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Various particle-size fractions of soil aggregates were obtained with the wet-screening method from the soil of a long-term stationary fertilization experimental field of Beijing Yanqing Lvfulong organic vegetables farms to analyze the effect of microbial communities on carbon distribution in brown soil aggregates under different fertilizations with sequence analysis by 16SrDNA-PCR-DGGE technology. Results showed that with different fertilization treatments, treatments OF(organic fertilizer) increased 0.25~2mm water stable aggregates by 109.0%; compared to CK (unfertilized), 0.053~0.25mm and 0~0.053mm particle aggregates decreased by 31.9% and 142.1%, respectively. Treatments OF significantly increased carbon content in aggregates of all particle sizes by 15.2%~46.9% compared to CK, and in the >2mm aggregates by 46.9%. The content of brown soil carbon was positively related to the content of the >2mm aggregates; significantly positive related to the content of the 0.25~2mm aggregates, but significantly negative related to the content of the 0.053~0.25mm aggregates; negative related to the content of the 0~0.053mm aggregates.