Frequent Flooding Drives Regional‐Scale Homogenization of Riparian Soil Microbial Communities in the Three Gorges Reservoir

ABSTRACT Aim This study aimed to investigate how frequent flooding events of varying intensities influence soil microbial diversity, community composition, and assembly processes in riparian ecosystems, with a focus on understanding the underlying mechanisms driving these responses. Location Fifteen riparian sites were selected along a ~600 km section of the Three Gorges Reservoir in central China. Methods Soil and vegetation samples were collected from sites experiencing different flooding intensities. Microbial α‐ and β‐diversity, community structure, and functional composition were assessed using high‐throughput sequencing; community assembly mechanisms were analysed using null model approaches, microbial communities and diversity were linked to soil physicochemical and vegetation characteristics. Results Despite an approximately 6% increase in microbial α‐diversity under high intensity flooding, both community heterogeneity (β‐diversity) and network complexity significantly declined, with the flooding effects being weaker for fungi than for bacteria. These changes in the microbial community were associated with alterations in soil properties and vegetation, which intensified with more severe flooding. Bacterial community assembly shifted toward stronger heterogeneous selection under high intensity flooding, indicating altered ecological processes. By contrast, assembly processes of the fungal community were dominated by dispersal limitation and were unaffected by the frequent flooding. Bacterial functional group composition shifted significantly with flooding intensity, with high‐intensity flooding increasing the abundance of microbial functional groups associated with nitrogen cycling (anammox), carbon cycling (methanol oxidation, methylotrophy, and fermentation), and sulfur cycling (dark sulfide oxidation and dark oxidation of sulfur compounds). Main Conclusions At the regional scale, flooding promoted the homogenization of riparian soil microorganisms, especially for the bacterial community, by enhancing environmental filtering and reducing dispersal limitation. The findings highlight the vulnerability of riparian ecosystems to hydrological changes and provide a framework for predicting microbial responses to flooding in riverine landscapes worldwide. Conservation strategies should account for these dynamics to protect watershed biodiversity and function.