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Summary Soil organic carbon (SOC) sequestration under elevated CO2 concentration (eCO2) is a function of carbon (C) input and C retention. Nitrogen (N) limitation in natural ecosystems can constrain plant responses to eCO2 and their subsequent effects on SOC, but the effect of eCO2 on SOC in N‐enriched agroecosystems with cultivars highly responsive to eCO2 is largely unknown. We reported results of SOC dynamics from a field free‐air CO2 enrichment experiment with two rice cultivars having distinct photosynthetic capacities under eCO2. A reciprocal incubation experiment was further conducted to disentangle the effect of changes in litter quality and soil microbial community on litter‐derived C dynamics. eCO2 significantly increased total SOC content, dissolved organic C and particulate organic C under the strongly responsive cultivar, likely due to enhanced organic C inputs originated from CO2 stimulation of shoot and root biomass. Increases in the residue C : N ratio and fungal abundance induced by eCO2 under the strongly responsive cultivar reduced C losses from decomposition, possibly through increasing microbial C use efficiency. Our findings suggest that applications of high‐yielding cultivars may substantially enhance soil C sequestration in rice paddies under future CO2 scenarios.

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