Multilevel Analysis of Response to Plant Growth-Promoting and Pathogenic Bacteria in Arabidopsis Roots

A major challenge in plant-microbe interaction research is understanding how plants distinguish between commensal and pathogenic microorganisms. We compared Arabidopsis responses to two contrasting bacterial strains, the plant growth-promoting (PGP) Pseudomonas sp. CH267 and the pathogen Burkholderia glumae PG1, using integrated multi-omics analyses. The pathogen triggered stronger transcriptional reprogramming and proteomic changes in roots than the PGP strain, and both strains also affected numerous leaf proteins, indicating systemic responses. Interaction with both strains increased the abundance of sulfur-containing metabolites camalexin, glutathione, and cysteine, in particular under pathogen treatment, which corresponded with elevated total sulfur in the leaves. Root and root exudate metabolomes significantly changed, with amino acids and tricarboxylic acid cycle intermediates accumulating in roots but being diminished in the exudates. Integrative analysis across the omics datasets revealed strong correlations between metabolite levels, protein abundance, and transcript levels, highlighting new links between sulfur metabolism, defense pathways, and mineral nutrition, including iron. Together, these findings uncover the complex multilayered nature of Arabidopsis responses to commensal and pathogenic bacteria and identify new connections across different regulatory levels. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.