Bio-organic fertilization promotes soil nutrient cycling and reduces CO2 emissions via regulating bacterial communities in vegetable production system

Organic fertilizer substitution plays a crucial role in improving soil quality and reducing carbon emissions. However, the microbial mechanisms underlying effects on soil nutrient cycling and carbon emissions, especially in vegetable cultivation systems, remain poorly understood. A five-year field experiment (2019–2023) was conducted to evaluate the effects of fertilization strategies, including no fertilization (CK), inorganic fertilization (CF), bio-organic fertilization (OF), and their combination (COF). The impact of bio-organic fertilization on soil nutrient cycling, carbon emissions, and carbon-cycling microbial communities was analyzed. The highest multi-nutrient cycling index was observed in COF treatment. Compared to the CF treatment, the bio-organic fertilization treatments (OF, 35.9 %; COF, 12.1 %) significantly ( P< 0.05) reduced soil CO 2 emissions. Bacterial diversity (Chao1 index and Shannon index) in the OF and COF treatments was significantly ( P< 0.05) higher than in the CF treatment, whereas fungal diversity (Shannon index) showed the opposite trend. Bacterial diversity played a crucial role in regulating soil nutrient status, as bacterial co-occurrence network exhibited a highly significant positive correlation with the multinutrient cycling index. Bio-organic fertilizer enhanced the activity of genes related to multiple systems ( pccA ), rTCA cycle ( icd ), reductive acetyl-CoA pathway ( cooC ), and Calvin cycle ( cbbL/R ), thereby promoting the conversion of CO 2 into stable organic compounds. Furthermore, structural equation modeling confirmed that soil carbon fixation genes, bacterial diversity, and network stability were key factors influencing CO 2 emissions. Overall, from a long-term perspective, organic fertilizer substitution can mitigate carbon emissions and promote nutrient cycling in greenhouse vegetable cultivation systems, representing a greener and more sustainable agricultural approach. • Bio-organic fertilizer substitution reduces CO 2 emissions while enhancing multinutrient cycling index. • Bio-organic fertilizer increased soil carbon fixation genes ( pccA , icd , cooC , cbbL/ R). • Bio-organic fertilizer increased bacterial diversity and suppressed fungal diversity. • Bacterial diversity, network stability, and carbon fixation genes are key regulators of soil CO 2 emissions.