Using multilocus sequence analysis to distinguish pathogenic from saprotrophic strains of Pseudomonas from stone fruit and kiwifruit

A variety of pseudomonads are associated with diseases of Actinidia and Prunus plants. A recently emerged virulent haplotype of Pseudomonas syringae pv. actinidiae (biovar 3) causes severe stem cankers on kiwifruit associated with dieback of canes. Pseudomonas syringae also causes one of the most important bacterial diseases affecting cherry orchards worldwide. Bacterial canker of cherry limits production in orchards in New Zealand. Less virulent and non-pathogenic pseudomonads also exist on both hosts, providing an opportunity to investigate the diversity of pseudomonads on these hosts, to find identifiers for new emerging highly pathogenic strains that could be used at the border to prevent incursions. In this study, genetic typing was used to explore the diversity of Pseudomonas on kiwifruit and a variety of Prunus plants. Multilocus sequence analysis (MLSA) of four house-keeping genes separated pseudomonads from kiwifruit and stone fruit plants into two major groups: one corresponding to P. syringae sensu lato and one corresponding to other Pseudomonas species. Within P. syringae sensu lato , strains were assigned to six of the nine previously described genomospecies or five of the seven previously described phylogroups. In the other major group, strains from both hosts clustered with a variety of well characterised non-pathogenic pseudomonads. The classification of strains into the two major groups is of practical diagnostic value since the most common pathogens of fruit trees belong to the P. syringae species complex. Furthermore, our analysis suggests that molecular diagnostics might be possible for the classification of strains into these two groups as a first tool to screen for exotic pathogenic pseudomonads on germplasm imports of both commodities.