Confluences characteristics determine the influence scope of microbial community from confluence hydrodynamic zone on river network

River confluences are crucial parts of the river networks, which connect different rivers and promote material exchange between them. Joining of two rivers would cause sharp shifts of flow dynamics and form confluence hydrodynamic zone (CHZ) with specific flow structure and biogeochemical processes. However, CHZs are small areas compared with river networks, whether and how the biogeochemical processes in CHZs would influence the lower reaches and even the whole river networks remain unclear. To address this gap, the present study focused on the nitrogen dynamics in a river network consisting a series of confluences, and combined molecular biological tools, gene-centric modelling approach and SourceTracker analysis to reveal the microorganisms induced nitrogen transformation processes in CHZs and other normal hydrodynamic zones (NHZs). Results illustrated that the enriched microbial species in CHZs were associated with nitrogen transformation, such as Terrimonas and Sphingobacterium, which were reported to be vital participants in nitrate and nitrite reduction processes. The reactions rates of different nitrogen transformation processes, calculated based on functional genes abundances, further revealed that N2 production rates were significantly higher in CHZs than NHZs (p < 0.05), demonstrating CHZs were the hotspots for nitrogen removal in the researched river network. Besides, the specific microbial communities and stimulated nitrogen removal processes in CHZ would sustain in lower reaches. SourceTracker analysis illustrated that microbial communities would exert significant influences on lower reaches, and the influence scope was controlled by confluences characteristics, such as flow ratio between tributary and main stream. Higher discharge ratio would increase the influence scope of microbial community in CHZ. These results indicate that reasonable design of confluence characteristics can be applied as a critical engineering measure for the improvement of ecological health of river networks.