A soil bacterium isolated from cucumber-growing fields has shown a marked ability to make cucumber plants taller, greener and heavier, and new research now offers a detailed picture of what happens below ground when the microbe is applied. In a study published in BMC Plant Biology, researchers report that Bacillus altitudinis strain JZBQ5, delivered by root irrigation, significantly increased plant height in pot trials, raised leaf chlorophyll readings, and improved growth and yield measures in field trials. The team then traced these effects to coordinated shifts in the rhizosphere bacterial community and in the expression of thousands of cucumber root genes.
The work began from a practical question: Bacillus species are well known for plant growth-promoting properties, but how B. altitudinis stimulates cucumber growth has not been fully understood. To close that gap, the researchers evaluated the strain’s growth-promoting effect and simultaneously examined the microbial and transcriptional responses in the rhizosphere after treatment. In the pot assay, plants treated with JZBQ5 at concentrations of 10 to the 7 and 10 to the 8 colony-forming units per millilitre reached average heights of 32.0 centimetres and 31.6 centimetres respectively, compared with 18.4 centimetres in untreated control plants. At the highest tested dose of 10 to the 9 colony-forming units per millilitre, leaf SPAD values, a proxy for chlorophyll content, climbed to 36.17, significantly above the control reading of 27.61.
Field trials reinforced the pot results. Treated cucumbers showed significant increases in plant height of 13.69 percent, root length of 32.75 percent, plant weight of 41.93 percent, chlorophyll a content of 101.91 percent, and total chlorophyll content of 63.08 percent relative to controls. Yield also responded: the average yield per ridge of first-crop cucumbers treated with JZBQ5 rose by 10.83 percent compared with the untreated group. Taken together, the agronomic data indicate that a single bacterial strain can deliver measurable gains across multiple growth parameters under both controlled and open-field conditions.
To understand the mechanism, the researchers turned to the rhizosphere, the narrow zone of soil surrounding and influenced by plant roots, where microbes and roots exchange nutrients and signals. Microbiome analysis of this zone revealed higher bacterial richness after JZBQ5 treatment and a treatment-associated shift in the overall community structure. Pseudomonadota remained the dominant phylum throughout, meaning the treatment reshaped the community without displacing its major bacterial group. Linear discriminant analysis effect size, a method for identifying biomarker taxa, together with genus-level comparisons, showed enrichment of several notable genera, including Pseudomonas, Bacillus, Streptomyces, Mesorhizobium and Bradyrhizobium.
The enrichment pattern is telling. Several of these genera are associated with functions that benefit plants, such as nutrient cycling and the production of growth-influencing compounds, so their increased abundance suggests that JZBQ5 does not act alone but recruits or favours a supportive microbial entourage. The finding that bacterial richness increased as well points to a broad stimulation of the rhizosphere ecosystem rather than a narrow takeover by the applied strain.
On the plant side, root transcriptome analysis identified 444 differentially expressed genes in treated roots, comprising 205 genes that were upregulated and 239 that were downregulated. Enrichment analysis against the KEGG pathway database highlighted four functional categories: plant hormone signal transduction, carbon fixation in photosynthetic organisms, alpha-linolenic acid metabolism, and glycolysis and gluconeogenesis. These pathways connect plausibly to the observed phenotypes. Hormone signalling governs growth and development, carbon fixation underpins photosynthetic capacity, alpha-linolenic acid metabolism participates in hormone-related signalling in plants, and glycolysis and gluconeogenesis regulate energy metabolism in root tissue.
Correlation analyses then tied the two layers of data together. The researchers found that JZBQ5 treatment strengthened statistical associations among rhizosphere taxa, carbon-fixation genes, chlorophyll accumulation and plant-growth traits. In other words, the microbial shifts, the gene-expression changes and the visible growth improvements did not occur as isolated outcomes but moved in statistically linked patterns after treatment. The authors present this as evidence that the strain may promote cucumber growth by influencing both the rhizosphere microbiome and host transcriptional regulation.
The study’s design supports cautious interpretation. The pot assay and field trials measured growth and yield directly, while the microbiome and transcriptome analyses describe associations observed after treatment; the correlation analyses indicate strengthened statistical links rather than proven causal chains from individual microbes or genes to individual traits. Even so, the consistency of the growth gains across pot and field settings, combined with the coherent pathway signals in the root transcriptome, gives the findings practical weight. The authors suggest that the results support further development of JZBQ5 as a biofertilizer for sustainable cucumber production.
For growers and researchers alike, the study adds a well-documented example of how a single beneficial bacterium can leave fingerprints at multiple scales at once: in the soil community surrounding the roots, in the expression of plant genes governing hormones, photosynthesis and energy metabolism, and in the final height, weight, chlorophyll content and yield of the crop. As cucumber production seeks tools that reduce reliance on synthetic inputs, strains such as JZBQ5, whose effects can now be tracked through both microbial and molecular lenses, offer a template for how next-generation biofertilizers might be evaluated before they reach the field.
Subject of Research: Growth-promoting effects of the bacterium Bacillus altitudinis JZBQ5 on cucumber, examined through rhizosphere microbiome and root transcriptome analysis.
Article Title: Rhizosphere microbiome and transcriptome uncover the growth-promoting effect of Bacillus altitudinis JZBQ5 in cucumber
Article References: Liu, Y., Zhao, J., Zhang, J., Zhang, T., Chen, L., Li, Y., Zhang, T., & Qin, W. (2026). Rhizosphere microbiome and transcriptome uncover the growth-promoting effect of Bacillus altitudinis JZBQ5 in cucumber. BMC Plant Biology. https://doi.org/10.1186/s12870-026-10247-9
Image Credits: AI Generated
DOI: 10.1186/s12870-026-10247-9
Keywords: Bacillus altitudinis, cucumber, plant growth-promoting bacteria, rhizosphere microbiome, transcriptome, biofertilizer, chlorophyll, Pseudomonadota, KEGG pathways, hormone signalling, sustainable agriculture, Rhizosphere
News Source: Morgan Morrow. (October 30, 2026). Soil bacterium Bacillus altitudinis JZBQ5 boosts cucumber growth through root and rhizosphere changes. Scienmag.
