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. 2021 Apr 16;118(16):e2100678118. doi: 10.1073/pnas.2100678118

Fig. 1.

Fig. 1.

A synthetic community comprised of 35 bacterial strains (SynCom35) modulates a sector of the Arabidopsis immune system. (A) Canonical analysis of principal coordinates (CAP) based on Bray–Curtis dissimilarities of 16S rDNA profiling reveals no significant effect of flg22 in the composition of root bacterial community. Significance of model terms was determined with a PERMANOVA analysis using 5,000 permutations (α = 0.05). (B) Number of differentially expressed genes (DEG) identified by RNA sequencing in roots treated with flg22 or not in the absence of bacteria, with heat-killed SynCom35 or with SynCom35 alive. (C) Overlap among the sets of flg22-responsive genes in the “No bacteria,” “Heat-killed SynCom35,” and “SynCom35” conditions. (D) Pearson correlation among flg22 responses in plants grown axenically (no bacteria) or in the presence of dead or living SynCom35. Note the low correlation between “SynCom35” and the other two conditions. (E) CAP coordinates shows that plants grown in the presence of SynCom35 display a unique transcriptional signature that is not differentiated by addition of flg22. (F) Hierarchical clustering of the 716 genes that responded to flg22 in at least one of the experimental conditions. SynCom35 triggers a transcriptional signature that is very similar to the flg22 response except for three sets of genes (Cluster SC1, Cluster SC7, and Cluster SC8), which display a remarkably different expression profile when compared to control plants. (G) Expression pattern of each of the clusters defined in the heatmap. The P values on the bottom refer to the comparison between groups (flgs22 vs. mock) for each condition using two-tailed t tests. (H) Gene ontology enrichment analyses showing enriched biological processes in each of the clusters. Cluster SC1, which is suppressed by SynCom35, contains defense genes that are activated by flg22. Cluster SC7, which is activated by SynCom35, is enriched in auxin metabolism. All results refer to plants exposed to the treatments for 12 d. HK, heat-killed SynCom35; FDR, false-discovery rate; NB, no bacteria; SC, SynCom35. The complete enrichment analysis and the associated statistics are shown in Dataset S3.