Integrated transcriptomic and metabolomic analyses reveal cultivar-specific growth promotion of lettuce by Bacillus velezensis

Lettuce ( Lactuca sativa L.) is an economically important leafy vegetable worldwide. Improving lettuce yield is vital to stabilize vegetable supply and satisfy market demand in China. Plant growth-promoting rhizobacteria (PGPR) represent a sustainable and environmentally friendly approach to facilitate crop growth. To uncover cultivar-specific growth responses of lettuce to PGPR and reveal the underlying molecular regulatory mechanisms, two Bacillus velezensis strains (JB0319 and SAAS-6–3) were tested on two newly bred lettuce cultivars, Huqian and Binfen-3. Our results revealed obvious cultivar-dependent growth phenotypes. Inoculation with either strain significantly improved the biomass of Huqian, with SAAS-6–3 showing superior growth-promoting efficiency compared with JB0319. However, neither strain induced significant growth stimulation in Binfen-3. Physiological measurements demonstrated that bacterial inoculation increased soluble protein concentration in Huqian leaves. Endogenous hormone quantification further confirmed elevated levels of gibberellin (GA₃) and auxin (IAA) upon inoculation. To dissect the molecular mechanism, integrated transcriptomic and metabolomic analyses were carried out on Huqian. We identified 672 differentially expressed genes (DEGs), mainly enriched in plant hormone signal transduction, zeatin biosynthesis, phenylpropanoid and anthocyanin biosynthesis pathways. The detected differentially accumulated metabolites (DAMs) were predominantly associated with ABC transporters, amino acid metabolism, carbohydrate metabolism and the tricarboxylic acid (TCA) cycle. Weighted gene co-expression network analysis (WGCNA) further identified two core modules (MEblue and MEyellow) closely linked to SAAS-6–3 treatment, forming a coordinated “material supply - signal regulation” cascade supporting lettuce growth. Collectively, strain SAAS-6–3 stimulates Huqian growth by activating IAA and GA₃ biosynthetic pathways. The increased endogenous phytohormones synergistically modulate central carbon and nitrogen metabolism as well as transport processes, eventually enhancing biomass accumulation. This work clarifies the cultivar-specific effects of B. velezensis and provides theoretical support for precision application of PGPR agents in sustainable lettuce cultivation.