Spatio-temporal distribution pattern of the picocyanobacterium Synechococcus in lakes of different trophic states: a comparison of flow cytometry and sequencing approaches

In this study, we aimed to investigate the spatio-temporal distribution patterns of the picocyanobacterium Synechococcus, an important contributor to primary production in many freshwater lakes. Our study sites were four lakes with different trophic states within the Osterseen Lake District in Southern Germany. Flow cytometry counts and next-generation sequencing were used from April to October 2015 to analyse the occurrence of Synechococcus and heterotrophic prokaryotes in relation to physical and chemical habitat properties. Synechococcus was identified as the main representative of the autotrophic picoplankton, but cell counts varied widely. The Synechococcus taxa identified by flow cytometry were confirmed by sequencing data, but the comparison of the flow cytometry counts and sequence data revealed discrepancies for cells in the exponential phase. The eutrophic Lake Schiffhuettensee was dominated by algae and had the highest abundance of heterotrophic prokaryotes. The presence of distinct operational taxonomic units of Synechococcus varied seasonally and was lake-specific, indicating local niche adaptation. Our study sheds light on the ecology of these important primary producers in freshwater systems. Furthermore, the discrepancy observed with the direct comparison of the widely used methods of next-generation sequencing and flow cytometry should serve as a caveat for future data analysis.