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Pythium Species Associated with Rooibos, and the Influence of Management Practices on Disease Development

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Pythium Species Associated with Rooibos, and the Influence of Management Practices on Disease Development PYTHIUM SPECIES ASSOCIATED WITH ROOIBOS, AND THE INFLUENCE OF MANAGEMENT PRACTICES ON DISEASE DEVELOPMENT By AMIRHOSSEIN BAHRAMISHARIF Thesis presented in partial fulfilment of the requirements for the degree of Master of Science in the Faculty of AgriSciences at the University of Stellenbosch Supervisor: Dr. Adéle McLeod Co-supervisor: Dr. Sandra C. Lamprecht March 2012 Stellenbosch University http://scholar.sun.ac.za DECLARATION By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the owner of the copyright thereof (unless to the extent explicitly otherwise stated) and that I have not previously in its entirety or in part submitted it for obtaining any qualification. Amirhossein Bahramisharif Date:……………………….. Copyright © 2012 Stellenbosch University All rights reserved Stellenbosch University http://scholar.sun.ac.za PYTHIUM SPECIES ASSOCIATED WITH ROOIBOS, AND THE INFLUENCE OF MANAGEMENT PRACTICES ON DISEASE DEVELOPMENT SUMMARY 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 Stellenbosch University http://scholar.sun.ac.za 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 non- pathogenic, 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. Stellenbosch University http://scholar.sun.ac.za 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. Stellenbosch University http://scholar.sun.ac.za PYTHIUM SPESIES WAT MET ROOIBOS GEASSOSIEER WORD, EN DIE INVLOED VAN BESTUURSPRAKTYKE OP SIEKTE-ONTWIKKELING OPSOMMING Omvalsiekte van rooibos (Aspalathus linearis), wat ‘n belangrike inheemse gewas in Suid-Afrika is, veroorsaak ernstige verliese in rooiboskwekerye, en word deur ‘n kompleks van patogene veroorsaak, waarvan oömysete, hoofsaaklik Pythium, ’n belangrike komponent is. Die bestuur van omvalsiekte in organiese rooiboskwekerye is problematies, aangesien fenielamied fungisiedes nie gebruik mag word nie. Alternatiewe bestuurstrategieë, soos rotasie-gewasse, kompos en biologiese beheer-agente, moet dus ondersoek word. Die bestuur van omvalsiekte vereis kennis, wat tans ontbreek, naamlik die Pythium spesies wat betrokke is, hul patogenisiteit teenoor rooibos, en twee kwekery rotasie-gewasse (lupiene en hawer). Pythium spesie-identifikasie kan moeilik wees aangesien die genus kompleks is en uit meer as 120 spesies bestaan. Spesie-identifikasie word egter grootliks vergemaklik deur analise van die interne getranskribeerde spasieerder (ITS) areas. Hierdie areas is ook gebruik om die genus in 11 filogenetiese “clades” (A tot K) te verdeel, met sommige “clades”, soos “clade” G, wat steeds swak gekarakteriseer is. Die eerste doelwit van die studie was om 12 Pythium “clade” G isolate te karakteriseer, wat vanaf omvalsiekte rooibossaailinge verkry is, tesame met ses bekende “clade” G spesies. Gevolglik is oligonukleotiede ontwerp ten einde twee rooibos- geassosieerde groepe, wat nuwe taksons kan verteenwoordig, te onderskei, en vir toekomstige gebruik in DNS makro-“array” analise. Filogenetiese analise van die ITS area en ‘n gekombineerde filogenie van vier geen-areas (ITS, -tubulien en, COX1 en COX2 [sitokroom c oksidase sub-eenhede I en II]) het vyf sub-“clades” binne Pythium “clade” G geïdentifiseer. Die rooibos isolate het twee groepe gevorm, Rooibos groep I (RB I) en II (RB II) wat twee groepe binne sub-“clade” 1 gevorm het, met goeie ondersteuning (64%-89% “bootstrap”, 1.00 waarskynlikheid). Die Pythium RB I isolate het P. iwayamai as sy naaste verwant, en
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