Regional variability in soil organic carbon responses to chemical fertilizer and manure slurry driven by microbial functional pathways

Soil organic carbon (SOC) dynamics are profoundly influenced by fertilization regimes and regional environmental conditions. In this study, we compared the impacts of chemical fertilizer and manure slurry application on SOC content and microbial functional gene composition across three geographically distinct regions in China: Harbin, Yiyang, and Nanyang. Our results revealed contrasting SOC responses among regions. Manure slurry application significantly enhanced SOC in Harbin, resulting in a 54% increase compared with chemical fertilizer, mainly due to a pronounced accumulation of particulate organic carbon (POC). In contrast, SOC responses to manure slurry were minor in Yiyang and Nanyang, indicating that fertilization effects on SOC were strongly site-dependent. Metagenomic analyses showed that manure slurry increased the abundance of carbon fixation genes in Harbin, particularly those involved in the reductive pentose phosphate cycle and reductive tricarboxylic acid cycle, which increased by 9.57% and 6.38%, respectively. In contrast, manure slurry in Yiyang primarily enhanced genes involved in labile carbon degradation. Integrating soil properties, microbial functional genes, and enzyme activities revealed that fertilization affected SOC mainly through indirect pathways mediated by soil nutrient conditions and microbial functional traits. Changes in soil nutrients were closely associated with shifts in microbial carbon fixation and degradation gene abundances, which were more strongly linked to SOC and POC than to mineral-associated organic carbon. Overall, our findings indicate that the effectiveness of manure slurry versus chemical fertilizer in promoting SOC sequestration is not universal but strongly context-dependent, emphasizing the need for site-specific strategies in sustainable soil carbon management. • Manure slurry does not always outperform chemical fertilizer in SOC accrual. • Microbial C fixation and degradation pathways exhibited contrasting responses. • Fertilization influences SOC via soil properties and microbial C fixation. • Site-specific fertilization strategies are required to optimize SOC sequestration.