Shifts in Fertilization Regime Alter Carbon Cycling in Paddy Soils: Linking the Roles of Microbial Community, Functional Genes, and Physicochemical Properties

Fertilization regimes impact the carbon cycle processes in paddy soils. However, the effects of shifting fertilization regimes on the structure of microbial communities and functional genes involved in soil carbon (C)-cycling remain unclear. A long-term field experiment was established with three paired fertilization shift treatments: chemical fertilizer (CF) and CF to normal-rate organic fertilizer (CF-NOM); normal-rate organic fertilizer (NOM) and NOM to CF (NOM-CF); high-rate organic fertilizer (HOM) and HOM to CF (HOM-CF). Metagenomic sequencing and bioinformatics analysis were employed to investigate the effects of fertilization shifts on soil C-cycling microbial community structure, functional genes, and environmental factors. The results showed that compared to CF treatment, CF-NOM significantly increased soil organic carbon (SOC), mineral-associated organic carbon (MAOC), particulate organic carbon (POC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), and the emissions of CO2 and CH4 (p < 0.05). The NOM-CF led to significant reductions in MAOC, MBC, DOC, and CO2 and CH4 emissions. The HOM-CF shift caused significant decreases in SOC, MAOC, POC, MBC, DOC, and CO2 and CH4 emissions. Fertilization shifts had no significant effect on the α-diversity of C-cycling microbial communities (p > 0.05), but β-diversity showed a significant restructuring of community composition. Network analysis indicated that fertilization shifts increased positive microbial correlations while reducing network modularity. C-cycling functional genes responded sensitively to fertilization disturbances, especially key genes in the carbon fixation pathway (cdhDE, cooS). Redundancy analysis indicated that soil bulk density (BD) and POC are key environmental factors regulating functional differences in carbon metabolism, which collectively influenced microbial community structure and functional gene abundance along with other factors. We concluded that the C-cycling process in paddy soil was greatly altered by shifts in fertilization regimes, influenced by microbial diversity, functional genes, and network structure linked to soil characteristics.