Abstract
Efficient fertilization is vital for rice production and sustainable agriculture. Conventional fertilization (CK) suffers from low efficiency and environmental pollution, whereas side-deep fertilization (SF) offers an efficient, eco-friendly alternative. The changes in microbial carbon cycling functional genes induced by SF in paddy soils remain unclear. This study investigates the effects of SF and CK on soil organic carbon (SOC), total nitrogen (TN), microbial communities, and carbon- and nitrogen-cycling genes in double-cropping rice paddies through field experiments. Results reveal that SF significantly increases TN in deeper soil layers (10–20 cm), enhancing the expression of nitrogen fixation genes (e.g., K02591 and K02588) and nitrogen metabolism pathways, alongside boosting Chloroflexi and Planctomycetes abundance. In contrast, CK promotes SOC accumulation and upregulates carbon metabolism genes (e.g., K01179 and K01728) in surface layers (0–10 cm). In deeper layers, SF elevates nitrogen reduction gene abundance (e.g., K02591) while suppressing denitrification and assimilatory nitrate reduction, whereas CK enhances dissimilatory nitrate reduction (e.g., K02568). Redundancy analysis (RDA) shows that soil properties (pH, SOC, and TN) drive microbial community structure, with Actinobacteria positively linked to SOC and TN. These findings demonstrate that SF optimizes nitrogen cycling in deeper soil by improving nitrogen use efficiency and functional microbial growth, while CK favors shallow-layer carbon sequestration. This study provides a scientific foundation for tailoring fertilization strategies to soil depth, leveraging carbon- and nitrogen-cycling gene dynamics to enhance soil fertility and sustainability in rice production.