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The nanocrystalline minerals contents predominantly and positively controlled the sizes of intermediate and stable SOC pools, and the mean residence time of intermediate SOC pool. Biotic and climatic factors (i.e., microbial biomass, available N for microbes, and excess precipitation) controlled the labile SOC pool. Compared with topsoil, stabilized organic matters were more in the intermediate rather than in the stable SOC pool, and the temperature had a more significant effect on the stable SOC pool in subsoil than in topsoil. Availa