A set of PCRs for rapid identification and characterization of Pseudomonas syringae phylogroups

Aims The aim of this study was to develop a rapid PCR-based method for the specific detectionof individual phylogroups of the Pseudomonas syringaecomplex. Methods and Results Seven primer pairs were developed by analysing whole genomes of 54 Ps. syringae strains. The specificity and sensitivity of these primer pairs were assessed on 236 strains from a large and comprehensive Ps. syringae collection. The method was also validated by characterizing the phylogenetic diversityof 174 putative Ps. syringae isolates from kiwifruit and apricot orchards of southeastern France. Conclusion Our PCR-based method allows for the detection and characterization of nine of the 13 Ps. syringae phylogroups (phylogroups 1, 2, 3, 4, 7, 8, 9, 10 and 13). Significance and Impact of the Study To date, phylogenetic affiliation within the Ps. syringae complex was only possible by sequencing housekeeping genes. Here, we propose a rapid PCR-based method for the detection of specific phylogroups of the Ps. syringae complex. Furthermore, for the first time we reveal the presence of Ps. syringae strains belonging to phylogroups 10 and 13 as epiphyteson plants, whereas they had previously only been observed in aquatic habitats.