Native Bacillus subtilis strains cultivated in a low-cost medium enhance maize growth and suppress seed-borne fungi by defense activation and rhizosphere colonization

• Native Bacillus subtilis strains suppressed seed-borne fungi in maize. • Inoculation enhanced expression of plant growth and defense-related genes. • Auxin levels, chlorophyll content, and antioxidant activity increased. • Repeated applications improved rhizosphere colonization at root apex. • Low-cost bacterial cultivation supports sustainable maize production. We evaluated two native Bacillus subtilis strains (CtpxS2-1 and CtpxS3-5) cultivated in low-cost DSF40–MOL5 medium as seed inoculants for maize ( Zea mays ). This study extends previous work by integrating molecular, physiological, and ecological endpoints under greenhouse conditions. Seed treatment with these strains enhanced germination rates and seedling vigor, suppressed seed-borne fungal pathogens, and promoted systemic defense responses. Quantitative RT-qPCR revealed upregulation of defense-related genes ( PR-1, PR-4, SOD-2 ) and growth regulators ( ZmYUC1, PIN-3 ), while biochemical assays confirmed increased auxin, chlorophyll, and antioxidant enzyme activities resulting in greater shoot and root biomass. Longitudinal monitoring demonstrated sustained rhizosphere colonization at the root apex and improved plant height and chlorophyll index over 90 days. These findings highlight DSF40-MOL5 as a cost-effective formulation enabling scalable Bacillus -based bioinoculants for sustainable maize production.