Broccoli
Similar to Arabidopsis, inoculation of Broccoli roots with each of the three rhizobacterial strains resulted in substantial alteration of the shoot metabolome. From the 1908 detected metabolites, 933 (49%) were significantly different between at least two treatments. For this set of metabolites, HCA revealed eight distinct metabolite clusters of the host metabolome. PCA further showed that the metabolome of Broccoli seedlings inoculated with different rhizobacteria is clearly different from the control and from each other. The first three PCs explained 84% of the total variance (Figure 2c1 ). PC1, representing 47% of the total variance, was associated with metabolites that discriminate both the control and MB samples from the Pbg and Pf SS101 samples. These metabolites were either significantly increased or decreased in plants inoculated by Pbg or Pf SS101 (Figure 2c2 decreased cluster 3 and induced clusters6 and 7 ) that represent effective and ineffective partnerships with the host, respectively. The indole glucosinolate glucobrassicin also showed a significant increase in plants inoculated with Pbg and Pf SS101. PC2 explained 22% of the total variance and corresponded to metabolites that were either specifically altered in the Pbg or Pf SS101 treatments (Figures 2c1 and 2c2 induced (clusters 8 (Pf SS101) and9 (Pbg )) or reduced by Pbg inoculation (cluster4 )). Metabolites that were specifically induced in the ineffective partnership between Pf SS101 and the host were dominated by flavonoids such as kaempferol, quercetin glycosides and glucosinolates including glucoibervirin, neoglucobrassicin and 4-methoxyglucobrassicin. Furthermore, several hydroxycinnamates conjugated or not with quinic acid, including chlorogenic acid (caffeoyl-quinic acid), coumaroyl quinic acid, sinapic acid and ferulic acid, were predominant in those metabolite clusters (clusters 7and 8 ). PC3 explained 15% of the total variation and corresponded to MB-induced metabolites represented in cluster 1and induced metabolites by all three rhizobacteria in cluster2 . Hexose 1-phosphate in cluster 1 showed a MB-specific increase. Meanwhile, some of the putatively annotated metabolites in cluster 2 including tryptophan, a precursor of indole glucosinolates, was reduced by all three rhizobacterial treatments.