Localized root colonization by Trichoderma afroharzianum T22 is associated with host transcriptional reprogramming and beneficial bacterial enrichment under salinity stress in sorghum.

Salinity is a major abiotic stress that severely restricts crop productivity. Despite considerable potential, the role of Trichoderma afroharzianum T22 in the molecular responses and root microbiome dynamics associated with salinity tolerance remains poorly understood in sorghum. In this study, T. afroharzianum inoculation alleviated salinity-induced stress by improving chlorophyll content, growth parameters, and nutrient balance, while restricting root-to-shoot Na+ translocation. Split-root experiments showed that T. afroharzianum application to a single root compartment was insufficient to improve whole-plant performance under salinity, whereas inoculation of both compartments restored growth and chlorophyll-related traits. RNA-seq analysis showed the upregulation of genes involved in symbiosis, hormone signaling, antioxidant defense, and ion homeostasis, accompanied by repression of genes involved in ethylene biosynthesis and senescence in the roots. KEGG enrichment analysis further revealed activation of secondary metabolic pathways involved in stress adaptation. Furthermore, 16S rRNA sequencing showed that T. afroharzianum inoculation was associated with shifts in the root bacterial community without significantly altering alpha diversity, while selectively enriching putatively beneficial taxa, including Dyella mobilis, Luteibacter rhizovicinus, and Luteibacter yeojuensis under salinity. In addition, a conserved core microbiome was retained across treatments and was dominated by Streptomyces, Rhizobium, Dyella, and Labrys. Further, Janibacter was identified as a characteristic indicator taxon of T. afroharzianum inoculation, while Streptomyces showed the highest overall indicator value. Multi-omics integration analysis revealed that T. afroharzianum-associated microbial taxa were strongly associated with hormone signaling, redox homeostasis, mineral transport, and secondary metabolism under salinity stress. Particularly, Streptomyces and Luteibacter were the two genera most strongly associated with plant growth traits, whereas Rhizobium and Mucilaginibacter showed stronger positive correlations with tissue Na+ accumulation. Collectively, these findings provide new insights into T. afroharzianum-mediated salinity tolerance in sorghum and highlight its potential as a microbial biostimulant, warranting further validation across diverse sorghum genotypes in field conditions.