AI-integrated metabolomics maps functional divergence of microbial consortia in field-grown maize.

key messageThe study provides actionable insights into modes of action of the three microbial biostimulants on maize plants under field conditions. The postulated framework indicates a divergence model involving (i) photoprotection, structural reinforcement, and defense priming, (ii) systemic metabolic reprograming for growth and defense, and (iii) hormonal signalling modulation for stress response. These insights offer a data-driven blueprint for the next generation of sustainable, effective, and field-ready bioformulations. Microbial consortia are currently recognized as a promising strategy for sustainable agriculture due to their ability to enhance plant growth, improve soil health, and mitigate environmental stresses. However, the biochemical and molecular mechanisms governing these beneficial effects on crops under field conditions remain poorly understood, and differential effects due to different microbial formulations are enigmatic. This study, therefore, aims to unravel the metabolic alterations, in maize plants, induced by three microbial biostimulants, under field conditions at different growth stages. Leaves from biostimulant-treated and untreated control maize plants were harvested at different time points. Metabolites were extracted using methanol. The extracts were analyzed on LC-MS/MS system. Computational metabolomics workflows and AI-driven strategies such as molecular networking and machine learning methods (PCA and OPLS-DA) were applied to mine and interpret spectral data. Machine learning models revealed the common and unique significant metabolites among the consortia at the vegetative stage. One of the key findings was that hydroxycinnamic acid (HCA) derivatives are the discriminatory metabolites differentiating the effects of the three microbial consortia on maize plants. Moreover, the results showed that consortia application significantly impacted primary and secondary maize metabolism, reprogramming biological pathways such as phenylalanine, tyrosine, and tryptophan biosynthesis, tyrosine metabolism, the citrate cycle (TCA cycle), flavone and flavonol biosynthesis, and flavonoid biosynthesis. These pathways are associated with plant defense, priming and development. Thus, this study sheds light on the complex molecular interactions between maize and microbial biostimulants under real-world conditions. It reveals that distinct microbial formulations differentially influence plant metabolism by reprogramming defense- and growth-related pathways. These actionable insights establish a foundational framework for functionally characterizing microbial consortia and pave the way for the rational design of next generation biostimulants tailored to specific crop needs and growth stages.