Integrative Metabolomic and Agronomic Analyses Reveal the Impact of Pseudomonas fluorescens -Based Bioinputs on the Micro-Tom Tomato ( Solanum lycopersicum ) Model System

Abstract Microbial biostimulants, bioinputs based on microorganisms, have emerged as an alternative to increase crop yield and quality while reducing the environmental impact. Particularly, the plant growth-promoting bacterium Pseudomonas fluorescens exhibits high potential for application in this field due to its production of a range of specialized metabolites (SMs). Research in this area mainly focuses on the use of active bacterial cells, whose efficacy depends on the success of host colonization. In this regard, we evaluated the treatment effect of two bioinputs from P. fluorescens ATCC_13525 (with active and inactive bacterial cells) on Micro-Tom tomato growth, productivity, nutrient accumulation, and metabolism. The bioinput with active bacterial cells promoted a few beneficial effects on the plant, the main one being associated with an increase in the calcium (Ca) concentration in fruits through foliar application. The cell-free bioinput primarily promoted an increase in leaf area, root biomass, and phosphorus (P) and molybdenum (Mo) concentrations in fruits. Specifically, its application by the foliar method exhibited a balance between the Brix degree and the maintenance of productivity. Untargeted metabolomic analysis of tomato leaves treated with this method indicated modulation of phenolamides and glycerophospholipids. On the other hand, an increase in the abundance of tryptophan and the indole lycoperodine-1 occurred when the treatment was carried out via soil. The results highlight that the cell-free formulation modulates plant responses and enhances plant performance in certain aspects under the evaluated application conditions, suggesting an important biostimulant effect of the metabolites present in the cell-free microbial culture for growth promotion and improvement in fruit quality. Notably, the findings demonstrate that microbial metabolites alone can drive significant plant responses, opening new perspectives for next-generation bioinputs in sustainable agriculture.