VNTR typing of the bacterial rice pathogen Burkholderia glumae reveals the coexistence of several diverging lineages in a single field in Colombia.

Bulkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. In order to estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. In order to detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or Variable Number Tandem Repeats, as well as part of the Toxoflavin toxA gene, in all strains. Results show that (i) the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan, (ii) data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, (iii) five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.