Alternative stable states of multi-trophic microbiota in long-distance water diversion systems

Whether hydro-engineering habitat switching can drive repeatable alternative stable states in multi-trophic microbial communities remains poorly understood in long-distance water diversion systems. Here, we applied an alternative stable states framework to bacterial, fungal, protistan, and micro-metazoan communities across seasonal and spatial gradients in a large engineered water diversion system. Multi-trophic communities exhibited cyclical state transitions over time, with spring and the subsequent spring converging toward similar community configurations. Along the spatial gradient, most microbial groups formed two alternative stable states, with State A mainly associated with high-disturbance sections and State B with hydraulically stable reservoir sections. Community state transitions were strongly structured by hydro-engineering habitats, and reservoirs repeatedly acted as major transition zones. State differentiation was accompanied by systematic shifts in diversity and taxonomic composition: bacterial diversity was higher in State A, whereas eukaryotic groups were generally more diverse in State B. Cross-trophic state consistency was associated with greater network stability, whereas state mismatches coincided with network simplification and reduced stability. State differentiation was jointly driven by environmental filtering, stochastic assembly processes, and cross-trophic coupling; notably, eukaryotic states were strongly and positively linked to bacterial states (path coefficient = 0.749, P < 0.001). These findings show that engineered water diversion systems can harbor repeatable multi-trophic stable states and that hydraulic habitat switching plays a central role in shaping microbial state transitions and ecological stability.