Effects of different concentrations of exogenous methyl jasmonate on tuber metabolism and rhizosphere bacterial community dynamics in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua is a traditional medicinal and edible plant valued for its tubers, which are rich in bioactive components such as polysaccharides, flavonoids, and saponins. The phytohormone methyl jasmonate (MeJA) regulates plant secondary metabolism and stress responses, promoting the accumulation of medicinal compounds in P. cyrtonema. However, the temporal dynamics of the rhizosphere microbiome and its association with the tuber metabolism under different MeJA concentrations remain poorly understood. In this study, three-year-old P. cyrtonema plants were treated with rhizosphere sprays of 200 μmol L −1 and 400 μmol L −1 MeJA. Plants were sampled at 7, 14, 21, and 28 days post-treatment to evaluate tuber physiology and metabolite profiles, and metagenomic sequencing was used to characterize the structure and function of the rhizosphere bacterial community. Application of 200 μmol L −1 MeJA significantly enhanced tuber peroxidase (POD) activity, which peaked at 2.29 times that of the control on day 14 ( P < 0.05), and increased total flavonoid and saponin contents by 22.58% and 13.85%, respectively ( P < 0.05). In contrast, 400 μmol L −1 MeJA mainly inhibited antioxidant enzyme activities and delayed the induction of secondary metabolism. Metagenomic analysis revealed that the two MeJA concentrations shared the same dominant bacterial phyla but showed concentration-dependent differences in relative abundance dynamics, alpha diversity trajectories, and temporal patterns of community structure. The 200 μmol L −1 MeJA group exhibited a directional temporal shift (PERMANOVA R² = 0.79, P = 0.003) and continuously rising alpha diversity, whereas the 400 μmol L −1 treatment showed nonspecific stress fluctuations, with reduced alpha diversity, a weaker temporal gradient in community structure, and increased community homogenization. At the functional level, the 200 μmol L −1 MeJA group had higher relative abundances of microbial genes associated with nitrogen, carbon, and secondary metabolic pathways. In contrast, the 400 μmol L −1 MeJA group showed disrupted coordination among functional genes and persistently higher abundances of genes involved in antioxidant pathways. Correlation analysis identified associations between specific phyla and host traits: Nitrospirota was positively correlated with POD activity (r = 0.48, P < 0.05); Methylomirabilota was positively correlated with total flavonoid and saponin contents (r ≥ 0.41, P < 0.05); and Verrucomicrobiota was negatively correlated with these components (r < −0.55, P < 0.01). These findings suggest that 200 μmol L −1 MeJA promotes the accumulation of bioactive metabolites in P. cyrtonema through two proposed ways: the direct activation of host metabolism and the indirect association with shifts in potentially beneficial rhizosphere microbial taxa. This study provides a practical foundation for selective MeJA concentrations in medicinal plant cultivation.