Isolation and identification of dark septate endophytes from sorghum roots and the effects of Alternaria destruens HN16G1 on drought and low-nutrient tolerance in sorghum seedlings

Introduction Dark septate endophytes (DSE) are root-associated fungi that can enhance host stress tolerance, yet their diversity and function in sorghum remain unclear. Here, we investigated the culturable DSE community across 29 sorghum varieties and evaluated the symbiotic potential of key isolates. Methods Culturable DSE were isolated from sorghum rhizosphere soil and roots via plate isolation, microscopy, and colonization assessment to screen efficient colonizers. Pot experiments then analyzed symbiotic compatibility with major Chinese cultivars to identify strains with high colonization efficiency. Finally, the selected strain was evaluated for salt tolerance and its effects on drought resistance, growth promotion, and low-fertility tolerance in seedlings. Results and discussion A total of 94 DSE isolates were obtained, accounting for 30.72% of the total fungal isolates, and were classified into 30 morphotypes. The genus Alternaria emerged as the dominant group, comprising 46.67% of the isolates. Among them, strain HN16G1, isolated from Hongnuo 16 and identified as Alternaria destruens via internal transcribed spacer sequencing, demonstrated superior root colonization capability. Strain HN16G1 established stable symbiosis with all 10 commercial cultivars tested, maintaining colonization rates and intensities above 50.0 and 16.0%, respectively. Physiologically, HN16G1 exhibited moderate halotolerance, with low NaCl concentrations (0.1–0.2 mol/L) promoting mycelial growth, whereas high salt stress (0.6 mol/L) induced adaptive responses including enhanced sporulation and reduced hyphal septal distance. The strain also displayed substantial indole-3-acetic acid production, reaching 181.56 μg/mL. Inoculation with HN16G1 (5.0 × 10 5 CFU/mL) significantly improved seedling emergence and early vegetative growth in sorghum under combined drought stress (40% field capacity) and low-nutrient conditions. Notably, varieties “Hongnuo 16” and “Jinnuo 3” exhibited the most pronounced responses, with growth parameters approaching optimal levels. Colonization parameters (rate and intensity) correlated positively with plant height, root length, and biomass. Overall, these findings highlight the rich DSE diversity in sorghum roots and identify A. destruens HN16G1 as a broad-compatibility, multifunctional endophyte with promising potential for the development of microbial inoculants to enhance stress tolerance in sorghum production systems.