Browsing by Author "Gouws, Reinette"

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    Ecology and characterization of Streptomyces species associated with common scab disease conducive and biofumigated soils in South Africa
    (Stellenbosch : Stellenbosch University, 2013-03) Gouws, Reinette; McLeod, Adele; Mazzola, M.; Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology.
    ENGLISH ABSTRACT: Common scab of potato is a serious cosmetic disease in South Africa as well as internationally. The disease affects the appearance and quality of potatoes resulting in major annual losses. Potato producers in South Africa, in the commercial, emerging and processing potato industries, struggle to manage the incidence of common scab, especially soilborne inoculum. Existing products and management programs against common scab are often insufficient. The two main aims of the study were to i) characterize and determine the pathogenic Streptomyces spp. occurring in potato production regions in South Africa and ii) investigate the mechanisms through which Brassica soil amendments can reduce common scab and ways in which it can be included in a sustainable management program. In South Africa, Streptomyces scabiei is still regarded as the main causal agent of common scab. However, world-wide, the disease is caused by a complex of Streptomyces species, with the dominant species varying in different regions. Therefore, a total of 132 Streptomyces isolates collected from six South African potato production regions were characterized. Potato pot trials showed that 53 % of the isolates were pathogenic. Analyses using species specific primers and phylogenetic analyses (16S rRNA phylogeny and multilocus phylogeny) showed that S. scabiei was the most prominent species in South Africa comprising 51.4 % of the pathogenic isolates, followed by S. europascabiei (30 %), S. cavisabies (5.7 %), and S. stelliscabies (1.45 %). The remaining 11.45 % of the pathogenic isolates comprised three taxa, which are related and fit within phylogenetic clades that do not contain common scab isolates from any country other than South Africa. The taxa are named here Streptomyces strains RSA1 (5.7 %), RSA2 (4.3 %) and RSA3 (1.45 %). Streptomyces strain RSA1, which occurred in two production regions, is of special concern since these isolates produce fissure scab symptoms that result in severe cosmetic tuber damage. Fissure scab has not been reported from any other region of the world and is of concern in South Africa since it occurs on the cultivar Mondial that is tolerant to typical common scab. PCR analyses targeting three marker pathogenicity island (PAI) genes (txtAB, nec1, tomA) showed that among the pathogenic isolates nec1 occurred in 89 % of the isolates, tomA in 81 % and txtAB in 89 % of the isolates. The isolates (11 %) that did not contain the txtAB gene and also did not produce thaxtomin, belonged to S. caviscabies and Streptomyces strains RSA2 and RSA3. The incorporation of Brassica tissue into soil has recently shown some potential for reducing common scab disease incidence. Brassica crop residues contain glucosinolates (GLN) that upon cell disruption are hydrolysed by the enzyme myrosinase to yield a diversity of biologically-active hydrolysis products that are toxic to soil microbes. This control mechanism is known as biofumigation. The current study showed that common scab was significantly reduced under field conditions through incorporation of fresh or air-dried residues of Brassica oleracea var. capitata (cabbage) in two consecutive potato plantings. The in-vitro effect of volatile emissions from various Brassica species towards Streptomyces was evaluated using two bioassay methods. An in-vitro agar plate bioassay showed that, in general, volatile emissions from water activated freeze-dried tissue of a B. juncea/S. alba mix and B. napus were superior to those from B. oleracea var italica and B. oleracea var capitata for suppression of growth and sporulation of Streptomyces. In a gas chamber bioassay that used freshly macerated Brassica tissue, B. oleracea var capitata and a B. juncea/S. alba mix suppressed sporulation but not hyphal growth of Streptomyces. The gas chamber bioassay showed that the biofumigation effect was bacteriostatic, i.e. isolates recovered after volatile exposure. Both bioassays showed that significant components of both the pathogenic (50 %) and non-pathogenic (20 %) Streptomyces population examined were unaffected by the Brassica tissue derived volatiles. Mechanisms of disease reduction through Brassica amendments are not limited to biofumigation, but changes in the structure of microbial communities involved in systemic induced resistance and/or general microbial suppression may also contribute to disease suppression. In the current study a potato split-root experiment that spatially separated the progeny tubers and roots of Brassica juncea/ Sinapus alba (mustard mix) and Brassica oleracea var oleracea (cabbage) amended soil sub-units from non-amended soil sub-units, showed that induced resistance induced in plants was involved in common scab suppression. The role of toxic GLN hydrolysis products was ruled out in the induced resistance mediated disease suppression, since volatiles were released from Brassica amended soil prior to initiating the experiment. Increased microbial activity in the Brassica amended units was evidenced by significant increases in ß-glucosidase and urease activities. Principal component analyses revealed some trends in the overall soil, tuber and root associated microbial genera (Trichoderma, Pseudomonas, Streptomyces, total bacteria and Fusarium) in the Brassica amended and non-amended units. The mustard amended treatment, and to a lesser extend the cabbage amended units, showed trends towards increases in soil Fusarium and Trichoderma and root Trichoderma populations, and decreases in total bacterial and Streptomyces populations in soil and tubers, and Streptomyces in roots. This study has contributed towards our knowledge of the Streptomyces species causing potato common scab in South Africa, and mechanisms through which Brassica soil amendments can reduce common scab. Several Streptomyces species, including novel pathogenic taxa, are involved in causing common scab and their differential virulence, and responses to being suppressed by Brassica amendments will require the implementation of an integrated management program. The planting of cabbage as a cash crop, with the subsequent incorporation of residues into soil shows promise as a management strategy for subsistence farmers. The mechanisms involved in common scab suppression through Brassica amendments were shown to involve systemic induced resistance in plants and general microbial suppression. Altogether, knowledge obtained in this study can be used to i) optimize management strategies for sustainable potato production, ii) further elucidate the mechanisms involved in disease suppression and iii) develop molecular techniques, such as quantitative real-time PCR for rapid identification and quantification of common scab-causing species in South Africa.