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Summary Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run‐off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early‐ and late‐season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment – locally known as red soil pollution – and caused moderate increases of macronutrients, especially SiO2 and PO43−, with up to 25 and 0.5 μM respectively. We detected shifts in relative abundances of marine and terrestrially derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run‐off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short‐lived and bacterial communities quickly recovered following both storm events. The early‐ and late‐season storms caused different physicochemical and bacterial community changes, demonstrating the context‐dependency of extreme storm responses in a subtropical coastal ecosystem.

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