Piriformospora indica enhances salt and alkali tolerance in Glycine max by modulating plant physiology, soil properties, and rhizosphere microbial communities

• P. indica inoculation markedly improves soybean growth and productivity under salt, alkali, and combined salt–alkali stress. • The fungus enhances stress tolerance through a dual mode of action: directly regulating antioxidant defense and ion homeostasis, and indirectly improving soil properties and reshaping microbial communities. • Integrated plant–soil–microbe analyses and structural equation modeling (SEM) reveal a distinctive mechanism of endophytic fungi in stress adaptation. Salt and alkali stress severely impacts the growth and productivity of Glycine max (soybean), posing a major challenge to agricultural sustainability. The symbiotic fungus Piriformospora indica ( P. indica ) has been reported to enhance plant salt tolerance, yet its mechanisms in soybean remain poorly understood. In this study, soybean seedlings were inoculated with a P. indica suspension, and root colonization was confirmed after 20 days. Plants were then subjected to salt stress (150 mmol·L -1 NaCl), alkali stress (200 mmol·L -1 NaHCO 3 , pH 8.5), or mixed salt-alkali stress (144 mmol·L -1 Na + , pH 9.0). Inoculated soybeans showed markedly improved growth, with pod numbers increasing by 60-77% under stress compared with controls. Enhanced tolerance was associated with elevated activities of superoxide dismutase (SOD) and peroxidase (POD), together with significantly reduced levels of malondialdehyde (MDA, ↓32–45%), hydrogen peroxide (H 2 O 2 , ↓28–41%), and superoxide anions (O 2 - , ↓25–39%). In addition, Na + /K + homeostasis was stabilized through the upregulated expression of ion transport-related genes ( NHX6, SOS2, PM H⁺-ATPase ). In soils, P. indica inoculation increased enzyme activities (urease, acid phosphatase, catalase) and nutrient availability, while selectively influencing rhizosphere microbial composition. Structural equation model (SEM) explained 98% of the growth variation, indicating that P. indica primarily enhances antioxidant defenses and ion balance with soil properties and microbial changes providing indirect reinforcement. Collectively, these findings highlight the potential of P. indica as a biotechnological tool to improve soybean performance under salt-alkali stress and to promote soil health.