Microeukaryotic communities and habitat-based assessment in a large plateau river system

Understanding how environmental conditions and anthropogenic activities shape microbial biodiversity is essential for ecological assessment of large river systems. However, the structure, assembly mechanisms, and environmental drivers of eukaryotic microbial communities in the upper Yellow River remain poorly understood. Here, we conducted a basin-scale survey across more than 1,000 km of the upper Yellow River in Gansu Province, sampling both trunk streams and tributaries during wet and dry seasons, and analyzed eukaryotic microbial communities using high-throughput sequencing. Our results show clear spatial and seasonal differentiation in community structure. Natural upstream regions exhibited significantly higher microeukaryotic diversity and more complex co-occurrence networks than downstream anthropogenically influenced areas. Community assembly was predominantly driven by stochastic processes, although the relative contributions of dispersal limitation and environmental selection varied across river sections and seasons. In addition, tributary communities were more strongly associated with habitat quality and land-use patterns than trunk-stream communities, highlighting distinct environmental controls across river types. Importantly, integrating habitat assessment and land-use indicators revealed strong and consistent relationships with microbial community variation, suggesting their potential as practical ecological indicators for microbial biodiversity assessment. These findings improve our understanding of microbial ecological processes in large river systems and provide a potential indicator-based framework for river ecological evaluation and management.