual sampling and light microscopy counts. Although providing detailed taxonomic information the method is labor intensive restricting the frequency of data collected. Long-term monitoring is often executed with only a few samples per year targeting different seasons, even weekly sampling monitoring stations being rare. Alternative methods to follow the phytoplankton community composition and succession traditionally include optical fluorescence detection of different phytoplankton pigments, such as chlorophyll a, phycocyanin, and phycoerythrin, and satellite remote sensing. Fluorometers provide a cost-effective solution to follow the community in high temporal resolution, but the taxonomic composition stays unresolved. Satellite remote sensing allows monitoring of large spatial scales, but similarly, lacks taxonomic information and relies on clear skies. Within recent decades novel methods, such as eDNA and pulse shape and imaging flow cytometry, have been emerging providing more detailed information on the phytoplankton communities. While eDNA cannot be yet used in high temporal resolution, high-frequency in situ imaging and cytometry provide autonomous and automated alternatives to follow the community composition and dynamics, however, their downside is the slightly lower taxonomic resolution. The long-term monitoring programs and data series collected using light microscopy methods are the key reference to understand the shifts in phytoplankton communities in the changing climate. The rapid uptake of the novel methods allows collection of more fine-grained datasets, but demands an understanding of how they compare to the existing methods. Here we present the results of the comparison of different methods, with an emphasis on the in situ instrument Imaging FlowCytobot. The results suggest that in situ imaging is an excellent addition to monitoring phytoplankton communities and to studies for enhancing our understanding of community dynamics and succession in relation to environmental forcing. However, novel methods should be adopted as an additional way of collecting information and used in parallel with ongoing monitoring activities to understand how the different methods describe the communities also in the long run.