Trade-Offs of Soil Quality, Wheat Yield and Nutrient Efficiency Under Long-Term Combined Chemical and Manure Fertilization in Vertisols

Organic fertilization is a key strategy for improving soil structure and fertility in China’s Vertisols, yet the trade-offs among soil quality enhancement, grain yield performance, and nutrient use efficiency under different organic amendment regimes remain insufficiently elucidated. Based on a unique 43-year field fertilization experiment, this study systematically evaluated the effects of long-term chemical fertilization (NPK) alone, low-dose (NPKLS) and high-dose straw incorporation (NPKHS), combined chemical fertilizer with cattle manure (NPKCM), and pig manure (NPKPM) fertilization on soil physical, chemical properties, crop yields and plant nutrient utilization efficiency. The results showed that NPKCM and NPKPM significantly improved soil physical properties by reducing soil bulk density, improving soil pore structure, and enhancing soil water retention capacity and saturated hydraulic conductivity. Although long-term manure application led to slight soil salt accumulation, the rate of accumulation remained substantially lower than that associated with commercial organic fertilizers and did not approach the crop salinity damage threshold, suggesting low ecological risk. Compared with NPK treatment, manure amendment effectively counteracted soil acidification induced by prolonged chemical fertilization, while also significantly increasing soil total phosphorus and available phosphorus content, and elevated the proportion of active phosphorus (PAC). The improved soil phosphorus activation capacity and comprehensive soil quality further contributed to substantial increases in wheat grain yield under NPKCM and NPKPM treatments. Despite these agronomic benefits, the additional nitrogen and phosphorus inputs from manure resulted in soil nutrient surpluses, which considerably reduced nitrogen and phosphorus partial factor productivity as well as agronomic efficiency. In contrast, straw incorporation treatments (NPKLS, NPKHS) sustained stable crop yield without notable declines in nutrient efficiency, positioning them as a greener and more sustainable approach to balancing grain production with resource use efficiency. These findings highlight the need to integrate nutrient credits from manure into fertilization program. Given the 43-year evidence, fertilization strategy should consider not only the nutrients supplied by manure but also the quantities exported through harvested products, with adjustments based on annual soil fertility analyses. Such nutrient budgeting is essential to maximize fertilizer use efficiency, prevent excessive phosphorus accumulation, and maintain balanced soil fertility over time.