Parallel Analysis of 16S sequencing and Imaging Flow Cytometry (IFC) data of microbial and phytoplankton communities in Lake Mesocosm Warming Experiment

Phytoplankton communities within freshwater ecosystems are characterized by high heterogeneity and complexity. With increasing evidence on the effect of climate change on aquatic systems, there is a need to better understand how such heterogeneous communities respond to environmental changes at contrasting temperatures. Dynamics of bacterio- and phytoplankton communities were monitored for two months using three outdoor mesocosms with three temperature regimes, varying nutrient levels, and two sampling depths. The collection of 46 water samples was followed by 16S rRNA amplicon sequencing and parallel analysis of phytoplankton composition by FlowCAM-based imaging flow cytometry (IFC). Nanopore-based sequencing was successfully applied for the classification of nearly 200 species in most mesocosm samples, with the detection of picoplankton and low-abundance/rare (<0.01%) species. Complementary IFC-based classification of nearly 3,500,000 recorded images revealed bloom dynamics of major phytoplankton groups. Nonmetric multidimensional scaling (NMDS) analysis revealed a significant effect of temperature on the composition of both microbial and phytoplankton communities. We conclude that an integrative approach of both optical and molecular methods provides a comprehensive assessment of complex spatial and temporal ecosystem dynamics at the mesocosm scale.