Fertilization impacts the conversion of microbe-derived and plant-derived carbon in particulate organic matter (POM) and mineral-associated organic matter (MAOM), affecting the storage and stability of soil organic carbon (SOC). However, it is still unclear how fertilization influences the microbial mechanisms underlying this conversion in paddy soil. To fill this gap, amino sugar and lignin, as well as enzyme activities, were determined in a 12-year field experiment. Organic fertilizer increased the SOC content by 33.01%, and combined organic and inorganic fertilizers increased SOC stability by 7.07%. Specifically, organic fertilizer increased the lignin content by 17.09% (particularly in POM) and decreased the (Ad/Al)v, indicating the selective preservation of lignin. The increased bacterial PLFA/fungal PLFA and Ln(cellulase)/Ln(ligninase) demonstrated a shift in microbial communities towards bacteria and a decrease of lignin utilization. The microbial necromass carbon (MNC) content increased by 46.75% (particularly in MAOM), and the GluN/MurN decreased, showing organic fertilizer increased the contribution of MNC to SOC (especially bacterial necromass). The increased microbial biomass carbon (MBC) and r-strategy bacterial relative abundance indicated the promotion of fast-growing microorganisms. Therefore, SOC sequestration was improved with the increase of lignin and amino sugars under organic fertilizer. The combined application of organic and inorganic fertilizers decreased the lignin content by 11.20% (particularly in POM) and increased the (Ad/Al)v in MAOM, indicating the acceleration of lignin decomposition. The increment of Ln(cellulase)/Ln(ligninase) and bacterial PLFA/fungal PLFA were smaller than those of other fertilization treatments, showing a stronger promotion effect on fungi and an increase of lignin use. The MNC increased by 45.26% (particularly in MAOM), but the GluN/MurN was lower than that of other fertilization treatments, showing the combined organic and inorganic fertilizers increased the contribution of MNC to SOC (especially fungal necromass). The MBC and the relative abundance of r-strategy bacteria and k-strategy fungi increased, indicating that the promotion of both fast-growing and slow-growing microorganisms. Therefore, the increase of MNC and the decrease of lignin improved the stability of SOC. Overall, fertilization affects the storage and stability of SOC by regulating the conversion of plant-derived and microbial-derived carbon.
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