Functional replacement of ancestral antibacterial secretion system in a bacterial plant pathogen

Two distinct molecular machineries, T4SS and T6SS, have been found within the order Xanthomonadales to be involved in outcompeting other bacterial species through the secretion of toxic effector proteins. However, the ecological and evolutionary basis leading xanthomonads to evolve two secretion systems with such similar functions remain unclear. Here we show that Xanthomonas translucens (Xt) lineages have switched from an X-T4SS-mediated to T6SS-i4-mediated bacterial killing strategy. T6SS-i4 was only found in Xt strains lacking X-T4SS and vice versa, resulting in a patchy distribution of the two nanoweapons along the Xt phylogeny. Using genetic and fluorescence-based methods, we demonstrated that X-T4SS and T6SS-i4 are crucial for interbacterial competition in Xt, but not Xt T6SS-i3. Combined comparative genetic and phylogenetic analyses further revealed that the X-T4SS gene clusters have been subject to degradation and had several loss events, while T6SS-i4 was inserted through independent gain events. Overall, this research supports the ancestral state of X-T4SS and provides new insights into the mechanisms promoting Xt survival within their ecological niches.