Global and specific rhizobacteria-induced changes in the plant shoot metabolome
LC-MS-based non-targeted metabolite profiling was used to investigate the global and specific effects of each of the three rhizobacterial strains on the occurrence and relative abundance of semi-polar secondary metabolites in shoots of Arabidopsis, Artemisia and Broccoli. Emphasis was given to metabolic alterations that differentiate effective from ineffective plant-rhizobacteria partnerships. An overview of metabolites that were significantly increased or reduced revealed that root inoculation with Pbg exerted the largest alteration of the shoot metabolomes of Artemisia and Arabidopsis, combinations that represent the most effective and ineffective partnerships, respectively (Supplementary Material, Figure S3 and Table S3 ). Furthermore, most of the differential metabolites were unique for plants inoculated with Pbg , i.e they were below the detection limit in untreated control plants. In Broccoli, the ineffective partnership with Pf SS101 accounted for the largest share of the ‘upregulated’ metabolites, whereas its effective partnership withPbg accounted for the largest share of ‘down-regulated’ metabolites (Supplementary Material, Figure S3 andTable S3 ). ANOVA with correction for multiple testing (Benjamini and Hochberg), principal component analysis (PCA) and hierarchical cluster analysis (HCA) were performed to investigate and visualize metabolite clusters that were significantly altered (p < 0.05, fold change > 2) in a rhizobacteria-plant specific manner (Figure 2 ). Below, we will discuss the most significant changes for each of the three plant species and the interacting rhizobacterial strains.