Systems-Level Plant Responses Reveal Pseudomonas-Mediated Growth Promotion in Brachypodium Under Nitrogen Limitation

Plant growth-promoting bacteria can enhance plant performance under nutrient limitation, yet the underlying plant molecular responses remain incompletely resolved. We investigated growth promotion by Pseudomonas koreensis in Brachypodium distachyon under contrasting nitrogen (N) regimes using time-resolved phenotyping, elemental analysis, lipidomics and proteomics. Shoot phenotyping revealed rapid responses to N availability, whereas beneficial effects of bacterial inoculation emerged only during prolonged growth under low N. Under N limitation, inoculated plants accumulated significantly more biomass and total N than uninoculated controls, reaching levels comparable to high N plants, while no inoculation effect was observed under high N. Biomass increases were accompanied by only modest changes in tissue N concentration, indicating enhanced whole-plant N-use efficiency rather than disproportionate N enrichment. Proteomics identified N availability as the primary determinant of proteome structure, with bacterial inoculation under low N conditionally modulating selected modules towards High N states. Lipidomic profiles were largely N-driven, with only transient inoculation effects at early stages. Despite the presence of N fixation-associated genes in P. koreensis, δ¹⁵N analyses did not support substantial in planta N fixation. Together, these results support a plant-centric model in which bacterial inoculation enhances growth under N limitation by modulating plant-encoded N acquisition and metabolic organization within an N-defined framework.