Characterization of Pectobacterium carotovorum subsp. carotovorum and brasiliense from diseased potatoes in Kenya

Using a DNA-based typing method, 48 bacterial strains isolated from infected potato (Solanum tuberosum) tubers originating from Kenya were characterized. The pel gene specific primers showed that all the 48 bacterial strains were pectolytic. Subspecies-specific primers EXPCCF/EXPCCR and Br1f/L1r identified 66 % of the strains as Pectobacterium carotovorum subsp. carotovorum while 34 % were identified as Pectobacterium carotovorum subsp. brasiliense based on their characteristic band sizes of 550 and 322 bp, respectively. Amplification of the 16S-23S rDNA (ITS) region did not yield observable differences in banding patterns between the Kenyan strains. However, PCR-RFLP analysis together with partial nucleotide sequences of the housekeeping mdh and gapA genes confirmed the results obtained by the specific primers. Phylogenetic analysis of the concatenated partial gene sequences grouped Pectobacterium carotovorum subsp. carotovorum and Pectobacterium carotovorum subsp. brasiliense Kenyan strains together with those identified in other parts of the world with 90 % and 99 % bootstrap support values, respectively. Pathogenicity assays using representative Kenyan strains demonstrated varied levels of tuber maceration ability. The Pectobacterium carotovorum subsp. carotovorum and Pectobacterium carotovorum subsp. brasiliense Kenyan strains were shown to be less aggressive in causing soft rot when compared to type strains. This study describes for the first time the genetic diversity of pectolytic bacteria causing soft rot disease of potatoes in Kenya.