The influence of ozone pollution on CO2, CH4, and N2O emissions from a Chinese subtropical rice–wheat rotation system under free-air O3 exposure

•We evaluate the effects of O3 on GHG emissions in rice–wheat system and their GWP.•Effects of elevated O3 on GHG fluxes differed among crop variety, coverage and GHG type.•Elevated O3 increased CO2 fluxes in rice–wheat system but not for CH4 and N2O fluxes.•Elevated O3 added the GWP in rice–soil system but did not increase it in bare soil.•Reducing the GWP needs reduced CO2 emissions and plant O3-tolerant crop cultivars. A better understanding of the effects of ozone (O3) on greenhouse gas (GHG) emissions in rotational rice (Oryza sativa L.)–wheat (Triticum aestivum L.) systems is essential for reducing potential GHG emissions in agroecosystems due to the projected increase in O3 concentrations. Rice and wheat were rotationally grown in a free-air O3 enrichment platform, and crop production and N2O, CH4, and CO2 emissions from the soils were investigated as well as the global warming potential (GWP) of the GHGs. Exposure to elevated O3 (50% greater than ambient O3) slightly reduced the total biomass of wheat and significantly decreased that of rice, significantly decreased the root to total biomass ratio of wheat and slightly increased that of rice. Elevated O3 significantly increased the CO2 emission but did not influence the CH4 and N2O emissions in the rice–soil system; however, elevated O3 did not influence the CO2 emission, significantly increased the CH4 emission, and significantly reduced N2O emissions in the root-free soil during the rice season. Elevated O3 increased the CO2 emission and decreased the CH4 and N2O emissions in the wheat–soil system and root-free soil during the wheat season, although the decrease in N2O emission in the wheat–soil system was not significant. The effects of elevated O3 on GHGs emissions and biomass accumulation were related to crop species, plant coverage, and GHG type. Elevated O3 significantly increased the GWP in the rice–soil system and the GWP per unit of rice yield; however, it did not change the GWP in the wheat–soil system or in the root-free soil during the wheat–rice growing period, nor did it change the GWP per unit of wheat yield. Considering the decreases in wheat and rice dry matter, reducing CO2 emissions and planting O3-tolerant crop cultivars during future elevated O3 scenarios, especially during the rice-growing season, should be a primary focus of the research aimed at reducing the GWP and increasing the soil C and N sequestration of rotational rice–wheat cropping systems.