Unveiling key metabolic pathways in Bacillus subtilis-mediated salt tolerance enhancement in Glycyrrhiza uralensis Fisch. through multi-omics analysis

Glycyrrhiza uralensis Fisch. (licorice), an essential medicinal herb, predominantly thrives in arid and semi-arid desert grasslands, where its unique ecological conditions confer upon it a certain degree of salt tolerance. However, the elevated salinity in saline-alkali soil can induce osmotic stress leading to the demise of licorice. Currently, the application of microbial agents stands as a primary strategy to alleviate salt stress. Bacillus subtilis (Bs), known for conferring non-biological stress tolerance in various plants, holds significant promise in mitigating salt stress in licorice. This study investigates the physiological responses, transcriptomic, and metabolomic changes in licorice seedlings inoculated with Bs under different concentrations of salt stress. Under Bs inoculation, the antioxidant enzyme activity, proline content, and malondialdehyde (MDA) levels in licorice seedlings decreased. Concurrently, Bs inoculation stimulated plant growth, photosynthetic capacity, and increased the content of polysaccharides, anthocyanins, and other substances. Metabolomic analysis identified 74 differential metabolites involved in Bs-mediated salt stress responses, including phenylalanine, flavonoids, and amino acid metabolites. Transcriptomic analysis elucidated Bs involvement in salt stress-related secondary metabolism, fatty acid metabolism, amino acid metabolism, cell wall synthesis, and signal transduction pathways, primarily implicating differential genes such as XET, GPX, COMT. Integrated multi-omics analysis revealed that under salt stress, Bs primarily enriches licorice in three crucial metabolic pathways: arginine and proline metabolism, phenylpropane, and flavonoid biosynthesis. In conclusion, the genetic regulatory network uncovered the response mechanisms of Bs in mediating licorice's salt stress.