A Plant Growth-Promoting Bacterial Isolate, Bacillus velezensis 41S2, Enhances Seed Protein, Isoflavone Accumulation, and Stress Resilience in Soybean Under Salt–Alkaline Soil Conditions

Salt–alkaline soil poses a significant challenge to soybean productivity. While plant growth-promoting rhizobacteria (PGPR) offer a sustainable strategy for stress mitigation, their field-level application remains underexplored. Here, a field experiment was conducted in the Yellow River Delta of Shandong, China, a typical salt–alkaline region. In this study, we evaluated the effectiveness of Bacillus velezensis 41S2 in enhancing soybean performance under salt–alkaline soil through integrated field trials and transcriptomic analysis. Inoculation with strain 41S2 significantly improved plant biomass, yield components, and seed yield under salt–alkaline soil, and notably increased seed protein and isoflavone contents. Physiological analyses revealed that strain 41S2 markedly reduced hydrogen peroxide (H2O2) accumulation, indicating alleviation of oxidative stress. Moreover, strain 41S2 modulated the levels of soluble sugars and amino acids, contributing to osmotic regulation and carbon–nitrogen (C-N) metabolic balance. Transcriptome profiling further indicated that strain 41S2 upregulated genes involved in antioxidant response, C–N metabolism, and phenylpropanoid biosynthesis, highlighting its role in coordinating multilayered stress response pathways. Overall, these findings highlight the potential of B. velezensis 41S2 as a multifunctional bioinoculant for improving salt tolerance and presents a promising tool for sustainable crop production and ecological restoration in salt–alkaline soil.