Toward deciphering the molecular dialogue in the rhizomicrobiota: transcriptomic profiling of Trichoderma in rhizobia interaction

Microbial interactions are of key importance for the emergent properties of microbiota and ecosystems, playing a pivotal role in plant health, growth, and productivity. This study explores the interactions between soil fungi and rhizosphere bacteria, focusing specifically on fungi belonging to the genus Trichoderma and the plant symbiotic bacterium Sinorhizobium meliloti. Our aim is to provide evidence of the impact of different strains of the same bacterial species on the fungus. By analysing the effects of four S. meliloti strains on gene expression of T. velutinum, we revealed the presence of several differentially expressed genes (DEGs) (from 139 to 254 genes) indicating a remodelling of its metabolism and growth. Remarkably, the majority of the DEGs (∼90 %) could not be assigned to function, indicating the presence of a large genetic “unknown space” potentially involved in fungal-bacterial interactions. Moreover, results indicated that transcriptomic profiles of T. velutinum significantly changed with respect to the four S. meliloti strains, suggesting the ability of the fungus to perceive the presence of specific bacterial strains. Our study emphasizes that strain specificity of microbial interactions could play crucial role in shaping microbiota functions, and highlights their potential impact on the success of bioinoculants.