Long-term fertilization can result in changes in the nitrogen (N) cycle in maize rhizosphere soil. However, there have been few reports on the impacts of plant–soil–microbe regulatory mechanisms on the N cycle in soil. In this study, soil samples were collected from a long-term experimental site located at Jilin Agricultural University, Changchun City, Jilin Province, Northeast China. We then analyzed the changes in the functional genes related to the N cycle, soil enzyme activity, and maize root exudates under long-term fertilizer application using metagenomics and liquid chromatography analysis. We aimed to investigate the response of the N cycle to long-term fertilizers, the interaction among plant, soil, and microbes, and the effect of the plant–soil–microbe system on the N cycle. Long-term fertilization had a significant effect on soil N contents, N₂O emissions, and enzyme activity related to the N cycle in maize rhizosphere soil. The functional genes of the N cycle were mainly enriched in the N degradation pathway in maize rhizosphere soil. N fertilizer application decreased the abundance of functional genes related to N fixation and degradation, denitrification, and assimilatory nitrate reduction (ANRA) and increased the abundance of functional genes participating in dissimilatory nitrate reduction (DNRA) and anaerobic ammonia oxidation/hydroxylamine oxidation. The soil environment was positively related to soil enzyme activity and negatively related to the microbial community composition and amino acids in root exudates. The contribution rate of microorganisms to the N cycle was the highest (r² = 0.900), followed by amino acids (r² = 0.836) and the soil environment (r² = 0.832). Therefore, we concluded that N fertilizer is the main factor limiting the soil N cycle and that microorganisms are the main factor regulating the N cycle in the plant–soil–microorganism system.

Long-term fertilization can result in the changes in carbon (C) cycle in the maize rhizosphere soil. However, there have been few reports on the impacts of microbial regulatory mechanisms on the C cycle in soil. In the study, we analyzed the response of functional genes that regulate the C fixation, decomposition and methane (CH₄) metabolism in maize rhizosphere soil to different fertilization treatments using metagenomics analysis. As the dominant C fixation pathway in maize rhizosphere soil, the abundance of the functional genes regulating the reductive citrate cycle (rTCA cycle) including korA, korB, and IHD1 was higher under the chemical nitrogen (N) fertilizer treatments [nitrogen fertilizer (N), compound chemical fertilization (NPK), the combination of compound chemical fertilizer with maize straw (NPKS)] than maize straw return treatments [maize straw return (S), the combination of phosphorus and potassium fertilizer with maize straw (PKS)]. The NPK treatment decreased the abundance of functional genes involved in 3-hydroxypropionate bicycle (3-HP cycle; porA, porB, and porD), which was one of the major C fixation pathways in soil aside from dicarboxylate-hydroxybutyrate (DC/4-HB cycle) and Calvin cycle. The abundance of functional genes related to C degradation was higher in S, PKS and NPKS treatments than N and NPK treatments, and chemical N fertilizer application had a significant effect on C degradation. The dominant Methanaogenesis pathway in maize rhizosphere soil, used acetate as a substrate, and was significantly promoted under chemical N fertilizer application. The functional genes that were related to CH₄ oxidation (i.e., pmoA and pmoB) were reduced under N and NPK treatments. Moreover, soil chemical properties had a significant impact on the functional genes related to C fixation and degradation, with SOC (r² = 0.79) and NO₃⁻-N (r² = 0.63) being the main regulators. These results implied that N fertilization rather than maize straw return had a greater influence on the C cycle in maize rhizosphere soil.