The impacts of biochar application on the carbon (C) and nitrogen (N) cycles in soil profiles in vegetable fields have rarely been reported. A three-year field experiment (CK, control; BC, biochar; N, nitrogen fertilizer; BCN, biochar and nitrogen fertilizer) was conducted in fluvo-aquic soil with a wild cabbage-Chinese cabbage rotation to investigate biochar effects on soil organic carbon (SOC) sequestration, N retention, and nitrate (NO3−) leaching in the soil profile (topsoil, 0–20 cm; subsoil, 20–50 cm; third-layer soil, 50–100 cm). The results showed that the biochar-induced increase in topsoil SOC under N fertilization was greater for Chinese cabbage season than for wild cabbage season. Excluding biochar-N, biochar application caused an extra increase in topsoil total nitrogen (TN) under N fertilization. Biochar decreased the NO3−-N concentration of third-layer soil solution, particularly under N fertilization, indicating that biochar reduced the potential source of NO3− leaching. Under N fertilization, biochar reduced the abundances of carbon-degrading bacteria (Streptomyces, Bacillus, Mycobacterium, and Sphingomonas) and genes (sga, xylA, lig, and pgu) in the topsoil, as well as the abundances of ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) and gene (amoA) in the third-layer soil. However, biochar increased the abundance of ammonia-assimilating bacteria (Rhodococcus) and gene (glnA) in the topsoil. Biochar inhibited the microbial function associated with C degradation by affecting soil TN, thus enhancing topsoil SOC sequestration. Biochar promoted the soil microbial function related to ammonia assimilation by affecting dissolved organic carbon (DOC), subsequently enhancing ammonia assimilation. Moreover, biochar initially inhibited ammonia oxidation in the third-layer soil by increasing soil DOC, subsequently affecting nitrite oxidation and ultimately reducing soil NO3− leaching. Biochar significantly increased the N use efficiency of vegetables in the last two years. This study provides insights into biochar effects on the changes in soil microbial function, which promoted SOC sequestration, enhanced N retention and mitigated nitrate leaching in a vegetable rotation field.
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