Little information is known on whether carbon (C) and nitrogen (N) immobilization is synchronized in different sizes of aggregates under different agricultural management practices. Carbon and N concentrations and the C/N ratios in different sizes of aggregates down to 40 cm depth were determined after long-term application of chemical fertilizers combined with manure or without manure in a wheat-rice cropping system. Manure application usually produced significantly (P < 0.05) higher C and N concentrations and lower C/N ratios in bulk soil and in different sizes of aggregates down to 20 cm depth than the other treatments, and the 1.5 MNPK treatment at 0-10 cm depth had the highest SOC concentration of 26.3 g/kg. The C and N concentrations in bulk soil and all aggregate fractions decreased markedly with increasing soil depth. Among water stable aggregates in all soil depths, the highest C (48.2-66.4%) and N (47.8-68.3%) concentrations as a percentage of SOC were found in the small macroaggregates (2000-250 μm, SM). Manure application significantly (P < 0.05) increased the mass and C and N concentrations of SM and SM fractions down to 20 depth. The mean C/N ratios of silt-clay within large and small macroaggregates (inter-SC) were 1.57 and 1.46 units lower than those of silt-clay particles, respectively, indicating that inter-SC had relative high N availability. Moreover, the C and N content of SM down to 40 cm depth tended to saturation with increasing C input rate. Overall, manure application effectively improved soil structure, SM were the dominant particles involved in soil C and N storage, and inter-SC were the main particles responsible for N availability.
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