Harnessing novel endophytic fungi for synergistic plant growth promotion and charcoal rot disease management in soybean

Crop plants harbor diverse endophytic fungi that establish mutualistic associations, often contributing to improved growth, stress tolerance, and enhanced resistance against pathogens. This study isolated and characterized soybean endophytes and evaluated their potential to suppress charcoal rot caused by Macrophomina phaseolina while promoting plant growth. Forty-seven endophytic fungal isolates were obtained from various tissues of four soybean cultivars using culture-based techniques. Diversity assessment indicated that stem tissues harbored the highest endophytic richness, with cultivar JS 95-60 exhibiting comparatively greater diversity than the other varieties examined. Of the 47 isolates, eight exhibited strong antagonistic activity against M. phaseolina in vitro, primarily through the secretion of cell wall–degrading enzymes and antifungal metabolites. These isolates tolerated abiotic stress under laboratory conditions and displayed multiple plant growth–promoting attributes, including phosphorus solubilization, nitrogen fixation, and indole-3-acetic acid production. In controlled experiments, they significantly reduced charcoal rot severity and enhanced defence-related enzyme activities in soybean plants. Under epiphytotic field conditions, EF 57 (Mucor circinelloides) emerged as the most promising isolate, lowering charcoal rot severity by 53.68% relative to the untreated control. In addition to its protective effect, EF 57 markedly improved yield and related traits, including pod number, plant height, and seed index. Principal component analysis further demonstrated a clear positive relationship between EF 57 application, disease reduction, and enhanced plant performance. Overall, the study identifies M. circinelloides (EF 57) as a promising biocontrol agent with dual functionality in charcoal rot management and yield enhancement in soybean, highlighting its potential application in sustainable disease management strategies.