Contrasting molecular responses in tomato to pathogenic stress and beneficial microbial interactions as revealed by proteo-metabolomic approach

Plants display distinct molecular mechanisms in their responses to differentiate between beneficial microbial and biotic stress (pathogen) interactions. We investigated molecular responses of tomato ( Solanum lycopersicum L.) to the beneficial bacterium Bacillus halotolerans IIVRBB3-BV4 and the fungal pathogen Alternaria solani with the help of integrated proteo-metabolomic approach. Untargeted LC-MS/MS based metabolomics analysis revealed that beneficial microbial interaction induced moderate molecular reprogramming with 185 upregulated and 109 downregulated metabolite features, and 133 upregulated and 113 downregulated proteins. In contrast, pathogenic interaction triggered extensive metabolic perturbation, yielding 959 upregulated and 803 downregulated metabolite features and 484 upregulated and 417 downregulated proteins. Pathway enrichment analysis demonstrated that beneficial interactions primarily enhanced photosynthesis, reductive pentose-phosphate cycle, and carbohydrate metabolism, while pathogenic stress activated defense-related pathways including phenylpropanoid biosynthesis, tryptophan metabolism, and glutathione accumulation. ROC-based biomarker analysis identified glutamyl putrescine, phosphatidylcholine, and pheophytin a as key metabolite biomarkers for beneficial interactions, whereas jasmonic acid, guanidinobutyraldehyde, and tetramethyl myricetin characterized pathogenic responses. Network analysis revealed that beneficial interactions exhibited compartmentalized protein-metabolite networks with discrete functional modules, whereas pathogenic interactions displayed densely interconnected networks with extensive cross-talk across multiple cellular processes. The findings elucidated plant’s discriminatory mechanisms underlying plant-microbe interactions at molecular level and yielded metabolite biomarkers. The outcomes have potential implications for early diagnostics of the pathogen interaction and development of biostimulant-based disease management strategies in tomato.