Bacterial and microeukaryotic assemblage transitions during a harmful algal bloom in the Nakdong River

Harmful algal blooms (HABs) represent major ecological disturbances that can alter microbial community composition and reduce ecosystem resilience. Here, we investigated bacterial and microeukaryotic assemblage transitions during a bloom-affected period in the Nakdong River, a regulated river system in South Korea. By integrating microcystin (MC) measurements, cyanobacterial dominance, water-quality parameters, and amplicon-based community profiling (16S rRNA gene and ITS2), we characterized how microbial communities reorganized along gradients of bloom intensity. MC concentrations increased markedly across the sampling period, and early-phase qPCR data showed concurrent increases in mcyE gene abundance through 6 August 2021. Bacterial communities shifted from Actinobacteriota- and Proteobacteria-dominated assemblages toward Microcystaceae-enriched communities. Microeukaryotic communities similarly transitioned from diverse Chlorophyta, fungi, and ciliates to Chlamydomonadaceae- and ciliate-dominated assemblages under high-MC conditions. Both domains exhibited significant reductions in alpha diversity with increasing bloom intensity, although microeukaryotic responses were comparatively moderate. Correlation analyses revealed strong associations of MC concentration and Microcystis abundance with declining pH, elevated BOD, and the enrichment of bloom-associated taxa. These results indicate that bloom-associated conditions in this regulated river system were accompanied by parallel restructuring of bacterial and microeukaryotic assemblages. The integration of environmental and microbial indicators presented here provides a framework for understanding HAB-associated microbial reorganization and for informing monitoring strategies in hydrologically altered freshwater ecosystems.