Rhizosphere microbiome and transcriptome uncover the growth-promoting effect of Bacillus altitudinis JZBQ5 in cucumber

Bacillus species are well-known for plant growth-promoting (PGP) properties, but how Bacillus altitudinis stimulates cucumber growth is not fully understood. In this study, we evaluated the PGP effect of B. altitudinis JZBQ5 in cucumber and investigated its associated rhizosphere microbial and root transcriptional responses after root-irrigation treatment. In the pot assay, JZBQ5 treatment significantly increased cucumber plant height, reaching 32.0 ± 7.07 and 31.6 ± 10.69 cm at 10 7 and 10 8 CFU/mL, respectively, versus 18.4 ± 6.71 cm in the control. Application at 10 9 CFU/mL raised leaf SPAD values to 36.17 ± 6.74, which was significantly greater than the control (27.61 ± 3.82). Field trials showed that JZBQ5 significantly increased plant height (13.69%), root length (32.75%), plant weight (41.93%), chlorophyll a (101.91%), and total chlorophyll content (63.08%). The average yield per ridge of first-crop cucumbers treated with JZBQ5 increased by 10.83% compared to the control group. Rhizosphere microbiome analysis showed higher bacterial richness after JZBQ5 treatment and a treatment-associated shift in community structure, with Pseudomonadota remaining the dominant phylum. LEfSe and genus-level analyses further showed enrichment of taxa including Pseudomonas , Bacillus , Streptomyces , Mesorhizobium , and Bradyrhizobium . Root transcriptome analysis identified 444 differentially expressed genes, including 205 upregulated and 239 downregulated genes, and KEGG enrichment highlighted plant hormone signal transduction, carbon fixation in photosynthetic organisms, alpha-linolenic acid metabolism, and glycolysis/gluconeogenesis. The correlation analyses indicated that JZBQ5 treatment strengthened statistical associations among rhizosphere taxa, carbon‑fixation genes, chlorophyll accumulation, and plant‑growth traits. These findings suggest that JZBQ5 may promote cucumber growth by influencing rhizosphere microbiome and host transcriptional regulation, supporting its further development as a biofertilizer for sustainable cucumber production.