Long-term manure drives divergent carbon stabilization: Enzymic latch-mediated POC in paddies and MEMS-associated MOC in uplands

Soil organic carbon (SOC) stabilization is governed by land-use-specific biogeochemical processes, but the divergent roles of plant- vs. microbial-derived carbon in SOC fractions (particulate organic carbon, POC; mineral-associated organic carbon, MOC) remain unclear under long-term fertilization. Here, we investigated two over-35-year field experiments in red soil of China, comparing paddy (anaerobic) and upland (aerobic) systems under four fertilization regimes: no fertilizer (CK), mineral nitrogen (N), mineral NPK, and NPK plus manure (NPKM). We quantified plant- and microbial-derived carbon using biomarkers (lignin phenols for plant residues; amino sugars for microbial necromass) and identified key drivers via random forest modeling. Long-term NPKM significantly increased SOC in both systems, but through contrasting stabilization pathways.. In paddy, SOC gains under NPKM were dominated by POC (62% of total SOC increment), with plant-derived carbon (2.90 g kg⁻¹) being 3.1-fold higher than microbial-derived carbon (0.94 g kg⁻¹). This was primarily driven by β-glucosidase activity (relative importance: 37%), consistent with the "enzymic latch" mechanism that preserves plant residues under anaerobic conditions. In upland, SOC gains under NPKM were dominated by MOC (71% of total SOC increment), where microbial-derived carbon (1.91 g kg⁻¹) exceeded plant-derived carbon (1.14 g kg⁻¹). The synergy between total nitrogen (TN, relative importance: 42%) and leucine aminopeptidase (LAP, relative importance: 28%) accelerated microbial turnover and necromass stabilization, supporting the Microbial Efficiency–Matrix Stabilization framework. Our findings demonstrate that manure-based fertilization is the key to enhancing targeted SOC fractions: it sustains the "enzymic latch" for plant-derived POC accumulation in paddy and strengthens TN-LAP synergy for microbial-derived MOC accrual in upland. These results highlight the pivotal role of organic manure in tailoring fertilization strategies to enhance SOC sequestration in agricultural ecosystems.