Isolation and characterization of Pseudomonas syringae pv. porri from leek in Flanders

Pseudomonas syringae pv. porri causes bacterial leaf spot and blight of leek (Allium porrum) and is in wet crop seasons responsible for substantial losses. The local diversity within this pathogen in Flanders, Belgium, was investigated to obtain insights into its epidemiology. Therefore, symptomatic leek leaves were collected from 112 fields and bacteria were isolated. An oxidase negative, HR positive, fluorescent Pseudomonas was consistently recovered from the diseased tissues. Isolates were identified as P. syringae pv. porri by rpoD gene sequencing and by confirmation of pathogenicity in leek. Genomic profiles generated with BOX-PCR subdivided them into two groups, with one group containing 5 of the 37 analyzed strains. Those five isolates were all obtained in 2012 and the plant origins indicated seed transmitted infection. Draft genome sequences were produced for a P. syringae pv. porri strain from each BOX group and sequences of seven housekeeping genes were extracted for multi locus sequence analysis (MLSA). This resulted in the clustering of both P. syringae pv. porri strains with the P. syringae pv. oryzae strain 1_6 as did the whole genome sequence comparisons by ANI analysis. The P. syringae pv. porri isolates, designated LMG 28495 and LMG 28496, differed in a type III effector gene, HrpW, and in the number of mobile elements in the genome. Overall, the data demonstrate that two P. syringae pv. porri variants are present in symptomatic leek in Flanders which can be discriminated and possibly traced using a genomic profiling method such as BOX-PCR . Furthermore, the draft genome sequences of both strains will facilitate the development of sensitive and specific methods for early detection.