Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study

Abstract The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in above-ground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.