Integrated microbiological and metabolomic analyses reveal the mechanism by which P addition affects the quality of Anisodus tanguticus

Anisodus tanguticus , a rare medicinal plant producing clinically vital tropane alkaloids: anisodine, anisodamine, scopolamine, and atropine, faces challenges in sustainable cultivation due to wild resource scarcity and suboptimal farming practices. While P addition is known to influence secondary metabolites, its microbiome mediated effects on alkaloid synthesis remain unclear. Therefore, in this study, we systematically analysed the mechanism of P on the association between alkaloid content of Anisodus tanguticus and microbiome by setting P addition gradients (LP: 120 kg/hm 2 , MP: 180 kg/hm 2 , HP: 240 kg/hm 2 ). The results demonstrated that P addition significantly reduced the content of 4 alkaloids in roots, stems and leaves. While microbial α-diversity remained unresponsive, but induced a structural reorganization of the microbial community, encompassing rhizosphere and bulk soil bacteria, which exhibited a marked association with alkaloids, intensified nutrient competition through the nitrogen cycling and organic matter catabolism pathways. Concurrently, the abundance of pathogenic functions within the fungal community underwent a significant increase with P addition. In this study, it was demonstrated that the addition of P inhibits alkaloid accumulation through dual pathways: (1) soil C:N:P stoichiometry imbalance interferes with plant secondary metabolism resource allocation; and (2) the introduction of pathogenic fungi hinders alkaloid synthesis and accumulation in plants. These findings provide a theoretical basis for the cultivation of Anisodus tanguticus by reducing the amount and increasing the efficiency of chemical fertilisers. The study suggests that precise fertilisation of medicinal plants needs to take into account the balance of soil nutrients and microbial function regulation. By suppressing the pathogenic bacterial flora and optimising the abundance of soil probiotic bacteria, it is possible to reduce the amount of phosphorus fertiliser applied and at the same time increase the yield of medicinal active ingredients, which is of great practical value in achieving the sustainable use of ethnomedicinal resources. • The alkaloid content of Anisodus tanguticus decreased significantly after phosphorus application. • The relationship between soil microorganisms and alkaloid content was closer after phosphorus application than endophytes. • Phosphorus additions affect the quality of Anisodus tanguticus by disrupting the soil nutrient balance, placing it in an unfavourable growing environment, and introducing pathogenic fungi that reduce its alkaloid content.