Microbial Metabolic Configuration Reweights Plant Growth–Defense Regulatory Networks in Nicotiana benthamiana

Plant growth-promoting rhizobacteria (PGPR) enhance host fitness through phytohormone modulation, induced systemic resistance, and pathogen suppression, yet whether variation in bacterial metabolic state independently shapes plant transcriptional architecture remains unresolved. Here, we compare genome-wide transcriptional responses of Nicotiana benthamiana to a characterized PGPR strain (JS) and a UV-induced mutant (MT) harboring frameshift disruptions in nadB and sacX , genes encoding enzymes involved in NAD⁺ biosynthesis and carbon catabolite regulation. MT-treated plants retained the directional framework of JS-induced transcriptional responses but exhibited attenuated amplitude and redistributed module weighting, consistent with transcriptional buffering rather than qualitative regulatory reprogramming. JS exposure coordinated pathways associated with energy metabolism, terpenoid and phenylpropanoid biosynthesis, and plant-pathogen interaction, whereas MT redistributed metabolic emphasis toward carbon and lipid metabolism categories. Hormone-associated analyses revealed that JS promoted coordinated auxin-, gibberellin-, and jasmonate/ethylene-centered signaling, while MT exhibited differential salicylic acid- versus jasmonate-associated weighting, implicating bacterial metabolic configuration as a key determinant of the growth-defense hormonal balance. Transcription factor profiling identified reconfigured AP2/ERF, GRAS, Dof, and MADS-box family representation under MT, indicating that metabolic perturbation propagates through upstream regulatory hierarchies. Phenotypically, MT reduced shoot growth promotion while preserving root architecture and antifungal efficacy, revealing a functional decoupling between metabolically tunable growth-promoting outputs and resilient biocontrol traits. These findings establish microbial metabolic architecture as a quantitative modulatory parameter that reshapes the amplitude and coordination of plant growth- and defense-associated regulatory networks without altering their directional polarity, and support incorporating bacterial metabolic profiling alongside strain identity as a rational selection criterion for next-generation bioinoculant development in sustainable agriculture.