Fig. 4: Homologs of ef90 are prevalent among Arabidopsis thaliana colonizing Pseudomonadota.

a The number of RND-type efflux pump system inner-membrane subunits in each Gram-negative bacterial genome of a 185 member genome sequenced isolate collection of bacteria collected largely from Arabidopsis thaliana roots. b A gene tree of all inner-membrane subunits in the 185-member isolate collection (bacterial class in the outer circle) based on sequence similarity (see “Methods”), and position of the functionally tested genes from Paraburkholderia bryophila MF376 (orange dot) and Pseudomonas simiae WCS417 (cyan dot). The clades related to the shoot (green) and root (purple) RND efflux pump systems were identified by the most recent common ancestor (MRCA) branch of the functionally tested genes. The functionally tested shoot-specific genes are in a shallow clade while the root-specific genes are in a deep and divergent clade. c In the genomes of each of the tested classes of Pseudomonadota, the vast majority of isolates encode an ef90 homolog from the shoot clade (78% of Alphaproteobacteria, 100% of Betaproteobacteria and 91% of Gammaproteobacteria). d Most isolates encode only a single copy of the shoot clade ef90 homolog, but seven of the 63 strains encode two copies. e A subtree of the shoot-specific clade colored by bacterial family marking one representative from each major family (family with more than two isolates, black circle). Five of the seven duplicated genes in Fig. 5d are from a divergent group of genes in five Variovorax strains (Comamonadaceae, orange long branch). f Expression of ef90 is induced in Arabidopsis thaliana Col-0 macerated leaf extract compared to bacteria in medium for five of seven representative strains (e) from all classes (n = 3 biologically independent cultures, Two sided T test P value <0.05).