Extended Data Fig. 2: Both Pseudomonas and total bacterial load are driven primarily by synthetic communities.

a. Cumulative bacterial load (ratio of bacterial and host read counts, which is dimensionless; Methods) in plant rosettes after control treatment or infection with each of the three synthetic communities. Cumulative load was analysed for (i) all bacterial reads classified at the genus level (‘total bacterial load’), (ii) all reads classified as ‘Pseudomonas’, and (iii) all reads not classified as ‘Pseudomonas’ at the genus level. Unclassified reads were discarded. b. Load mean differences between plants infected with each of the synthetic communities to control plants. (See panel A for absolute loads.) Mean difference was calculated per cumulative load type (Total bacterial load, Pseudomonas load and non-Pseudomonas load), using the model [log₁₀ (Cumulative load) ~ treatment + error], that is, the same model was computed for all three data subsets. Dots indicate the median estimates, vertical lines 95% Bayesian credible intervals of the fitted parameter, and the dashed line the control baseline. c. Load mean difference between the cumulative non-Pseudomonas to Pseudomonas load in plants treated with control, or each of the three synthetic communities. Mean difference was calculated per treatment (control, PathoCom, CommenCom and MixedCom) using the model [log₁₀ (Cumulative load) ~ Genus_classification + error] that is, the same model was computed for all four data subsets. The ‘Genus_classification’ predictor was set to either Pseudomonas or non-Pseudomonas Classification. Dots indicate the median estimates, vertical lines 95% Bayesian credible intervals of the fitted parameter, and the dashed line the Pseudomonas load baseline. DNA of Ey15-2 plants was randomly sampled across the two experiments, and among the four treatments. n=17 for control plants, n=12 for PathoCom-infected plants, n=18 for CommenCom-infected plants, and n=24 for MixedCom-infected plants. The V4 16S region, as well as the A. thaliana gene GIGANTEA were targeted³⁰.