Rhizosphere Microbiome and Transcriptome Uncover the Growth-Promoting Effect of Bacillus altitudinis JZBQ5 in Cucumber

Bacillus species are well-known for plant growth-promoting properties, but how B. 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 markedly improved plant height at 10 ⁸ and 10 ⁷ CFU/mL and increased leaf SPAD values at specific concentrations. In the field trials, JZBQ5 significantly increased plant height, root length, plant weight, chlorophyll a, and total chlorophyll content. 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 plant-beneficial 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. Heatmap and correlation analyses indicated that JZBQ5 reconfigured auxin- and cytokinin-related transcriptional modules and strengthened the association between beneficial rhizosphere bacteria, carbon-fixation genes, chlorophyll accumulation, and growth traits. These findings suggest that JZBQ5 promotes cucumber growth through coordinated rhizosphere microbiome remodeling and host transcriptional regulation, supporting its further development as a biofertilizer for sustainable cucumber production.