Early-stage intercropping modulates rhizosphere soil properties, microbiome composition, and photosynthetic physiology of Phellodendron chinense: a comparative analysis of five cultivation systems

Introduction Phellodendron chinense is an important medicinal plant in China. However, continuous monoculture has caused soil degradation and physiological constraints, which have become a key bottleneck limiting its sustainable production. Intercropping with companion plants is an effective approach to break this dilemma. Methods We selected five representative cultivation systems commonly practiced of Phellodendron chinense and systematically measured their rhizosphere soil properties, microbial community composition, and leaf gas-exchange traits. The overarching goal was twofold: (i) to characterize the intercropping-induced variations in these three dimensions (soil properties, microbial communities, and photosynthetic physiology, and (ii) to elucidate the coupling relationships among these three dimensions. Results and Discussion The results demonstrated that total nitrogen(N), total sodium(Na), and magnesium(Mg) contents in the T4 and T2 patterns were significantly higher than those in other patterns. The T2 and T4 patterns significantly enhanced microbial community α-diversity. In contrast, the T3 pattern caused significant soil acidification (pH 4.69) and elevated the relative abundance of the tolerant phylum Chloroflexi. T4 and T2 patterns significantly alleviated stomatal limitations in P. chinense , achieving optimal net photosynthetic rate(Pn) and stomatal conductance(Gs). Correlation analysis showed that Pn was significantly and positively correlated with soil P and Mg contents, while Gs was significantly and positively correlated with soil Na content, and N and Na were the critical factors affecting the structural variation of bacterial and fungal communities. Overall, this study demonstrates that intercropping promote soil nutrient accumulation enhances rhizosphere microbial diversity to facilitate the alleviation of photosynthetic physiological limitations. Intercropping P. chinense with bamboo or tea synergistically mitigates the host’s photosynthetic physiological limitations through a belowground positive feedback pathway. These findings provide an important theoretical basis for the efficient and sustainable cultivation of this rare medicinal plant.