Coupled regulation effects of sanqi-pine intercropping systems on soil fertility and heavy metals mediated by ammonia-oxidizing microorganisms

Background While the Sanqi-pine intercropping system enhances soil fertility and mitigates heavy metal accumulation, the dynamic interactions among soil properties, heavy metals, and microorganisms across different intercropping patterns and full growth stages remain poorly understood. Here, we established monoculture systems of Pinus armandii (Pa) and Pinus yunnanensis (Py), alongside their respective intercropping systems with Sanqi (PaS and PyS). Over a 24-month monitoring period, we determined key edaphic properties, heavy metal concentrations, and the abundance of ammonia-oxidizing microorganisms, aiming to systematically uncover the regulatory mechanisms underlying these interactions. Results Both PaS and PyS systems significantly improved comprehensive soil fertility and effectively reduced the contents and pollution risks of heavy metals. The relative closeness of soil fertility increased by 19.35% and 18.18%, while the relative closeness of heavy metals decreased by 41.03% and 61.36% in the PaS and PyS systems, respectively. Notably, the pollution levels were all classified as GradeⅠ(clean/safe) in all the systems. Sensitivity analysis revealed that ammonium nitrogen (NH 4 + –N) and Cu were the core factors affecting soil fertility and heavy metal indices, respectively. Further correlation analysis demonstrated that soil fertility was significantly negatively related to heavy metal contents. Structural equation modeling (SEM) confirmed that ammonia-oxidizing bacteria (AOB) and the archaea–to–bacteria ratio (AOA/AOB) directly influenced Cu content by regulating NH 4 + –N transformation, thereby reducing heavy metal accumulation in the soil. Conclusion This study confirms that both PaS and PyS systems improve soil fertility and mitigate heavy metal risks, while the PyS system exhibits superior comprehensive performance under its environmental conditions. These findings provide an important theoretical basis for the ecologically safe cultivation of Sanqi and the sustainable management of soil health.