Fig 1. Maximum likelihood phylogenetic tree of the isolates.

A) Ninety-nine orthologous gene sequences present in single copies in all 19 isolates of this study, 15 type strains of the P. putida group and 518 strains of other eight Pseudomonas groups were aligned, concatenated and used to generate a MLSA phylogenetic tree, which is rooted in the P. aeruginosa group. B) Zoom in of the P. putida group. The tree was rooted in the P. putida group and the clades containing strains from the other groups of Pseudomonas spp. were collapsed and used as outgroup. The isolates assessed in this study are labeled in green font (rhizosphere) or brown font (bulk soil); the reference strains are labeled in black font; and the type strains of the P. putida group are labeled in red font. The bootstrap values are shown below each branch (100 bootstrap tests).