Warming reshapes the rice rhizosphere microbiome to impair post-heading nitrogen supply and reduce yield

Climate warming poses a significant threat to global rice security. While research heavily emphasizes aboveground physiological acclimation to heat stress, belowground dynamics—particularly how temperature-induced shifts in rhizosphere ecology affect sustained nutrient availability—remain largely unresolved. Using a two-year field-based free-air temperature enhancement system, we investigated the temporal dynamics of rhizosphere microbial functioning, nitrogen (N) cycling, and rice performance from jointing to maturity. Warming initially stimulated plant N accumulation before heading but induced a severe N deficit during critical reproductive phases, ultimately reducing grain yield by 22.80%-23.44%. This yield penalty was driven by substantial depletions in soil organic carbon and available inorganic N pools during heading and grain filling. Furthermore, warming reshaped the rhizosphere microbiome, reducing α-diversity while increasing network complexity, indicating intensified biotic interactions under resource limitation. Taxonomically, warming drove a successional shift toward oligotrophic and stress-tolerant assemblages (e.g. Chloroflexi and Acidobacteriota ). Functionally, it intensified organic matter decomposition and denitrification while suppressing nitrification. These findings demonstrate a critical “temporal decoupling” between rhizosphere N supply and crop demand: although warming transiently increases early-season N availability via stimulated rhizosphere priming, it fails to sustain N supply due to accelerated carbon depletion and gaseous N loss. This study elucidates the microbial feedbacks governing rice resilience to climate stress and highlights the necessity of stage-specific N regulation to maintain yield stability in warming agroecosystems. • Warming caused yield loss via severe post-heading N accumulation. • Soil organic carbon and available N rapidly declined after heading. • Microbial shifts enhanced mineralization and denitrification potentials. • Early resource overdraw created a mismatch between supply and demand.