<i>Lysobacter</i> Orchestrates Plant–Microbiome Crosstalk to Enhance Tomato Fruit Quality

<i>Lysobacter</i> can promote plant growth and induce disease resistance, but its potential contribution to fruit quality remains understudied. This study investigated the role of <i>Lysobacter fragariae</i> P25 in regulating tomato fruit quality through integrated metabolomics, transcriptomics, and metatranscriptomics. We found that P25 inoculation modified fruit flavor and nutrition by increasing the accumulation of soluble sugars, unsaturated fatty acids, and essential amino acids and decreasing the tomatidine content. Fruit color and functional quality were enhanced upon inoculation with higher levels of flavonoids, lycopene, vitamins, and phenolic acids. The inoculated soil showed greater fertility and biological activity coupled to heightened microbial diversity and recruitment of potentially beneficial taxa in the rhizosphere, shifting community functions and networks toward healthier patterns. Cross-kingdom interactions between microbial genes and fruit metabolites were identified, linking rhizosphere microbiomes to fruit quality. Our results demonstrate P25-mediated plant-microbiome crosstalk in tomatoes, which drives metabolic reprogramming and consequently enhances the overall fruit quality.