Modulation of Sorghum-Associated Fungal Communities by Trichoderma Bioinoculants: Insights from ITS Amplicon Sequencing

Sorghum (Sorghum bicolor L. Moench) is a major cereal crop cultivated in semi-arid regions, but its yield is often constrained by soilborne fungal pathogens that affect plant growth and grain quality. This study explored how Trichoderma-based bioinoculants restructure the structure and functional composition of fungal communities in distinct sorghum compartments (soil, root, seed, and stem) using ITS amplicon sequencing. Two cultivars, Kalatur and Foehn, were evaluated under control and inoculated conditions. Alpha diversity indices revealed that inoculation reduced overall fungal richness and evenness, particularly in seed and stem tissues, while selectively enhancing beneficial taxa. Beta diversity analyses (PERMANOVA, p < 0.01) confirmed significant treatment-driven shifts in community composition. LEfSe analysis identified Trichoderma and Mortierella as biomarkers of inoculated samples, whereas Fusarium, Alternaria, and Penicillium predominated in controls. The enrichment of saprotrophic and symbiotrophic taxa in treated samples, coupled with the decline of pathogenic genera, indicates a transition toward functionally beneficial microbial assemblages. These results demonstrate that Trichoderma bioinoculants not only suppress fungal pathogens but also promote the establishment of beneficial ecological groups contributing to plant and soil health. The present work provides insight into the mechanisms through which microbial inoculants modulate host-associated fungal communities, supporting their use as sustainable tools for crop protection and microbiome management in sorghum-based agroecosystems.