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Biochemical and genetic diversity of pectolytic enterobacteria causing soft rot disease of potatoes in New Zealand

Pitman, Andrew R., Wright, Peter J., Galbraith, Matthew D., Harrow, Sally A.
Australasian plant pathology 2008 v.37 no.6 pp. 559-568
Dickeya, Pectobacterium carotovorum, Pectobacterium wasabiae, genes, genetic variation, internal transcribed spacers, phylogeny, polymerase chain reaction, potatoes, restriction fragment length polymorphism, ribosomal RNA, stems, tubers, virulence, New Zealand
The diversity of 89 pectolytic enterobacteria collected from potatoes in New Zealand was investigated by comparing their physiological, biochemical and genetic characteristics with those of type strains of Pectobacterium and strains previously identified as isolates of the genus Dickeya. Biochemical and physiological analyses demonstrated that the predominant pectolytic enterobacterium present in New Zealand is Pectobacterium carotovorum subspecies carotovorum. Isolates of Pectobacterium atrosepticum and strains closely related to Dickeya were also detected. Species and subspecies-specific PCR confirmed the identity of the majority of the P. carotovorum subsp. carotovorum and P. atrosepticum strains. However, several atypical isolates classified by Biolog as P. carotovorum subsp. carotovorum failed to grow at 37°C or to amplify the pectate lyase-encoding gene (pel gene) characteristic of this subspecies. Restriction fragment length polymorphism (RFLP) analyses of the 16S-23S intergenic transcribed spacer (ITS) also identified atypical isolates with unique ITS-RFLP profiles. Further characterisation of the atypical strains, by phylogenetic analysis of their 16S rRNA sequences, clustered them into four groups distinct from pectolytic enterobacteria previously found on potato. Several of the atypical strains proved highly virulent on both tubers and stems of potato, suggesting that a variety of novel species or subspecies are responsible for soft rot of potatoes in New Zealand, including Pectobacterium wasabiae.