Masters Degrees (Plant Pathology)
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Browsing Masters Degrees (Plant Pathology) by Author "Bahramisharif, Amirhossein"
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- ItemPythium species associated with rooibos, and the influence of management practices on disease development(Stellenbosch : Stellenbosch University, 2012-03) Bahramisharif, Amirhossein; McLeod, Adele; Lamprecht, Sandra, C. ; Stellenbosch University. Faculty of AgriSciences. Dept. of Plant Pathology.ENGLISH ABSTRACT: Damping-off of rooibos (Aspalathus linearis), which is an important indigenous crop in South Africa, causes serious losses in rooibos nurseries and is caused by a complex of pathogens of which oomycetes, mainly Pythium, are an important component. The management of damping-off in organic rooibos nurseries is problematic, since phenylamide fungicides may not be used. Therefore, alternative management strategies such as rotation crops, compost and biological control agents, must be investigated. The management of damping-off requires knowledge, which currently is lacking, of the Pythium species involved, and their pathogenicity towards rooibos and two nursery rotation crops (lupin and oats). Pythium species identification can be difficult since the genus is complex and consists of more than 120 species. Species identification is, however, greatly facilitated by analyses of the internal transcribed spacer (ITS) regions. These regions, have also been used to divide the genus into 11 phylogenetic clades (A to K), with some clades, such as clade G, still being poorly characterised. The first aim of the study was to characterize 12 Pythium clade G isolates that were obtained from damped-off rooibos seedlings, along with six known clade G species. Subsequently, oligonucleotides were designed for differentiating two rooibos associated groups that may represent new taxons, for future use in DNA macro-array analyses. Phylogenetic analyses of the ITS region and a combined phylogeny of four gene regions (ITS, -tubulin and, COX1 and COX2 [cytochrome c oxidase subunits I and II]) identified five sub-clades within Pythium clade G. The rooibos isolates formed two groups, Rooibos group I (RB I) and II (RB II) that clustered into two groups within sub-clade 1 with good support (64%-89% bootstrap, 1.00 probability). The Pythium RB I isolates had P. iwayamai as its nearest neighbour, and may represent a new species. The Pythium RB II isolates had P. canariense and P. violae as their closest relatives and may, along with other isolates contained in the RB II sub-clade, represent several new species. Morphological analyses of the rooibos isolates were inconclusive, since the isolates all contained similar morphological characteristics that did not correspond to the description of known Pythium species. The Pythium RB I and II isolates were all non-pathogenic toward rooibos, lupin and oats seedlings. For each of the two rooibos groups, one newly developed oligonucleotide was able to differentiate the isolates from clade G reference isolates using DNA macro-array analyses. The second aim of the study was to determine the oomycetes species associated with rooibos in nurseries and in a native rooibos site, and their pathogenicity towards rooibos and two nursery rotation crops (lupin and oats). Since some isolates were shown to be nonpathogenic, another aim was to determine whether these isolates, along with the previously characterised non-pathogenic Pythium RB I and RB II isolates, could suppress pathogenic oomycetes. Characterisation of isolates from 19 nurseries and one native rooibos site revealed the presence of five Pythium species (P. acanthicum, P. irregulare, P. mamillatum, P. myriotylum, and P. pyrilobum) and Phytophthora cinnamomi. In nurseries, P. irregulare was the most common species (81%) followed by P. myriotylum (14%). Similarly, P. irregulare was also the most prevalent species (57%) in native rooibos, but P. pyrilobum (26%) was second most prevalent. Pathogenicity studies on rooibos showed that all species, except P. acanthicum, were highly virulent causing 100% damping-off. On lupin, P. acanthicum was also the only non-pathogenic species, with the other species being less virulent on lupin than on rooibos. Only P. irregulare, P. myriotylum, and P. pyrilobum were pathogenic towards oats, and were also less virulent on oats than on rooibos. On lupin and oats, not all off the isolates from a specific species was pathogenic. Non-pathogenic Pythium species (P. acanthicum, Pythium RB I and II) was only effective at suppressing disease on the less susceptible crops of lupin and oats, but not on rooibos. The third aim of the study was to investigate the management of rooibos damping-off using two composts (A and B), and composts combined with non-pathogenic Pythium species. Evaluation of the suppression by composts of Ph. cinnamomi and 29 Pythium isolates, which represented the four pathogenic Pythium rooibos species, showed that both composts were able to suppress some, but not all of the pathogenic Pythium isolates. Both composts were very effective at, and the highest percentage control was achieved, with suppression of Ph. cinnamomi. Most isolates of P. mamillatum and P. pyrilobum were suppressed by composts, whereas most P. irregulare (> 62%) and P. myriotylum (>50%) isolates were not suppressed. Non-pathogenic Pythium species combined with either of the two composts were able to significantly reduce damping-off caused by P. irregulare or a combination of pathogenic species (P. irregulare, P. mamillatum, P. myriotylum, P. pyrilobum, and Ph. cinnamomi), compared to than when only the pathogens were present. In the absence of non-pathogenic species, neither of the composts was able to suppress the aforementioned pathogenic isolates. This study has improved our knowledge of the oomycete species that are involved in rooibos damping-off, and has identified possible management strategies for use in organic nurseries. Several oomycete species are involved in causing damping-off and their differential virulence, and responses to being suppressed by composts, will require the use of integrated management strategies. Management strategies that showed promise include the combined use of compost and non-pathogenic Pythium taxons. The use of oats, which is susceptible to fewer oomycete isolates than rooibos, could also be valuable as a rotation crop. Altogether, knowledge obtained in this study can be used to (i) optimize integrated management strategies for organic nurseries, (ii) elucidate the mechanisms involved in disease suppression and (ii) develop molecular techniques, such as DNA macro-arrays and quantitative PCR (qPCR) for the rapid assessment of the species involved, and the quantification of inoculum in nursery soils.