Urbanization reshapes planktonic and benthic microbial communities and networks along a river continuum

Rivers are essential components of urban-rural river and lake system. Increasing urbanization and climate change have introduced significant longitudinal and vertical variability in environmental factors and river habitats; however, the underlying patterns remain largely unclear. This study selected a representative river with significant rural-urban gradients to analyze microbial community diversity, co-occurrence patterns, and spatiotemporal variation mechanisms to clarify the impacts of urbanization and differences in medium characteristics (surface water vs. sediment) on planktonic and benthic microorganisms. Vertically, the differences between water and sediment lead to distinct microbial community assembly processes. The community assembly of planktonic microorganisms was more influenced by stochastic processes, whereas deterministic processes had a greater influence on the assembly of the benthic microbial community. The differences in the medium characteristics also resulted in divergent response mechanisms of planktonic and benthic microbial communities to urbanization: benthic communities were more sensitive to changes in environmental factors and developed more complex network structures. Longitudinally, from rural to urban areas, the Chao diversity of planktonic communities decreased from 1099 to 938, and the Chao diversity of benthic communities decreased from 3465 to 3047. Notably, the proportion of benthic communities derived from planktonic microorganisms dropped sharply from 52% in rural areas to only 8% in coastal areas, indicating severely hindered microbial exchange. Urbanization also disrupts microbial networks and reduces network complexity. In growing urbanization, understanding the shifts in river microbial community-building processes can help develop more efficient ecological restoration measures. • Media properties drive distinct dominant processes in planktonic and benthic microbial community assembly. • Media differences lead to divergent response mechanisms to urbanization in planktonic vs. benthic microbes. • Microbial networks were disrupted in urban areas and reconstructed in coastal zones.