Divergent Stochastic Reassembly of Bacterial and Fungal Communities Under Extreme-Rainfall-Induced Hydrological Pulses in a Managed Urban River–Pool System

Extreme rainfall can rapidly alter hydrological connectivity in managed urban aquatic systems, yet its association with microbial community reassembly remains insufficiently understood. In 2025, Beijing experienced an anomalous rainy season with extreme rainfall, providing a single-year natural opportunity to examine bacterial and fungal communities across a dry–rainy–dry hydrological sequence in a managed river–pool system at the China National Botanical Garden (Northern Garden). Using 16S rRNA gene and ITS amplicon sequencing, we analyzed in situ water samples together with rainfall and runoff inflow samples representing atmospheric and catchment-derived external inputs. Bacterial alpha diversity increased during the mid-rainy phase influenced by extreme rainfall, whereas fungal alpha diversity remained comparatively stable despite compositional turnover. Genus-level profiles revealed distinct event-based source signatures—rainfall samples were characterized by Acinetobacter and Massilia, whereas runoff inflow samples were enriched in Arcobacter, Segatella, and Plectosphaerella. Null model analysis indicated that microbial assembly was dominated by stochastic processes, with bacterial communities mainly associated with drift-related undominated processes and fungal communities showing stronger dispersal limitation. Co-occurrence networks suggested rainfall-associated expansion of bacterial associations and persistently modular fungal networks. These findings suggest that extreme-rainfall-induced hydrological pulses are associated with divergent bacterial and fungal reassembly pathways in managed urban aquatic systems.