Hydrodynamic Disturbance Drives Habitat‐Dependent Assembly of Microalgae: Divergent Adaptive Strategies in a Heavily Sediment‐Laden River Ecosystem

Hydrological connectivity and sediment‐driven disturbance structure microbial communities in river ecosystems, but most studies focus on single habitats. Consequently, the assembly mechanisms of cyanobacterial and eukaryotic microalgae across interconnected habitats in sediment‐laden rivers remain poorly understood.

We investigated longitudinal and vertical assembly patterns of planktonic and benthic microalgae across 44 sections of the Yellow River (22 natural river and 22 reservoir‐affected sites) using 16S/18S rRNA gene amplicon sequencing combined with neutral modelling, network analysis and path modelling.

We hypothesized that cyanobacteria and eukaryotic microalgae adopt distinct adaptive strategies in response to hydrodynamic disturbance and habitat heterogeneity in sediment‐laden river.

We found that microalgal communities differed markedly between planktonic and benthic habitats, with sediment transport enhancing benthic cyanobacterial abundance. Deterministic processes dominated community assembly, particularly in benthic habitats. Along longitudinal and vertical gradients, cyanobacteria showed stronger dispersal limitation and habitat coupling than eukaryotic microalgae and reservoir sections exhibited weaker planktonic‐benthic connectivity.

These findings indicate that hydrodynamic disturbance and sediment dynamics differentially regulate cyanobacterial and eukaryotic assembly across habitats in sediment‐laden rivers, highlighting the importance of cross‐habitat perspectives for understanding microbial organization in large river systems.