Decadal manure substitution reshapes microbial communities to drive plant and microbial carbon accumulation in soil carbon fractions

• Pig manure surpassed inorganic fertilizer to increase SOC content and persistence. • 100% N as pig manure maximized SOC via necromass C and lignin accumulation. • 50% N fertilizer plus pig manure enhanced the proportion of mineral-stabilized SOC. • Microbial life strategies control lignin degradation and necromass C accumulation. The transformation of organic residues into particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) governs soil organic carbon (SOC) storage and stability. However, how long-term manure use steers plant- and microbe-derived SOC fractions in paddy soils remains unclear. The SOC in paddy soil was evaluated by measuring amino sugars, lignin and enzyme activities from a 12-yr field trial (rice–wheat rotation) with no fertilizer, 100% mineral N fertilizer, and pig manure (50% and 100% replacement of N fertilizer). Compared to mineral N, the 100% pig manure treatment increased SOC by 26%, mainly through enhanced lignin input and microbial necromass accumulation, leading to significantly higher POC and MAOC levels. Manure application, compared to mineral N, promoted rice growth, which increased total organic C input and nutrient availability, thereby selectively favoring r -strategist bacteria, as reflected by a lower vanillyl acid-to-aldehyde ratio, a higher ratio of cellulose- to lignin-degrading enzyme activity, and greater lignin and bacterial necromass production. In contrast, the combined NPK and pig manure treatment increased the proportion of MAOC in total SOC by 7% compared to the 100% manure treatment, yet this came with enhanced lignin degradation, a lower bacterial phospholipid fatty acid (PLFA)/fungal PLFA ratio, and greater abundance of K -strategist fungi, resulting in less POC accumulation. These findings demonstrate that substituting mineral N with pig manure reshapes microbial community, enhancing the microbial transformation of plant- and microbe-derived residue into stable and labile SOC pools, and more effectively promotes SOC sequestration and persistence than mineral fertilization alone in paddy systems.