A dissertation submitted to the Faculty of Science of the University of Witwatersrand, Johannesburg, in full fulfilment of the requirements for the degree of Master of Science, 2019 / Cassava, Manihot esculenta Crantz, is categorized as a food security crop, producing large starchy tubers that are gaining interest from both international and local agro-processing industries for products such as bioethanol, textiles, and food additives. However, cassava is currently under threat from a group of begomoviruses that cause cassava mosaic disease (CMD) in all countries in sub-Saharan Africa where cassava is cultivated. CMD can result in up to 100% crop loss. South African cassava mosaic virus (SACMV) is particularly a threat to the growing cassava industry in southern Africa. Despite extensive breeding programs over the past 70 years to develop CMD-resistant farmer-preferred cassava landraces, total resistance has not been achieved. Furthermore, the high mutational rates of begomoviruses, and mixed infections in the field, have exacerbated the problem. TME3 is a West African landrace that displays tolerance to begomoviruses, including SACMV. Infection of TME3 by SACMV leads to recovery, hallmarked by low virus loads and milder symptoms compared to a susceptible southern African landrace T200. The molecular processes that govern tolerance in crops, including cassava, are not well understood. However, systemic immune responses, which are controlled by hormoneresponsive transcription factors (TFs), are required by the plant to successfully combat an invading pathogen. Two different branches of systemic immunity have been described, namely systemic acquired resistance (SAR), facilitated by salicylic acid (SA) signalling, and induced systemic resistance (ISR), which is induced through jasmonic acid (JA) and ethylene (ET) signalling in the presence of beneficial rhizobacteria. In 2014, Allie et al. compared global transcriptomic responses occurring in TME3 and the T200 during early 12 days’ post inoculation (dpi), middle (32 dpi) and late (67 dpi) stages of SACMV infection. In order to give greater context to transcriptomic data, which is inheritably large and complex, network analysis may be implemented. By placing the differentially expressed (DE) gene homologs/orthologs identified from the cassava transcriptome datasets into protein-protein networks, functions of SACMV-responsive genes, interacting partners, and potential hubs, can be derived. Cassava gene functions are based on the model crop Arabidopsis thaliana, as despite the sequencing of the cassava genome, the annotations are incomplete. The aim of this study was to identify potential candidate TFs, and their associated hormones and other network partners, that confer either tolerance (TME3) or susceptibility (T200) to SACMV. / TL (2020)

Studies presented in this dissertation highlight the importance of fungal pathogens in forestry nurseries in South Africa. Both Acacia meamsii seedlings and Eucalyptus hybrid cuttings are shown to be affected by important nursery pathogens. Chapter one presents an evaluation of the potential importance of pathogens to Eucalyptus hedge plants maintained in hydroponics. Hydroponics is a new technology being used in South African forest nurseries, which allows for the rapid establishment of Eucalyptus hedge plants. However, no information is available on pathogens affecting Eucalyptus in hydroponics. By applying information on pathogens of other hydroponic crops, several potentially important pathogens were identified and these reside in the genera Phytophthora, Pythium and Fusarium. Possible disease symptoms in Eucalyptus caused by these pathogens include wilting, stem cankers and root rots. Implementation of appropriate control measures that include cultural, biological and chemical practices could prevent and/or reduce disease impact in hydroponics. Chapter two presents the results of a survey of the roots of Eucalyptus hedge plants grown in an ebb and flow hydroponic system. An interesting result of the survey was the discovery of Cylindrocladium pauciramosum in the hydroponic system. This is the first report of the pathogen in a hydroponic system. Other important pathogens in the genera Phytophthora and Pythium were also isolated. Two Pythium species, namely P. dissotocum and P. helicoids, found in the roots and nutrient solution are new to Eucalyptus. Several Fusarium species were also isolated of which two, namely F. nygamai and F. lateritium, are also new to Eucalyptus. Chapter three of this dissertation presents the results of a survey of Eucalyptus cuttings conducted at four forestry nurseries in KwaZulu-Natal, South Africa. Several well-known Eucalyptus nursery pathogens were isolated. Cylindrocladium pauciramosum was identified as the dominant pathogen on Eucalyptus cuttings. This was confirmed based on morphological characteristics and DNA sequence comparisons. Pathogenicity tests conducted using a spore suspension of C. pauciramosum indicated that this pathogen is capable of infecting most commercial Eucalyptus clones used in South Africa. Chapter four considers a serious disease of Acacia mearnsii seedlings caused by an unidentified species of Cylindrocladium. Cylindrocladium pauciramosum was isolated from A. mearnsii seedlings showing girdling and stem canker symptoms. The pathogen was identified based on morphological characteristics and DNA sequence comparisons. Pathogenicity tests with Acacia seedlings confirmed the susceptibility of this tree to C. pauciramosum infection. This dissertation clearly indicates that Cylindrocladium pauciramosum is an important nursery pathogen in South African forestry nurseries. This pathogen has already been shown to be limiting during production of planting stock. I hope to have highlighted the importance of C. pauciramosum and other nursery pathogens in forestry nurseries in South Africa. This study will also hopefully provide information to forestry nursery managers and help them improve production. / Dissertation (MSc)--University of Pretoria, 2004. / Microbiology and Plant Pathology / Unrestricted

Commercial AM fungi isolates, Rhizophagus clarus, Gigaspora gigantea, Funneliformis mosseae, Claroideoglomus etunicatum and Paraglomus occulum were tested on four seasonal ornamentals, Dianthus chinensis x barbatus, Impatiens wallerana, Petunia x hybrid and Viola x wittrockiana planted in peat-base medium. The experiment was conducted in a glasshouse with three replicates in a completely randomised design. Various vegetative (height, width, length, number of leaves, leaf area and dry biomass) and reproductive (number of flowers and buds) plant parts were measured in the course of three months. AM fungi was found to increase seedling growth and reduced seedling mortality rate of all the plants studied. Inoculated plants produced more leaves (16-33%) and grew taller (12-28%). Dry biomass of inoculated Dianthus, Impatiens and Viola plants were significantly increased by 25-53%. All plants under low colonisation rates displayed mycotrophic qualities and net growth output thereof were found to be similar to plants with equal or higher colonisation rate. Mortality were less frequent in inoculated plants and they were also less susceptible to transplant shock. / Agriculture, Animal Health and Human Ecology / M. Sc. (Ornamental Horticulture)

Thesis (MSc)--Stellenbosch University, 2000. / Full text to be digitised and attached to bibliographic record. / ENGLISH ABSTRACT: The cultivation of citrus in the Vaalharts region is a fairly recent development. With the introduction of this crop, an insect pest complex has also developed in this region. The presence of these pests was studied in eleven orchards, planted with three citrus cultivars and of varying ages, distributed in the 300 square kilometer cultivation area. Each orchard was inspected for the presence of pests by making use of two weekly sampling techniques. Ten of the most important insect pests of citrus in the Vaalharts region are briefly described by refering to their general appearance, life cycles, feeding and pest status and economic threshold. For every pest various control options, including operational systems, crop cultivation, biological and chemical control, are discussed and, where applicable, illustrated by means of graphic presentations. The seasonal presence of the cirtrus pests in the Vaalharts region is tabulated and discussed individually. With these details as background, an insect pest management programme for citrus in the Vaalharts region is compiled. / AFRIKAANSE OPSOMMING: Die verbouing van sitrus in die Vaalhartsgebied is 'n redelik onlangse ontwikkeling. Gepaard met die nuwe gewas het daar ook 'n insekplaagkompleks in die gebied ontstaan. Die voorkoms van die plae is in elt .boorde, beplant met drie sitruskultivars en van verskillende ouderdomme, verspreid in die 300 vierkante kilometer verbouingsareaal, bestudeer. Elk van die boorde is weekliks ondersoek vir die aanwesigheid van plae deur van twee moniteringstegnieke gebruik te maak. Die tien belangrikste insekplae van sitrus in die Vaalhartsgebied word kortliks beskryf deur na hulle algemene voorkoms, lewenssiklus, voeding en plaagstatus en ekonomiese drempelwaardes asook die moniteringsmetodes wat gebruik is, te verwys. Vir elke plaag word beheeropsies, wat operasionele stelsels, gewasverbouing, bloloqlese en chemiese beheer insluit, bespreek wat, waar toepaslik, aan die hand van grafiese voorstellings gemustreer word. Die seisoenale aanwesigheid van die sitrusplae word in 'n tabel aangedui en individueel bespreek. Met die gegewens as agtergrond is 'n insekplaagbestuurprogram vir sitrus in die Vaalhartsgebied opgestel.

Thesis (MScAgric)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: Various aspects of the biology and ecology of woolly apple aphid, Eriosoma lanigerum, were investigated, including initial galling damage caused by E. lanigerum to the roots of apple trees, the possible relationship between E. lanigerum and Xiphinema and Pratylenchus nematodes and the effectiveness of Biostart 2000® and Furfural® as possible control agents of E. lanigerum in the orchard. Preliminary root damage by first instar E. lanigerum feeding was characterized by the mechanical injury of endodermis and parenchyma tissues. Damage by second, third and fourth instar E. lanigerum was similar, but the symptoms were more pronounced. Damage caused by adults included a pronounced swelling at infected areas of the root. Cell walls hardened until the root was radially strengthened with sclerenchyma tissue and nonconducting xylem vessels while the cuticle expanded greatly through the growth of corklike cambium tissue. There was no direct relationship between the population dynamics of E. lanigerum and those of Xiphinema and Pratylenchus nematodes. The occurrence of E. lanigerum appeared to be seasonal while P. penetrans and Xiphinema numbers fluctuated erratically. Undamaged root nitrogen levels seemed to correspond with the normal root growth cycle. Nitrogen levels from galled roots were significantly lower than those of undamaged roots, probably due to E. lanigerum feeding. Soils rich in fine sand and clay sustained higher populations of E. lanigerum and Xiphinema than sandy soils. The number of E. lanigerum found in soil samples correlated well with the damage index allocated to the samples. The numbers of Xiphinema found in soil samples also correlated well with the damage index allocated to the samples according to suspected Xiphinema damage symptoms. Both Biostart 2000® and Furfural® were effective as control agents of woolly apple aphid. Furfural'Ï, a chemical waste product of the sugarcane industry, was however not as effective as Biostart 2000®, a product that includes an activator and three bacterial species, Bacillus laterosporus, B. chitinosporus and B. licheniformis. The bacteria in the Biostart 2000® treated pots could replicate themselves under suitable conditions while Furfural® dilutes with each watering. Biostart 2000® is also easier to prepare than Furfural® since the components of Biostart 2000® readily mix to form a paste easily thinned by water, whereas Furfural® is an oily substance that does not easily disperse in water. Root damage was initiated soon after E. lanigerum started feeding, however there was no apparent relationship between E. lanigerum and the nematode species. The most promising, environmentally friendly control measure was Biostart 2000®. / AFRIKAANSE OPSOMMING: Verskeie aspekte van biologie en die ekologie van die appel bloedluis, Eriosoma lanigerum, was ondersoek insluitende aanvanklike galvorming veroorsaak deur E. lanigerum op wortels van appelbome, die moontlike verwantskap tussen E. lanigerum en Xiphinema en Pratylenchus nematodes en die effektiwiteit van Biostart 2000® en Furfural® as moontlike beheeragente van E. lanigerum in die boord. Aanvanklike wortelskade deur eerste ins tar E. lanigerum voeding was gekenmerk deur die meganiese beskadiging van endodermale en parenchiem weefsel. Skade veroorsaak deur tweede, derde en vierde instar E. lanigerum was soortgelyk alhoewel die simptome meer beklemtoond was. Skade deur volwassenes het 'n meer duidelike swelsel by geïnfekteerde wortelareas ingesluit. Selwande het verhard totdat die wortel radiaalsgewys versterk was met skierenchiem weefsel en nie-geleidende xileemvate terwyl die kutikula grootliks toegeneem het deur die groei van kurkagtige kambiumweefsel. Daar was geen direkte verwantskap tussen die bevolkingsdinamika van E. lanigerum en dié van Xiphinema en Pratylenchus nematodes nie. Die voorkoms van E. lanigerum was seisoenaal terwyl P. penetrans en Xiphinema se getalle onvoorspelbaar gefluktueer het. Onbeskadigde wortel stikstofvlakke het ooreengestem met die normale wortel groeisiklus. Stikstof vlakke van galwortels was noemenswaardig laer as dié van onbeskadigde wortels, heel waarskynlik as gevolg van voeding deur E. lanigerum. Grond ryk aan fyn sand en klei het groter bevolkings van E. lanigerum en Xiphinema onderhou as sanderige gronde. Die aantal E. lanigerum in grondmonsters het goed ooreengestem met die skade indeks wat aan die monsters toegeken was. Die aantal Xiphinema in grondmonsters het ook goed ooreengestem met die beskadigingsindeks wat aan die monsters toegeken is weens vermoedelike Xiphinema skade simptome. Beide Biostart 2000® en Furfural® was effektief as beheeragente van die appelbloedluis. Furfural'", 'n afvalproduk van die suikerriet industrie, was egter minder effektief as Biostart 2000®, 'n produk bestaande uit 'n aktiveerder en drie bakterie spesies, Bacillus laterosporus, B. chitinosporus en B. licheniformis. Die bakterië in die Biostart 2000® behandelde potte kon vermeerder onder gunstige toestande terwyl Furfural® na elke besproeiing verdun het. Biostart 2000® is ook makliker om aan te maak as Furfural® aangesien die bestanddele van Biostart 2000® geredelik meng tot 'n wateroplosbare pasta, terwyl Furfural® 'n olierige vloeistofis wat moeilik 'n waterige suspensie vorm. Wortelskade het plaasgevind kort nadat E. lanigerum begin voed het, alhoewel daar geen duidelike verwantskap tussen E. lanigerum en nematode spesies voorgekom het nie. Die mees belowende omgewingsvriendelike beheermaatreël was Biostart 2000®.

Fusarium circinatum is a fungal pathogen that has had a serious impact on pine production throughout the world. It attacks most Pinus species including Pinus elliottii, Pinus patula and Pinus radiata. Infections in South Africa (SA) are largely on seedlings, and result in fatal seedling wilt. Accurate and quick detection systems suitable for field use are needed to monitor the spread of the disease and optimize fungicide applications. Detection of F. circinatum is currently based on visual observations of typical symptoms. However, symptoms are not unique to the pathogen and can be caused by other biotic and abiotic stress factors. Nucleic acid-based identification techniques using PCR are available for different fungal species. These are sensitive and accurate, but they are expensive and require skilled biotechnologists to conduct the assays. In this study an enzyme-linked immunosorbent assay (ELISA) was developed to identify F. circinatum in infected seedlings. This optimized ELISA is able to discriminate between F. circinatum and two other fungi that frequently affect pine. This method has advantages over other assays because of its ease of operation and sample preparation, sensitivity and the ability to run multiple tests simultaneously. Mycelium-soluble antigens from Diplodia pinea (=Sphaeropsis sapinea), F. circinatum and F. oxysporum were prepared in nutrient broth. Analysis of these antigens on SDS-PAGE indicated the presence of common antigens between the different fungal pathogens. Some antigens were expressed more by some isolates than by others. Separate groups of chickens were immunised with mycelium-soluble antigens from D. pinea, F. circinatum and F. oxysporum and exo-antigen from F. circinatum prepared in nutrient broth. A 34 kDa protein purified from SDS-PAGE specific for D. pinea was also used for immunisation. Five sets of antibodies were obtained including anti-D. pinea, anti-F. circinatum, anti-F. oxysporum, anti-F. circinatumexo and anti-D. pinea 34 kDa antibodies, respectively. Reactivity of these antibodies was evaluated against antigens prepared in nutrient broth using western blotting and ELISA. Western blot analysis indicated that immuno-dominant antigens for F. circinatum were larger than 34 kDa and their reactivity was not the same between different isolates. Each of the antibodies prepared using mycelium-soluble antigens showed increased reactivity when detecting its own specific pathogen, but cross-reactivity was observed. Anti-D.pineaantibodies showed minimal cross-reactivity with antigens from F. circinatum and F. oxysporum. Anti-F. circinatum antibodies cross-reacted with antigens from F. oxysporum but showed little cross-reactivity with D. pinea antigens. Anti-F. oxysporum antibodies showed more cross-reactivity towards antigens from F. circinatum than those from D. pinea. No reactivity was observed when anti-F. circinatum-exo antigen and anti-D. pinea 34 kDa antibodies were used in immuno-blotting analysis. Evaluation of antibody reactivity using indirect ELISA showed patterns similar to those observed on western blotting, where anti-D. pinea, anti-F. circinatum and anti-F. oxysporum antibodies showed the same cross-reactivity relationships. Anti-F. circinatum and anti-F. oxysporumantibodies showed a significant difference when reacting with antigens isolated from other pathogens including D. pinea, F. circinatum, F. oxysporum, F. solani, F. graminearum and F. culmorum (P = 0.001). No significant difference was observed when the antigens were detected with anti-D. pinea antibodies. Reactivity of anti-F. circinatum-exo and anti-D. pinea34 kDa antibodies was mostly similar to that of non-immune antibodies and showed no significant difference between detection of different antigens. Pine seedlings were artificially infected with the three fungal pathogens using a spore concentration of 1 – 1 x 106conidiaml-1.Infection was monitored using scanning electron microscopy. Results showed increased levels of mycelium growth on the stem and roots of the F. circinatum and F. oxysporum infected seedlings and on the leaves and stem in the case of D. pinea infected seedlings. These plant parts were used in ELISA tests for the detection of antigens. Isolation of antigens from the plant materials involved crushing plant parts in buffer and centrifugation of the suspension. The supernatant obtained was directly used in the assay. ELISA tests prepared in this study were sensitive enough to detect infection caused by 1 conidium ml-1at two weeks post inoculation. A positive reaction for detection of F. circinatum and F. oxysporum was indicated by an ELISA reading above an optical density at 405 nm. The plant material used in ELISA tests were further analysed using PCR. Results indicated that there was no cross-infection between seedlings and served as a confirmation of the disease-causing pathogen. This indicated that cross-reactivity observed was due to other factors such as common epitopes on the major antigens. Use of an ELISA dip-stick or ELISA using these antibodies should provide an easy, fast field test to identify infections of pine, discriminating between F. circinatum, F. oxysporum and D. pinea. / M.Sc.Agric. University of KwaZulu-Natal, Pietermaritzburg 2013.

Please read the abstract in the section 00front of this document / Dissertation (M Inst Agrar (Sustainable Insect Management))--University of Pretoria, 2005. / Zoology and Entomology / unrestricted

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: Grapevine trunk diseases are caused by invasive pathogens that are responsible for the slow decline of vines. In particular, Eutypa dieback of grapevine has had a devastating impact on vineyards worldwide, reducing growth and yield, eventually killing the grapevine. The causal organism of Eutypa dieback was first described as Eutypa armeniacae Hansf. & Carter, the pathogen that causes dieback of apricots, but since 1987 this species has been considered a synonym of Eutypa lata (Pers.:Fr.) Tul & C. Tul (anamorph Libertella blepharis A. L. Smith). Recently, it was proposed that at least two species that are capable of infecting grapevines are responsible for Eutypa dieback. Consequently, the molecular identification and characterisation of Eutypa dieback was used to delineate the species occurring on infected grapevines in South Africa. This involved the molecular analyses of three molecular markers, namely, the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA operon, and the -tubulin gene. The results obtained revealed the presence of a second species, namely, Eutypa leptoplaca (Mont.) Rappaz, that occurred together with E. lata on infected grapevines. Also co-habiting with these pathogens were related fungi form the Diatrypaceae family, Cryptovalsa ampelina (Nitschke) Fuckel and Eutypella vitis (Schwein.) Ellis & Everhart. Pathogenicity tests conducted on isolates representing C. ampelina, E. lata, E. leptoplaca, and E. vitis revealed that all were pathogenic to grapevine. Several species of Botryosphaeriaceae that commonly invade the woody tissue of grapevines are also pathogenic to grapevine. The symptoms in grapevine commonly associated with Botryosphaeriaceae are easily confused with the symptoms produced by Eutypa dieback which prompted the need for the development of a detection method that can correctly identify the presence of multiple pathogens. A reverse dot blot hybridisation (RDBH) method was subsequently applied to provide a rapid, accurate and reliable means of detecting the Eutypa species involved in the Eutypa disease complex, as well as those species of Botryosphaeriaceae known to cause disease in grapevines. The method involved the use of multiplex PCR to simultaneously amplify and label the regions of DNA that are used as pathogen specific probes. Consequently, membrane immobilised species-specific oligonucleotides synthesised from the ITS, - tubulin and LSU molecular data were evaluated during the application of this diagnostic method to detect Eutypa species. It was found that the species-specific oligonucleotides, designed from ITS sequence data, could consistently detect E. lata and E. leptoplaca. The application of the RDBH method for the detection of these Eutypa species, based on -tubulin and LSU sequence data, however, proved to be unsuccessful. Subsequently, a RDBH method, utilising species-specific oligonucleotides designed from elongation factor-1α sequence data, was successfully applied for the detection of Botyrosphaeria dothidea (Moug.:Fr.) Ces. & De Not., Neofusicoccum luteum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers, A.J.L. Phillips and Neofusicoccum ribis (Slippers, Crous & M.J. Wingf.) Crous, Slippers & A.J.L. Phillips. The method, however, was unsuccessful for the detection of Diplodia seriata De Not. In addition to the above-mentioned shortcomings, the RDBH was not amenable to the detection of pathogens directly from field or environmental samples, but required preparation of DNA from pure cultures. The method, however, allows for the identification of multiple pathogens in a single assay. As DNA extraction methods are amended, improved and honed to obtain DNA from environmental samples, so would it increase the usefulness of RDBH. / AFRIKAANSE OPSOMMING: Wingerd stamsiektes word veroorsaak deur patogene wat die vermoë het om wingerdplante te infekteer en dan stadige agteruitgang van dié wingerde te veroorsaak. Veral Eutypa terugsterwing het ‘n vernietigende effek op wingerde wêreldwyd deurdat dit groeikrag en oesmassa verlaag, maar ook omdat dit uiteindelik wingerdstokke kan dood. Die veroorsakende organisme is aanvanklik as Eutypa armeniacae Hansf. & Carter beskryf, die patogeen wat terugsterf by appelkose veroorsaak, maar sedert 1987 word hierdie spesies beskou as ‘n sinoniem van Eutypa lata (Pers.:Fr.) Tul & C. Tul (anamorph Libertella blepharis A. L. Smith). Dit is egter onlangs voorgestel dat ten minste twee spesies die vermoë het om wingerd te infekteer om Eutypa terugsterwing te veroorsaak. Gevolglik is molekulêre identifikasie- en karakteriseringstudies geloods om te bepaal watter spesies Eutypa terugsterwing in Suid-Afrikaanse wingerde veroorsaak. Dit het die molekulêre analise van drie molekulêre merkers behels, naamlik die interne getranskribeerde spasiëerderarea (“ITS”), die groot ribosomale subeenheid (“LSU rDNA”) en β-tubilien geen. Resultate van die filogenetiese analise dui daarop dat ’n tweede spesies, naamlik Eutypa leptoplaca (Mont.) Rappaz, saam met E. lata in geïnfekteerde plante voorkom. Saam met bogenoemde twee spesies het daar ook verwante spesies van die Diatrypaceae familie voorgekom, naamlik Cryptovalsa ampelina (Nitschke) Fuckel en Eutypella vitis (Schwein.) Ellis & Everhart. Patogenisiteitstudies wat uitgevoer is met verteenwoordigende isolate van C. ampelina, E. lata, E. leptoplaca, en E. vitis dui daarop dat almal patogene van wingerd is. Verskeie Botryosphaeriaceae spesies wat gereeld in houtagtige wingerdweefsel aangetref word, is ook patogene van wingerd. Interne simptome wat algemeen met Botryosphaeriaceae infeksies geassosieer word, kan baie maklik met dié van Eutypa terugsterwing verwar word en dit het die nood laat ontstaan om ‘n opsporingsmetode te ontwikkel wat akkuraat genoeg is om tussen veelvoudige infeksies te onderskei. ’n Omgekeerde-stippelklad-hibridisasie (OSH) metode is gevolglik aangewend om Eutypa spesies betrokke in die Eutypa-siektekompleks op ‘n vinnige, akkurate en betroubare manier op te spoor, sowel as die Botryosphaeriaceae species wat bekend is as patogene van wingerd. Die metode behels ’n saamgestelde PKR vir die vermeerdering en merk van DNS areas wat gebruik word as patogeen spesifieke peilers. Spesies-spesifieke oligonukleotiede ontwikkel vanaf die ITS, -tubilien en LSU molekulêre data is op ‘n membraan vasgeheg en gebruik om ’n diagnostiese toets te ontwikkel vir Eutypa species. Merkers ontwikkel vanaf die ITS kon E. lata and E. leptoplaca konsekwent opspoor. Die opspoor van Eutypa spesies met merkers vanaf die -tubulien en LSU gene met OSH was onsuksesvol. Die OSH metode met merkers vanaf die verlengingsfaktor-1α kon susksesvol gebruik word om Botyrosphaeria dothidea (Moug.:Fr.) Ces. & De Not., Neofusicoccum luteum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers, A.J.L. Phillips and Neofusicoccum ribis (Slippers, Crous & M.J. Wingf.) Crous, Slippers & A.J.L. Phillips op te spoor. Dié metode kon egter nie Diplodia seriata De Not. opspoor nie. Bykomend tot bogenoemde tekortkominge, kon die omgekeerde-stippelklad-hibridisasie metode ook nie aangepas word om patogene direk vanuit plantmateriaal op te spoor nie en word DNS afkomstig vanaf suiwer kulture benodig. Dié metode laat egter identifikasie van verskeie patogene in ‘n enkele toets toe. Soos DNS ekstraksie metodes aangepas, verbeter en verfyn word om DNS vanuit plantmateriaal te verkry, sal die bruikbaarheid van die omgekeerde stippelklad hibridisasie metode ook verbeter.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Very little is known about the diversity of fungi associated with Afromontane forests of the Cape Floristic Region (CFR) of South Africa. The ophiostomatoid fungi include many species, some known as pathogens in the CFR, while others are well-known saprophytes important in wood degradation. This study focused on the biodiversity and ecology of tree-associated ophiostomatoid fungi (Ophiostomatales) in the CFR. In addition to this, mites and subcortical beetles associated with the CFR trees were collected, regardless of whether they were associated with ophiostomatoid fungi or not. A relatively high diversity of ophiostomatoid fungi were collected from native trees, ten of which were newly described here. Three further fungal species, two of which are probably new to science, were also collected from exotic Pinus species growing in these forests. Four Ophiostomatales species (including three newly described species) were associated with subcortical beetles on Rapanea melanophloeos and Olea capensis ssp. macrocarpa. These were Sporothrix pallida, Sporothrix aemuluphilus, Raffaelea scabbardiae and Raffaelea rapaneae, associated with the beetles Lanurgus sp. 1, Ctonoxylon sp. 1, Xyleborinus aemuluphilus and a Platypodinae species. This represents a first study to explore the associations between subcortical beetles and ophiostomatoid fungi on native trees in the CFR. In addition to fungi associated with subcortical beetles, several members of the Ophiostomatales associated with wounds on Rapanea melanophloes trees were also collected. These included Ophiostoma stenoceras, Sporothrix reniformis, S. rapaneae, S. lunateae and S. noisomeae. All but O. stenoceras were new to science, and were formally described here. All of these wound-associated species from R. melanophloeos belong to the Sporothrix schenckii – O. stenoceras complex, except for S. noisomeae that was provisionally placed in the S. lignivora complex. Besides fungal taxa collected from wounds on Rapanea melanophloeos, other fungi were also collected from wounds on other host trees species. Three more previously undescribed ophiostomatoid fungal species were collected from this niche. They included Sporothix capensis collected from O. capensis ssp. macrocarpa, Graphilbum roseus collected from many different, unrelated host trees and Graphium ilexiense (Microascales), isolated from wounds on Ilex mitis. The latter represented the first isolation of an ophiostomatoid fungus from this host tree species. Two possibly new fungal species (Sporothrix sp. 1, Ceratocystiopsis sp. 1) and Ophiostoma ips, associated with three bark beetles (Orthotomicus erosus, Hylurgus ligniperda and Hylastes angustatus), were collected from Pinus. Several fungal species were collected from both native trees and non-native trees. These included Sporothrix fusiforme from Brabejum stellatifolium and Acacia mearnsii, O. quercus and O. pluriannulatum-like fungus from several native trees and from A. mearnsii. This suggests a possibility for host shifting of some of these fungi between native and non-native hosts or even between different native hosts. Eight non-ophiostomatoid fungi associated subcortical beetles taxa were found also to infest native trees in the Afromontane forests and in total more than 4500 beetle individuals were collected. Some species of ophiostomatoid fungi collected in this study were found to be associated with other arthropods such as mites. Four phoretic mites species associated with ophiostomatoid fungi (Dendrolaelaps quadrisetus, Histiogaster sp. 3, Elattoma sp. 1 & 2) were collected. In addition, sixteen species of tree wound-associated mites were collected from 12 native trees. Of these, nine were associated with several ophiostomatoid fungi (Graphilbum roseus, O. pluriannulatum-like, O. quercus) that were isolated from several different host trees. This suggests that they may aid in the transport of these fungi from one host species to another. The possible consequences of transfers of Ophiostomatales species between hosts were tested using pathogenicity tests, which highlighted that some fungi are pathogenic on several different trees. Transfers seemed most likely in fungal species isolated from wounds, especially those associated with mites, because the mites may aid in the vectoring of these. When phoretic mites were tested for their specificity to their vector beetles, they proved to be highly specific. Although some of the fungi associated with these mites and their sub-cortical beetles were also pathogenic, it is less likely for these fungi to be transferred to other host tree species due to the high specificity of their arthropod associates. This study represents one of a few studies that focused on ophiostomatoid fungi, subcortical beetles and mites associated with trees in the Afromontane forests of South Africa. Although we collected a high diversity of Ophiostomatales members, many more still await discovery. It is recommended that future studies focus on the complex inter-organismal interactions in many of the systems uncovered in this study. / AFRIKAANSE OPSOMMING: Baie min is bekend oor die diversiteit van fungi wat met die Afromontane woude van die Kaapse Floristiese Streek (KFS) van Suid Afrika geassosieer is. Die ophiostomatoïde fungi sluit baie spesies in, sommiges bekend as patogene in die KFS, terwyl ander bekende en belangrike saprofiete in houtdegradasie is. Hierdie studie het op die biodiversiteit en ekologie van die boom-geassosieerde ophiostomatoïde fungi (Ophiostomatales) in die KFS gefokus. Daarbenewens is myte en subkortikale kewers wat met die KFS bome geassosieer word ook versamel, ongeag of hulle geassosieerd was met ophiostomatoïde fungi of nie. „n Relatief hoë diversiteit van ophiostomatoïde fungi is van inheemse bome versamel, tien waarvan hier nuut beskryf is. Drie verdere fungi spesies, twee waarvan ook waarskynlik nuut is tot die wetenskap, is ook vanaf Pinus spesies versamel wat in hierdie woude gegroei het. Vier Ophiostomatales spesies (insluitend drie nuut beskryfde spesies) wat met subkortikale kewers op Rapanea melanophloeos en Olea capensis L. ssp. macrocarpa geassosieer is, is ook versamel. Hulle was Sporothrix pallida, Sporothrix aemuluphilus, Raffaelea scabbardiae en Raffaelea rapaneae, geassosieer met die kewers Lanurgus sp. 1, Ctonoxylon sp. 1, Xyleborinus aemuluphilus en „n Platypodinae spesie. Hierdie verteenwoordig die eerste studie wat die assosiasies tussen subkortikale kewers en ophiostomatoïde fungi op inheemse bome in die KFS ondersoek. Addisioneel tot fungi geassosieer met die subkortikale kewers, is verskeie lede van die Ophiostomatales vanaf wonde op Rapanea melanophloes bome versamel. Hulle sluit in Ophiostoma stenoceras, Sporothrix reniformis, S. rapaneae, S. lunateae en S. noisomeae. Almal behalwe O. stenoceras was nuut tot die wetenskap, en is hier formeel beskryf. Al hierdie wond-geassosieerde spesies vanaf R. melanophloeos behoort aan die Sporothrix schenckii – O. stenoceras kompleks, behalwe vir S. noisomeae wat voorlopig in die S. lignivora kompleks geplaas is. Benewens fungi taxa wat van die wonde op Rapanea melanophloes versamel is, is ander fungi ook vanaf die wonde op ander gasheer boom spesies versamel. Drie verdere ophiostomatoïde fungus spesies is in hierdie nis versamel. Hulle sluit in Sporothix capensis wat vanaf O. capensis ssp. macrocarpa versamel is, Graphilbum roseus wat vanaf baie verskillende, onverwante gasheer bome versamel is en Graphium ilexiense (Microascales), wat vanaf wonde op Ilex mitis versamel is. Laasgenoemde verteenwoordig die eerste isolasie van „n ophiostomatoïde fungus vanaf hierdie gasheer boom spesie. Twee moontlik nuwe fungus spesies (Sporothrix sp. 1, Ceratocystiopsis sp. 1) en Ophiostoma ips, geassosieer met drie baskewers (Orthotomicus erosus, Hylurgus ligniperda en Hylastes angustatus) is vanaf Pinus versamel. Verskeie fungi spesies is van beide inheemse en nie-inheemse bome versamel. Hulle het Sporothrix fusiforme vanaf Brabejum stellatifolium en Acacia mearnsii, O. quercus en O. pluriannulatum-like fungus vanaf verskeie inheemse bome en vanaf A. mearnsii ingesluit. Dit suggereer die moontlikheid van gasheer-skuiwing van sommige van hierdie fungi tussen inheemse en uitheemse gashere of selfs tussen verskillende inheemse gashere. Agt nie- ophiostomatoïde geassosieerde subkortikale kewers was ook versamel en in totaal is meer as 4500 kewer indiwidue versamel. Sommige ophiostomatoïde fungus spesies wat in hierdie studie versamel is, was met ander geleedpotiges soos myte geassosieer. Vier foretiese myt spesies wat met ophiostomatoïde fungi geassosieer is (Dendrolaelaps quadrisetus, Histiogaster sp. 3, Elattoma sp. 1 & 2), is versamel. Nege addisioneële myt spesies was met verskeie ophiostomatoïde spesies vanaf verskeie boomspesies geassosieer (Graphilbum roseus, O. pluriannulatum-like, O. quercus). Dit suggereer dat myte die vervoer van hierdie fungi van een gasheer spesie na die ander mag bewerkstellig. Die moontlike gevolge van die oordrag van Ophiostomatales spesies tussen gashere is getoets deur patogeniteitstoetse. Dit het beklemtoon dat sommige fungi patogenies is op verskeie onverwante boomspesies. Oordraag van spesies is mees waarskynlik in fungi spesies wat vanaf wonde geisoleer is, veral dié wat met myte geassosieer is, want die myte mag hierdie fungi help vervoer. Toe foretiese myte getoets is vir hulle spesifisiteit tot hulle vektore, is hulle hoogs spesifiek bevind. Alhoewel sommige fungi wat met hierdie myte en hulle geassosieerde kewers geassosieer word wel patogenies is, is dit minder waarskylik dat hulle na ander gasheer bome sal verskuif as gevolg van die hoë spesifisiteit van hulle geleedpotige assosiate. Hierdie studie verteenwoordig een van net enkele studies gefokus op ophiostomatoïde fungi, subkortikale kewers en myte wat met bome van die Afromontane woude van Suid-Afrika geassosieer is. Alhoewel ons „n hoë diversiteit van Ophiotomatale lede versamel het, wag baie meer fungi spesies waarskynlik nog op ontdekking. Daar word voorgestel dat toekomstige studies fokus op die komplekse inter-organismiese interaksies in baie van die sisteme wat in hierdie studie blootgelê is.

Thesis (MScConsEcol)--Stellenbosch University, 1970. / AFRIKAANSE OPSOMMING: Verskeie aspekte van die biologie van die wingerdfilloksera is bestudeer. Die ondergrondse lewensiklus is in spesiale teelbakke waargeneem en die ontwikkelingstydperk van elke stadium word afsonderlik aangegee. Dit is bepaal dat die ontwikkeling van n eier tot n volwasse radicicolae-wyfie gemiddeld 22 dae duur en dat die ontwikkeling van n eier tot n alata gemiddeld 30 dae duur. Die leeftyd en tydperk van eierlegging van n volwasse wyfie asook die aantal eiers wat geproduseer word, word aangegee. Verskillende gegewens wat in verband met oorwintering verkry is, word bespreek. Die tyd van voorkoms van die verskillende stadia van die radicicolae-siklus in die natuur, is bepaal. Die aktiewe · stadium duur vanaf September tot Mei, die oorwinterende stadium vanaf April tot Oktober en nimfe kom voor vanaf November tot April. Met die gegewens verkry, is die aantal generasies per jaar teoreties bepaal. Filloksera is tot op n diepte van 1.2 m in die grond gevind. Daar is vasgestel dat verskillende grondtipes n invloed op die fillokserabesmetting het. Die besmetting neem af soos die persentasie fyn plus medium sandinhoud van n grond styg. Opnames het getoon dat 95% van die wingerde met Jacquez as onderstok in die Stellenbosch-area besmet is en dat ongeveer 25% van alle wingerde in die Olifantsrivier-besproeiingsgebied besmet is. Met behulp van sekere vangapparate is alatae vir die eerste keer in Suid-Afrika in die natuur versamel. Die leeftyd en eierproduksie van alatae en verskillende aspekte van die voorkoms van die galicolae-siklus word bespreek. Twee metodes is toegepas om morfologiese rasse van filloksera·te onderskei. Met behulp van een van die metodes kon verskille tussen die populasies van die twee geografies verskillende areas wat ondersoek is, aangetoon word. / ENGLISH ABSTRACT: None