Soil and rhizosphere microbes correlate with altitude-dependent variation in flavor component of Amomum tsao-ko fruits

Environmental factors play a crucial role in regulating the accumulation of secondary metabolites in medicinal plants, which ultimately determines their pharmacological quality. Amomum tsao-ko is commonly used as spice and medicinal ingredient in China, known for its essential oil enriched with flavor compounds that serve as a critical quality indicator. However, the yield and quality of A. tsao-ko are commonly constrained by specific habitat requirements. While previous studies have mainly focused on the chemical constituents and bioactivities of the essential oils, the ecological factors influencing their quality variation remain insufficiently explored. This study utilized an integrated multi-omics approach to investigate how soil environment and rhizosphere microbial communities correlate with the accumulation of flavor compounds in A. tsao-ko fruits across different altitudes. Our finding revealed that the accumulation patterns of geraniol and geranyl acetate were opposite to those of citrals and bicyclononane aldehydes, with the former two compounds showing a significant increase with rising altitude. Additionally, the accumulation of geraniol and geranyl acetate was positively correlated with the levels of available nitrogen, iron (Fe), and zinc (Zn) in the soil. In contrast, the contents of citral and bicyclononane aldehydes were significantly positively associated with Pseudomonas and nitrogen-fixing bacterial taxa such as Zophobihabitans and Rhizobium . Furthermore, although terpenoid biosynthesis-related genes exhibited significant variation across altitudinal environments, their expression levels showed relatively weak correlations with soil environmental changes. Overall, our study reveals correlations with soil nutrients and rhizosphere soil microbial ecology in shaping the biosynthesis and accumulation of characteristic terpenoids in A. tsao-k o, which may impact fruit quality. These findings might provide valuable insights for optimizing fertilization practices and targeted rhizosphere microbial management to improve the quality of A. tsao-ko fruit. • Multi-omics linked soil nutrients and microbes to terpenoid metabolism in Amomum tsao-ko across altitude. • Geraniol/geranyl acetate showed oppositetrends to geranial and bicyclononane aldehydes with increasing altitude. • Geraniol and geranyl acetatecorrelated positively with soil available nitrogen, Fe, and Zn. • Citral and bicyclononane aldehydes were positively associated with Pseudomonas and nitrogen-fixing taxa. • PLS-PM model integratedsoil–microbe–monoterpenoid interactions across altitudinal gradients.