Mutants and plasmids used in this study.

Natural competence is one of the mechanisms of horizontal gene transfer, an important process that contributes to host-use evolution and other types of environmental adaptation in bacteria. Recently, the plant pathogen Xylella fastidiosa has undergone expansion of its host and geographic ranges. Natural competence has been empirically documented for a few strains of X. fastidiosa, but its prevalence across genotypes and populations is largely unknown. In this study, we characterized the natural competence in vitro of 142 X. fastidiosa strains from diverse hosts and geographic origins, and revealed substantial variability among strains, particularly across subspecies. X. fastidiosa subsp. fastidiosa strains were largely naturally competent, while only 15% of studied subsp. multiplex strains showed recombination, and none of the strains classified in other subspecies were competent. While recombination rates in vitro were associated with subspecies classification, host and climatic variables from the area of isolation did not explain differences in recombination across strains. A genome-wide association study identified several genes linked to variation in natural competence, including a heretofore unknown role for xadA2, which codes for a surface afimbrial adhesin, and the already known fimbrial adhesin type IV pili genes pilY1-1 and pilY1-3. Overall, this study highlights the variability of natural competence among X. fastidiosa strains, that could have an impact on their potential for adaptation to the environment.