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Aims <p>Plant growth-promoting rhizobacteria (PGPR) are vital for enhancing agricultural productivity. This study aimed to evaluate the growth-promoting efficacy of three preselected PGPR strains in seedling and field trials, and to elucidate their mechanisms in modulating the rhizosphere microenvironment for enhanced plant growth.</p> Methods <p>Three <i>Bacillus</i> spp. (JZ31, JZ38, JZ264), isolated from rhizosphere soils, were evaluated using cucumber (<i>Cucumis sativus</i> L.) as a model plant in single or combined inoculation assays. Core PGPR traits, including phosphate solubilization, potassium solubilization, and indole-3-acetic acid secretion, were characterized. Plant nutrient uptake, growth parameters, and rhizosphere microbial α- and β-diversity were measured. Functional profiling was conducted via integrated metagenomic and metabolomic analyses, with microbial biomarkers identified using LefSe and MetagenomeSeq. Correlation analyses linked metabolites to plant–microbe interactions.</p> Results <p>All three strains exhibited classic PGPR traits and directly promoted cucumber nutrient uptake and growth. Individual inoculation induced distinct restructuring of the rhizosphere microbial community. These strains selectively enriched potentially beneficial microorganisms linked to nutrient decomposition, plant growth promotion, and biocontrol, while simultaneously suppressing potential pathogens and other identified non-beneficial microorganisms. Functional annotation revealed that inoculation specifically activated pathways related to quorum sensing, gene expression, hormone signaling, and nutrient metabolism, thereby facilitating rhizospheric nutrient cycling and microenvironment optimization. Correlation analyses identified key metabolites mediating the strains’ regulation of plant–microbe interactions.</p> Conclusion <p>This study demonstrates that the three <i>Bacillus</i> strains promote plant growth through a multi-faceted mechanism involving the reshaping of rhizosphere microbial community structure, activation of beneficial metabolic pathways, and mediation of plant–microbe interactions via specific metabolites. <i>B. pumilus</i> JZ38 and <i>Bacillus albus</i> JZ264 demonstrated the greatest efficacy in promoting cucumber growth and yield when applied as a sole rhizosphere inoculant. These findings deepen the mechanistic understanding of PGPR-mediated rhizosphere regulation and contribute to the theoretical foundation for developing targeted microbial fertilizers.</p>

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Combined metagenomic and metabolomic analyses reveal the effects of three Bacillus spp. on the rhizosphere microenvironment and plant growth of Cucumis sativus L.

  • 期刊论文

  • 发表日期：

    2026年2月27日

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  • Junzheng Wang,
  • Peng Wang,
  • Zhenglun Li,
  • Zhimei Chen,
  • Jiaqi Pan,
  • Songshen Hu,
  • Abid Khan,
  • Yu Song,
  • Xiaohui Hu

摘要

Aims

Plant growth-promoting rhizobacteria (PGPR) are vital for enhancing agricultural productivity. This study aimed to evaluate the growth-promoting efficacy of three preselected PGPR strains in seedling and field trials, and to elucidate their mechanisms in modulating the rhizosphere microenvironment for enhanced plant growth.

Methods

Three Bacillus spp. (JZ31, JZ38, JZ264), isolated from rhizosphere soils, were evaluated using cucumber (Cucumis sativus L.) as a model plant in single or combined inoculation assays. Core PGPR traits, including phosphate solubilization, potassium solubilization, and indole-3-acetic acid secretion, were characterized. Plant nutrient uptake, growth parameters, and rhizosphere microbial α- and β-diversity were measured. Functional profiling was conducted via integrated metagenomic and metabolomic analyses, with microbial biomarkers identified using LefSe and MetagenomeSeq. Correlation analyses linked metabolites to plant–microbe interactions.

Results

All three strains exhibited classic PGPR traits and directly promoted cucumber nutrient uptake and growth. Individual inoculation induced distinct restructuring of the rhizosphere microbial community. These strains selectively enriched potentially beneficial microorganisms linked to nutrient decomposition, plant growth promotion, and biocontrol, while simultaneously suppressing potential pathogens and other identified non-beneficial microorganisms. Functional annotation revealed that inoculation specifically activated pathways related to quorum sensing, gene expression, hormone signaling, and nutrient metabolism, thereby facilitating rhizospheric nutrient cycling and microenvironment optimization. Correlation analyses identified key metabolites mediating the strains’ regulation of plant–microbe interactions.

Conclusion

This study demonstrates that the three Bacillus strains promote plant growth through a multi-faceted mechanism involving the reshaping of rhizosphere microbial community structure, activation of beneficial metabolic pathways, and mediation of plant–microbe interactions via specific metabolites. B. pumilus JZ38 and Bacillus albus JZ264 demonstrated the greatest efficacy in promoting cucumber growth and yield when applied as a sole rhizosphere inoculant. These findings deepen the mechanistic understanding of PGPR-mediated rhizosphere regulation and contribute to the theoretical foundation for developing targeted microbial fertilizers.