Partial substitution of synthetic nitrogen fertilizer with manure (organic substitution) is highly recommended to minimize environmental risks without compromising crop productivity in intensive agricultural systems. However, our understanding of the effect of organic substitution on soil organic carbon (OC) and total nitrogen (TN) in deep soil and its impact on crop productivity remains limited. Here we investigated OC and TN changes in soil profile down to 100 cm, crop yield, and sustainable yield index under synthetic nitrogen, phosphate, and potassium fertilizers (NPK), NPK plus straw (NPKS), and organic substitution (NPKM) treatments over two decades in four upland fields across different climate zones. Compared with the initial values, two decades of NPKM treatment significantly (p < 0.05) increased OC and TN stocks in either topsoil (by 25.6–103.8 and 15.8–89.8%) or deep soil (by 2.9–71.3 and 5.7–36.9%), respectively, across all sites. The increases in OC and TN stocks in 0–100 cm soil receiving NPKM were significantly higher than those receiving NPK at all sites and NPKS at three high-evaporation sites. Compared with NPKS and NPK treatments, crop yield and N uptake were significantly increased under NPKM treatment only at the Qiyang site. Furthermore, OC sequestration in the entire soil profile down to 100 cm and TN accumulation in topsoil exhibited significant positive correlations with crop N uptake, relative crop yield, and sustainable yield index. In conclusion, long-term partial substitution of synthetic N fertilizer with manure facilitates soil OC and TN sequestration in the entire 100 cm profile and thus maintains high crop productivity in upland areas.

Mitigating climate change necessitates a thorough understanding of soil organic carbon (SOC) decomposition and its response to warming. The overuse of synthetic fertilizers can alter SOC composition and affect carbon cycling, potentially changing the temperature sensitivity (Q₁₀) of SOC decomposition. This study evaluated the Q₁₀ of SOC decomposition after long-term (37-year) excessive fertilization in a loess soil. Four treatments were compared: control (no nutrient input, CK); recommended rates of synthetic nitrogen (N) and phosphorus (P) fertilizers (CF_r); excessive rates of N and P fertilizers (CF_h); and CF_h plus organic manure (MCF_h). The Q₁₀ of SOC decomposition was investigated via an incubation experiment at temperatures of 15 °C, 25 °C and 35 °C within 63 days. Compared with CF_r, long-term CF_h and MCF_h significantly increased SOC contents by 14% and 67%, and this increase was driven primarily by rises in mineral-associated organic carbon (MOC) of 28% and 62% and particulate organic carbon (POC) of 32% and 79%, respectively, under CF_h and MCF_h. While CF_h and MCF_h did not change the SOC composition, they increased the proportions of fine POC (fPOC) to SOC by 10% and 91%, and the ratio of light POC to SOC by 78% and 143%, respectively. Q₁₀ values ranged from 2.18 to 3.00 across all treatments, with a mean of 2.64. Both CF_h and MCF_h drastically enhanced the Q₁₀ values by 38% and 25% compared with CF_r at 15–25 °C. However, MCF_h significantly decreased the Q₁₀ value by 31% relative to CF_r at 25–35 °C. Partial least squares path modeling showed that soil physicochemical properties and labile carbon fractions differed significantly among treatments, with physical properties regulating labile carbon fractions. Fertilization significantly increased the Q₁₀ value at 15–25 °C owing to increased proportion of labile carbon fractions and decreased labile carbon content. Our results suggest that SOC gains from continuous addition of synthetic fertilizers are vulnerable to loss under warming. However, this loss could be alleviated by incorporation of organic manure. Thus, integration of organic manure into nutrient management practices could be an efficient way to counteract warming-induced SOC decomposition.