Proteomic analyses of the interaction between the plant‐growth promoting rhizobacterium Paenibacillus polymyxa E681 and Arabidopsis thaliana

Plant growth‐promoting rhizobacteria (PGPR) facilitate the plant growth and enhance their induced systemic resistance (ISR) against a variety of environmental stresses. In this study, we carried out integrative analyses on the proteome, transcriptome, and metabolome to investigate Arabidopsis root and shoot responses to the well‐known PGPR strain Paenibacillus polymyxa ( P. polymyxa ) E681. Shoot fresh and root dry weights were increased, whereas root length was decreased by treatment with P. polymyxa E681. 2DE approach in conjunction with MALDI‐TOF/TOF analysis revealed a total of 41 (17 spots in root, 24 spots in shoot) that were differentially expressed in response to P. polymyxa E681. Biological process‐ and molecular function‐based bioinformatics analysis resulted in their classification into seven different protein groups. Of these, 36 proteins including amino acid metabolism, antioxidant, defense and stress response, photosynthesis, and plant hormone‐related proteins were up‐regulated, whereas five proteins including three carbohydrate metabolism‐ and one amino acid metabolism‐related, and one unknown protein were down‐regulated, respectively. A good correlation was observed between protein and transcript abundances for the 12 differentially expressed proteins during interactions as determined by qPCR analysis. Metabolite analysis using LC‐MS/MS revealed highly increased levels of tryptophan, indole‐3‐acetonitrile (IAN), indole‐3‐acetic acid (IAA), and camalexin in the treated plants. Arabidopsis plant inoculated P. polymyxa E681 also showed resistance to Botrytis cinerea infection. Taken together these results suggest that P. polymyxa E681 may promote plant growth by induced metabolism and activation of defense‐related proteins against fungal pathogen.