Nitrogen fertilization modulates the endophytic bacteria of Aconitum carmichaelii Debx. and the quality of medicinal materials

Aconitum carmichaelii Debx. is a traditional medicinal plant with substantial economic value. Prolonged use of chemical fertilizers or high nitrogen (N) input may reduce the accumulation of pharmacodynamic compounds and adversely influence ecosystems. Although the impact of N fertilization on soil microorganisms has been extensively investigated, how N fertilization modulates the endophytic bacterial community and thus affects secondary metabolite accumulation in the host plant remains unclear. This study hypothesizes that moderate nitrogen fertilization enhances alkaloid accumulation by modulating endophytic bacterial communities, thereby altering plant metabolic pathways. The field experiment demonstrated that moderate N fertilization (N2: 350 kg N ha⁻¹) significantly increased the total alkaloid content in A. carmichaelii by 14.45% ( P < 0.05) compared with that in the zero N control. High-throughput 16S rRNA gene sequencing indicated that moderate N fertilization significantly increased the diversity (Chao 1 and Shannon index, P < 0.05) and altered the community composition (R² = 0.5081, P = 0.001) of endophytic bacteria. 64 endophytic bacterial taxa were identified differentially abundant taxa varying N treatments. Among them, 20 belonged to the N2 group, 16 of which demonstrated a strong positive correlation with alkaloid contents. Subsequent experiments confirmed that Bacillus subtilis JY-7-2L significantly enhanced alkaloid accumulation in A. carmichaelii ( P < 0.05) by producing alkaloids and inducing host metabolic pathways. Further analysis revealed that the metabolites from B. subtilis JY-7-2L remarkably up-regulated the genes related to signal transduction and alkaloid biosynthesis, thereby enhancing alkaloid accumulation in A. carmichaelii . This study demonstrated that rational fertilization significantly enhances plant–microbe interactions, particularly through the role of B . subtilis JY-7-2L in promoting alkaloid accumulation. These findings laid the foundation for optimizing the N fertilization strategy for A. carmichaelii cultivation and developing B . subtilis JY-7-2L strain into environmentally friendly biofertilizers to advance agricultural sustainability. • Nitrogen application (350 kg ha⁻¹) significantly increased total alkaloid content in A. carmichaelii by 14.45% compared to the zero-N control ( P < 0.01). • Endophyte diversity and composition had distinct responses to N fertilization. • Alkaloid accumulation correlated with variations in key microbial taxa. • B. subtilis JY-7-2L significantly increased alkaloid accumulation by 16.05% compared to the control ( P < 0.01). • JY-7-2L metabolites up-regulated host genes, enhancing alkaloid accumulation.