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Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe

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Abstract

Soft rot and blackleg can cause severe economic losses in potato production in South Africa and Zimbabwe depending on climatic conditions. The aim of the study was to identify the predominant bacteria causing potato soft rot and blackleg in these countries. Samples, comprising of stems and tubers from potato plants with blackleg and soft rot symptoms were collected from 2006–2009 from potato production areas where disease outbreaks occurred. The isolates from these plants and tubers yielded Gram negative, pectinolytic bacteria on crystal violet pectate and inoculated tubers. Identification was based on biochemical and phenotypic characteristics, rep-PCR, Amplified Fragment Length Polymorphisms and sequences of gyrB and recA genes. Isolates from Zimbabwe were identified as Pectobacterium carotovorum subsp. brasiliensis (Pcb) (21 isolates), Dickeya dadantii subsp. dadantii (Dd) (20 isolates), P. c. subsp. carotovorum (Pcc) (16 isolates) and P. atrosepticum (Pa) (4 isolates). Pcb, Pcc and Dd subsp. dadantii were isolated from samples collected from all the regions, while Pa was isolated from Nyanga the coolest region in Zimbabwe. In South Africa, however, Pcb was the most common causal agent of soft rot and blackleg. P. atrosepticum was the only pathogen isolated from samples collected in Nyanga, Zimbabwe, and was not isolated from any South African samples. AFLP analysis separated the Pcb strains into 12 clusters, reflecting subdivision in terms of geographic origin, and Pcc isolates were clearly differentiated from Pcb isolates. A large degree of DNA polymorphism was evident among these 12 clusters. The study identified all the pathogens associated with the blackleg/soft rot disease complex.

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Acknowledgements

This work was funded by Potatoes South Africa and the National Research Foundation of South Africa. The authors would like to acknowledge the help of Mr Charles Wairuri in sequence alignment and drawing of phylogenetic trees.

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Authors and Affiliations

  1. Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0002, South Africa

    Elizabeth Ngadze & Jacquie E. van der Waals

  2. Department of Crop Science, University of Zimbabwe, P.O. Box MP167, Mount Pleasant Harare, Zimbabwe

    Elizabeth Ngadze

  3. Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa

    Carrie L. Brady & Teresa A. Coutinho

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  1. Elizabeth Ngadze
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  4. Jacquie E. van der Waals
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Correspondence to Jacquie E. van der Waals.

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Supplementary Figure 1

Phylogenetic tree based on recA gene sequence showing the phylogenetic relationship among Zimbabwean strains, D. dadantii subsp. dadantii and different Pectobacterium spp. The phylogram was produced by the neighbour-joining programme (Tamura et al. 2007). The numbers on the branches indicate bootstrap value support based on neighbour-joining analyses of 1000 bootstrap replication. Accession numbers of reference strains in GenBank are in parenthesis. T, type strain (PDF 32 kb)

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Ngadze, E., Brady, C.L., Coutinho, T.A. et al. Pectinolytic bacteria associated with potato soft rot and blackleg in South Africa and Zimbabwe. Eur J Plant Pathol 134, 533–549 (2012). https://doi.org/10.1007/s10658-012-0036-z

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