Abstract
Abstract Our understanding of the interactions between bacteria and phytoplankton in the freshwater phycosphere, including the development of algal blooms, is very limited. To identify the taxa and compositional variation within microbial communities, we performed 16S rRNA amplicon sequencing research on samples collected weekly through summer from mesocosms that differed in temperature and mixing regimes. We investigated, for the first time, the abundance diversity of microalgae, including Chlorophyta, Cryptophyta, and Cyanobacteria species, using visualization-based FlowCAM analysis and classification of microbial communities to species level by nanopore next-generation sequencing. We found that nanopore metagenomics, in parallel with complementary imaging flow cytometry, can depict the fine temporal dynamics of microbiomes associated with visually identified Microcystis morphospecies, Chlorophyta, and Cryptophyta during algal bloom development. Our results showed that the temporal characteristics of microbiomes combined with a visual approach may be a key tool to predict the metacommunity structure and dynamics of algal blooms in response to anthropogenic effects and climate change.