Bacillus inoculation drives subtle taxonomic shifts in the bacterial communities of saline–alkaline wheat rhizosphere soil

BACKGROUND: Soil salinization severely restricts wheat production in the coastal regions of northern China, and inoculation with plant growth-promoting rhizobacteria (PGPR) is a promising strategy for alleviating salt stress. However, the response mechanisms of indigenous bacterial communities to PGPR remain unclear, partly because of the limitations of short-read sequencing in terms of taxonomic resolution. This study combined pot and field experiments with PacBio third-generation sequencing (TGS) to investigate bacterial community dynamics in rhizosphere and bulk soils after Bacillus inoculation. RESULTS: The dominant phyla across treatments were Proteobacteria, Acidobacteria, and Bacteroidetes, with Proteobacteria being enriched in rhizosphere soils. Bacillus inoculation altered the bacterial community structure, increasing diversity and reducing intergroup dissimilarity, particularly in the pot experiments. Key ASVs responsive to inoculation were identified by intergroup difference analysis, including the enrichment of Pseudomonas spp. (ASV4007) in the inoculated treatments, which exhibited syntrophic interactions with Bacillus. Inoculation increased the abundance of functional genes, which were annotated using PICRUSt2, involved in phosphorus and nitrogen cycling and improved bacterial co-occurrence network resilience reflected by the natural connectivity. CONCLUSIONS: This study demonstrated that Bacillus inoculation reshaped indigenous bacterial communities to mitigate salt stress, and TGS served as a powerful tool for identifying key functional taxa and supports the development of microbe-based saline soil remediation strategies.