Inter-basin water diversion drives microbial homogenization and a shift from generalists to specialists

Inter-basin water transfer is a critical strategy for alleviating freshwater scarcity. However, a central scientific question remains: how does large-scale water transfer reshape microbial community assembly and interaction networks in ways that regulate ecosystem multifunctionality? This study investigated rivers in the Beijing-Tianjin-Hebei region affected by the Middle Route of the South-to-North Water Diversion Project (SNWDP-MR), comparing microbial community dynamics between receiving and non-receiving water bodies before and after normalization water replenishment. Replenishment markedly increased the relative abundance of Cyanobacteriota in both bacterioplankton and bacteriobenthos, while driving a decline in the speciation and extinction rates of generalists, and species tending to shift from generalists to specialists. Community α diversity increased significantly, but while community homogenization also accelerated. In receiving water bodies, bacterioplankton assembly was primarily governed by stochastic processes, whereas bacteriobenthos was dominated by deterministic processes, showing an opposite pattern in non-receiving water bodies. Network analysis revealed that replenishment reduced the complexity and stability of bacterioplankton networks but enhanced those of bacteriobenthos. Structural equation modeling further indicated that water replenishment weakened the regulatory effect of network stability on ecosystem multifunctionality. Collectively, this study elucidated the coupling mechanisms among microbial community assembly, network structure and evolutionary dynamics under ecological water replenishment, providing new insights for assessing the ecological impacts of inter-basin water transfer projects and optimizing sustainable water resource management.