Theses and Dissertations (Plant and Soil Sciences)

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Spatial patterns of C4 grass-associated fungal endophyte communities
Harris, Mathew Andrew (University of Pretoria, 2025-05)
Foliar fungal endophytes represent ubiquitous and hyper-diverse symbionts of all lineages of plants. However, the factors that shape their diversity and composition from local to global scales has been little explored, relative to charismatic macro-organisms e.g. plants and animals. Additionally, certain regions of the globe have been scantly explored when it comes to micro-organisms in general, e.g. tropical and sub-tropical grassy biomes. This thesis aimed to fill these gaps by exploring the patterns and the factors that shaped the diversity and composition of foliar fungal endophytes associated with C4 grasses, sampled within tropical and sub-tropical grassy biomes at local, continental and international scales. More specifically, I examined whether foliar fungal endophyte diversity of the endophytes associated with two widely distributed and keystone grass species within tropical and sub-tropical regions of the Paleo-tropics followed the classical latitudinal diversity gradient in species richness. I then attempted to link the observed patterns to established macroecological theories commonly used to evoke the latitudinal diversity gradient in species richness for many taxa i.e. the species-energy hypothesis and the evolutionary-time hypothesis. Using this same dataset, I determined which factors drove the turnover of rare to increasingly common endophyte taxa at continental and intercontinental scales, by using a newly proposed zeta diversity framework which explicitly considers the frequency of occurrence and thus a taxa’s rarity or commonness. Lastly, I grew many different C4 grass species in a common garden to remove the effect of variable abiotic conditions and different inoculum sources could have on endophyte communities, to explicitly assess how plant traits effected the diversity and composition of foliar fungal endophytes. My thesis showed that foliar fungal endophytes associated with widespread C4 grass species did follow the classical latitudinal diversity gradient is species richness, and that a combination of energy availability (i.e. high growing season temperatures) and the evolutionary history of the grass hosts (i.e. grass hosts which were present in a location for longer periods of time, in millions of years) generally supported a higher diversity of foliar fungal endophytes. My findings highlighted that different factors shape the turnover or rare to increasingly common endophyte taxa at both the continental and intercontinental scales, with geographic distance being the only consistent driver of endophyte turnover for rare and common endophytes at both spatial scales. Lastly, plant traits, specifically leaf structural traits, had a significant effect on the diversity and composition of foliar fungal endophytes, and are thus important factors to consider for future research. My thesis demonstrated that many different factors shape the diversity and composition of foliar fungal endophytes, and that the factors that shape compositional turnover differ for rare and common endophytes at different spatial scales. Future efforts should be made to assess other macroecological patterns e.g. species-area relationships or distributional patterns of foliar fungal endophytes. This thesis advances our understanding of the factors that shape the diversity and composition of foliar fungal endophytes across different spatial scales, adding value sampling from under-represented tropical and sub-tropical grassy biomes.
Exploring the impact of agricultural practices, temperature, and CO2 on potato health and soil microbiome biodiversity
De Wet, Angelique (University of Pretoria, 2025-03)
Agriculture plays an important role in global food security, but significant challenges, including climate change and land degradation, threaten crop productivity and soil health. Potato (Solanum tuberosum L.) is one of the most important non-grain food crops worldwide. However, production of the crop faces major obstacles due to changing climatic conditions, particularly because of its sensitivity to heat stress. In addition, intensive agricultural practices have led to soil degradation, further reducing crop yields and negatively influencing soil ecosystem functioning. Central to these challenges is the soil microbiome, which plays a vital role in nutrient cycling, disease suppression, and plant resilience against environmental stressors. However, climate change and intensive agricultural practices lead to disruptions in soil microbial communities, posing a threat to soil biodiversity, agroecosystem stability, and long-term crop productivity. This study aimed to explore the complex interactions between climate change factors (elevated temperature and carbon dioxide (CO2) levels), agricultural practices, and the soil microbiome within potato production systems in South Africa. The effect of elevated temperature and CO2 was observed on microbial taxonomic shifts in the potato soil microbiome. Two growth chamber trials were conducted using four temperature-CO2 treatment combinations reflecting projected climatic conditions for South Africa. While alpha diversity remained stable under elevated temperature and CO2 conditions, significant shifts in beta diversity indicated changes in microbial community composition with CO2 as a primary driver. Notably, elevated temperature favoured thermo-tolerant taxa such as Gemmatimonadota and Bacillota, whereas elevated CO2 favoured genera such as Saccharomonospora and Flavobacterium, known for their roles in nutrient cycling and plant growth promotion. A mini-plot trial was conducted to evaluate the effect of different agricultural practices, namely chemical pest control, integrated pest management (IPM), and organic farming, on potato yield, tuber blemish diseases, soil chemistry, and soil microbial diversity. The IPM and organic treatments significantly increased tuber yield compared to the chemical treatment, particularly in the first season. Soil pH and potassium levels increased under the IPM and organic treatments. Soil microbiome analysis revealed that the IPM and organic treatments promoted higher bacterial diversity, whereas the chemical treatment promoted fungal diversity. When comparing the effects of climate change and agricultural practices, climate-induced shifts in microbial community composition emerged as more pronounced compared to shifts caused by agricultural practices. Elevated CO2 levels were identified as a primary driver of microbial communities, indicating that climate change had a stronger influence on the soil microbiome dynamics than the short-term changes induced by agricultural management practices. However, sustainable agricultural practices may be a potential mitigation strategy for climate change by enhancing soil microbial diversity and promoting ecosystem resilience. Notably, beneficial taxa associated with nutrient cycling and disease suppression were enriched under the IPM and organic treatments, suggesting these practices could be a potential buffer against the negative impacts of climate change.
Quantifying the roles of environmental, seasonal, and genome size variation in the expression of medicinally valuable compounds in Helichrysum kraussii Sch.Bip
Boshoff, Willem Hendrik (University of Pretoria, 2025-02)
South Africa is home to a vast array of medicinal plant species. Variations in their secondary metabolomes determine their medicinal potential. Intraspecific variations in these chemical profiles are commonplace and are caused by numerous genetic and environmental factors, including epigenetic modifications, point mutations, whole genome duplication, aneuploidy, topography, soil type, climate, and biotic interactions with herbivores and pollinators. Despite the prevalence of inter- and intrapopulation variation in geno- and phenotypes, its importance in medicinal plant research is often not considered and may influence the robustness of inferences made regarding a species’ medicinal value. The present study first aimed to establish intraspecific variation in the secondary metabolite profiles, antibacterial activity, and genome sizes of Helichrysum kraussii Sch. Bip and second elucidate the effects that geographic isolation and seasonal differences have on these attributes. Plant material was collected from nine populations and two seasons (autumn and summer). Ethanolic extracts were prepared from each of the 93 samples and used in high-performance thin-layer chromatography to evaluate their secondary metabolite profiles. Statistical analyses included principal component analysis (PCA), agglomerative hierarchical clustering (AHC) with bootstrap, and k-means analysis to determine how samples could be grouped based on similarities and differences in their secondary metabolite profiles. Permutational analysis of variance (PERMANOVA) using population, season, and their interaction was performed to determine whether these factors significantly contributed to the clustering of the samples. Partial least squares discriminant analysis was used to elucidate whether samples could be divided into specific chemotypes and which potential compounds contributed most toward their distinction. From the results, it was evident that sample provenance, collection period, and their interaction significantly (p < 0.05) influenced disparities in secondary metabolite profiles. Mantel tests using geographic distance and secondary metabolite profiles revealed that the entire dataset and the autumn subset showed poor correlations, R2 = 0.185, p = 0.263 and R2 = 0.213, p = 0.208, between spatial separation and interpopulation variation in secondary metabolite profiles, respectively. The same analysis on the summer subset indicated a significant negative correlation between population location and secondary metabolite profiles with R2 = -0.396 and p = 0.04. Samples were clustered into two chemotypes with robust support (5-fold validation indicating Q2 = 0.6, and permutation analysis yielding p < 0.01) by Partial Least Squares Discriminant Analysis (PLS-DA). Kaurenoic acid (KA), a ubiquitous secondary metabolite found across numerous plant families with several reported medicinal properties, including antibacterial activity, was present in the extracts, however, concentrations differed amongst the samples and were shown to be significantly influenced by the interaction of season and population by two-way analysis of variance (p < 0.05) but only between five population and season pairs. The antibacterial activity of some samples, as selected based on their cluster assignments, was evaluated against Cutibacterium acnes. The half-maximal inhibitory concentration (IC50) values of these samples ranged between 17.10 ± 4.16 μg/mL and 391.16 ± 15.02 μg/mL, whereas KA exhibited potent (IC50 = 37.94 ± 2.73 μg/mL) antibacterial activity. However, a linear regression model revealed that a poor correlation existed between the samples’ antibacterial activity and KA concentrations, suggesting that a different compound, or set of compounds, was responsible for the observed antibacterial activity. Flow cytometry, conducted using the Mountain Sanctuary Park, Groenkloof, Faerie Glen, Hedianga Farm, and Skuilkrans Kopje populations, indicated the presence of significant interpopulation differences in relative genome size when Pisum sativum L. was used as a standard. No correlation could, however, be found between secondary metabolite profiles and genome size differences. This study concluded that season, population, and their interaction drive interpopulation variation in secondary metabolite profiles in Helichrysum kraussii, but that these factors were not sufficient predictors of variance. The PLS-DA suggested that the H. kraussii samples were better categorised into two clusters, where no pattern regarding the samples’ population and season identity could be discerned. The previous studies on intraspecific variation within medicinal plant species suggest that variation in secondary metabolomes and medicinal activity is not limited to H. kraussii, and it is therefore recommended that medicinal plant research incorporates potential inter- and intrapopulation variation into its methodologies to ensure robust inferences regarding a species’ medicinal value.
The impacts of a hot fire on the population dynamics of Vachellia erioloba
Howard, Joscelyn (University of Pretoria, 2024-03-01)
The Savanna Biome is one of the largest in southern Africa, extending across a wide range of rainfall conditions. A major factor in the occurrence of Savannas in Africa is the presence of fire and herbivory disturbances that influence vegetation structure and enable tree-grass coexistence. The Kalahari is an arid Savanna home to many important and endangered species. Vachellia erioloba is one of those species and is essential to the survival of a range of other plants and animals. The role of fire in arid Savannas has been neglected as fire is considered much rarer in arid Savannas compared to mesic systems. Thus, few studies have focused on the impacts of fire on V. erioloba individuals and populations. Additionally, studies focused on the species’ population dynamics have not always considered the long-term dynamics of this long-lived tree. In September of 2021 a large, intense fire burnt through Benfontein Nature Reserve (BNR) causing many large and old V. erioloba trees to topple and even die. This study was conducted across 1100 ha of Kimberley Thornveld in BNR. Individual, burnt adults were surveyed to determine their survival and resprouting abilities after the fire. Sapling traits and densities were measured and compared between 2003 and 2022 following which, the adult population density was analysed from 1940 to 2023 to understand some of the long-term population dynamics and the impacts of the 2021 fire. Finally, the demographic bottleneck index was determined what limits the growth of this population. I determined that V. erioloba trees are able to survive burning but their strategies change with age from fire tolerance to fire resistance and avoidance. Saplings recovered surprisingly well and fast after burning, with a greater density observed in 2022 than in 2003. The adult population showed little change from 1940 to 2017, but the 2021 fire caused a drastic decline. The population’s demographic bottleneck is at the sapling recruitment to adult stage. Fire, herbivory, frost, rainfall, and competition are considered to be drivers of the demographic bottleneck. This research emphasizes that this species and landscape can be slow to change and if the population is going to recover from the fire, then efforts must be made to reduce restrictions to sapling growth and encourage recruitment to the adult life stage.
Improvement of irrigation efficiency in citrus orchards by lowering dripper emitter delivery rate
Snyman, Christiaan Mauritz (University of Pretoria, 2024-03-01)
Most of the world’s freshwater is used by the agricultural industry, with irrigation of crops being one of the main uses. In water scarce countries, like South Africa, it is important that this water is used sustainably. Citrus is one of the most irrigated fruit crops in South Africa at around 99 000 ha, making it a very large and important water user. The growth of the industry, 35 000 ha increase since 2014, has placed pressure on current water resources and growers are in search of more efficient irrigation methods to maximise the water at their disposal. Drip irrigation has emerged as a very effective method for the irrigation of citrus and recent advances in drip irrigation technology have reduced emitter delivery rates by 70% compared to conventional drip, in an attempt to increase irrigation efficiency by decreasing drainage and increasing water storage in the rootzone. These systems, commonly referred to as low flow drip (LFD), have been widely adopted in the citrus industry with little research on the effects they have on plant and soil water relations and general irrigation management. This study therefore attempted to determine the differences between conventional and LFD irrigation systems in both soil and plant water relations. Furthermore, current FAO-56 crop coefficient values were evaluated with two treatments where a 20% and 40% deficit of crop evapotranspiration (ETc) were applied to test the hypothesis that current crop coefficient values overestimate ETc for low flow drip systems. This was done by a randomised trial design consisting of five treatments in a mature Mandarin orchard (Citrus reticulata cv. ‘Nadorcott’) where treatment 1 (1.6 l h-1), treatment 2 (2.3 l h-1) and treatment 3 (0.7 l h-1) were irrigated with no deficit and treatment 4 and 5 (0.7 l h-1) were irrigated at -20% and -40% of ETc respectively. The results indicated that LFD decreased drainage (D) below the root zone and increased water stored in the root zone, which resulted in an increase in transpiration. When soil water content was evaluated from capacitance probe data the LFD treatments had the highest average water content in the active rootzone, with treatment 3 (0.7 l h-1) at 92% followed by treatment 4 (0.7 l h-1 -20%) and 5 (0.7 l h-1 -40%) at 88%, the conventional drip followed with treatment 2 (2.3 l h-1) at 87% and finally treatment 1 (1.6 l h-1) at 85%, indicating that LFD stored more water higher in the profile. There were also differences in wetted area between treatments, with treatment 2 (2.3 l h-1) creating the smallest wetted area with an average of 51% of the interpolated area having plant available water (VWC > 0.13 cm3 cm 3) compared to treatments 1 (1.6 l h-1) and 3 (0.7 l h-1) with an average of 56% and 59 % of the total area having plant available water (VWC > 0.13 cm3 cm 3) respectively. There were, however, no differences observed in stomatal conductance (gs) and both pre-dawn (Ψpd) and midday stem water potential (Ψsmd) between treatments, with all readings well below the thresholds for stress, indicating that all treatments were well watered at the time of measurements. There were no significant differences in yield and quality between treatments illustrating that LFD is an effective and viable option for citrus irrigation. Furthermore, this also confirms the hypothesis that current FAO-56 values are overestimated for LFD and that it could be reduced between 20-40% with no influence on yield, size and quality in this sub-tropical climate. The final part of this study reviewed irrigation and yield data of Mandarin orchards (Citrus reticulata cv. ‘Nadorcott’) from a wide variety of production areas in South Africa. The main objective was to determine water productivity (WP) benchmark values and to evaluate if there are distinct differences between irrigation methods. No distinct differences were observed between conventional drip and LFD irrigation systems in terms of WP, but there was a noticeable decrease in applied Kc values (season total irrigation ÷ season total ETo) with a reduction in emitter delivery rate, suggesting improved application efficiency. The findings of this study suggest that irrigation water productivity (WPi) for ‘Nadorcott’ in a winter rainfall area is ~ 9.0 kg m-3 and ~ 18 kg m-3 for summer rainfall areas. When the effective rainfall (Pe) was calculated the summer rainfall regions ranged between 60% -80% and the winter rainfall areas between 40%-60%. These values will ultimately impact the applied Kc, as was the case in this study with much lower applied Kc values realised than recommended in FAO-56 for citrus. Due the impact of climatic differences on irrigation requirements, a normalised crop water productivity (WPn) was proposed in this study, which does not only take total water used (TWU) into account but also ETo and the contribution of rainfall to irrigation. Further research is warranted to gain a deeper understanding of and make meaningful comparisons between summer and winter rainfall regions with regards to WPc and the contribution or utilization of rainfall.
Redeveloping an introductory plant sciences course : content, competencies and barriers to change
Roberts, Megan Jennifer (University of Pretoria, 2023-12)
The need to produce well-trained graduates that are capable and competent enough to enter the working world and tackle the problems they will be facing has never been greater. In light of some departmental changes and a national call for the transformation of university curricula, the decision to reform the introductory plant sciences course at the University of Pretoria was taken. The aim was to produce a course that is of an international standard, by aligning the course with the Vision and Change document, but also to ensure the content remains relevant and locally applicable. Using the Delphi Technique, this study aimed to determine broad learning objectives for an introductory plant science course, in terms of content and competencies, based on the opinion of plant science lecturers from top universities around South Africa. The Delphi Technique involves asking a series of questions, over a number of iterations, to a group of experts with the goal of reaching a consensus amongst the experts’ opinions. Secondly, I aimed to explore the potential barriers that could arise throughout the process of implementing curricular changes in an introductory plant science course. Results indicated a clear majority of opinions within the participants with regards to the inclusion of specific areas of content in the curriculum as well as in the inclusion of the process of science as a competency. Results also indicated a clear majority in regard to the purpose of an introductory plant science course being to spark interest in the field rather than instil basic knowledge. The exploration of the potential barriers to change show a number of common themes. The data suggest that the largest barrier to change is found in resistance to change from lecturing staff, followed by meeting specific curriculum and institutional requirements. Limitations to change due to issues around students, such as large classes and under-preparedness are also discussed. Further studies should aim to include industry representatives in the discussion in order to help increase student preparedness in the work place, as well as creating more specific learning objectives for the course.
Phosphonate sensitivity of phytophthora nicotianae in South African citrus orchards and nurseries
Theron, Eloff (University of Pretoria, 2024-01)
The first citrus trees introduced into South Africa were orange seedlings from St. Helena, brought to the Cape by the Dutch East India Company, and planted in the Company’s gardens in 1654. Seven years later, commander Jan van Riebeeck and his wife picked the first oranges from these original trees. By then, numerous other plantings had occurred, including that of 1162 citrus seedlings at Boschheuvel, van Riebeeck’s private estate. However, it was not until 1895 that citrus cultivation in South Africa grew to a commercial scale under the guidance of horticulturists from California, who brought with them the scientifically based methods of the time. In 1907, the first substantial volume of citrus, consisting of 3000 cases, was shipped to England. By, 2022, exports of fresh citrus had grown to 2.6 million tons, making South Africa a world leader and citrus an important asset to the agricultural economy. Citrus trees can have a lifespan of more than a century. During this time, they face a constant barrage of biotic and abiotic challenges. Among these are diseases caused by members of a genus named Phytophthora, which literally means the plant destroyer. Phytophthora species are the most important soil- and water-borne pathogens of citrus and cause a variety of diseases symptoms including, fibrous root rot, crown rot, gummosis, and brown rot of the fruit. The two most important citrus pathogens in this genus are Phytophthora nicotianae and Phytophthora citrophthora. They have been implicated in devastating epidemics on citrus in 19th century Europe. Phytophthora nicotianae is the predominant species in South Africa, with a country-wide distribution, while P. citrophthora is mainly found in the cooler production regions. The management of Phytophthora diseases of citrus involves the use of oomycide chemicals. Ever since the introduction of fosetyl-Al in 1977, phosphonates have formed an integral part of the chemical arsenal against Phytophthora. The name ‘phosphonate’ refers to the esters and salts of phosphonic acid. They have been described as the ideal oomycide due to their ambimobility, complex, multipronged mode of action, persistence in plants yet transient non-toxic nature in the environment, and affordability. It is because of this complex mode of action that phosphonates are considered to be at low risk to resistance development. Despite this, there have recently been reports of reduced phosphonate sensitivity in Phytophthora species, including P. nicotianae and P. citrophthora from citrus. In some instances, this translated into reduced disease control. This is a cause for concern. There is limited knowledge concerning the phosphonate sensitivity of Phytophthora isolates from South African citrus growing areas. To prolong the effective life of phosphonates, resistance management strategies guided by evolutionary principles should be considered. This includes accounting for fitness costs associated with resistance traits. Theoretically, a fitness cost can prevent or slow the development of pesticide resistance, given adequate time between pesticide treatments. Conversely, resistance without a fitness cost will persist, rendering the pesticide permanently ineffective. Therefore, fitness costs have implications for resistance management decisions. Information on fitness costs associated with reduced phosphonate sensitivity in Phytophthora is lacking. Accordingly, the literature review of Chapter 1 summarised the current knowledge on phosphonates as a treatment modality for Phytophthora diseases, with special emphasis placed on citrus and the most relevant Phytophthora species in South Africa. A deeper investigation was carried out into the mode of action of these chemicals and, most importantly, into their current efficacy. Recent reports of reduced phosphonate sensitivity in Phytophthora warranted a discussion of resistance management practices driven by evolutionary principles. Fitness costs associated with resistance and its relevance to resistance management were also discussed in depth. The first experimental work aimed to investigate the phosphonate sensitivity of P. nicotianae isolates from South African citrus production regions, to establish whether phosphonates are still effective at controlling citrus root rot caused by this pathogen. Following the collection and identification of P. nicotianae isolates from citrus growing areas across the country, they were screened for their in vitro sensitivity to potassium- and ammonium phosphite. None were found to be resistant although some had reduced sensitivity, albeit less than previously reported. Furthermore, previous phosphonate exposure did not appear to play a role in the isolate’s phosphonate sensitivity. Subsequently, the efficacy of foliar phosphonate applications against these isolates, was tested on rough lemon seedlings. The phosphonates failed to reduce root rot severity or P. nicotianae concentrations. Although these results could suggest that reduced phosphonate sensitivity has developed in the South African P. nicotianae citrus population, it is unlikely the case. Other factors, such as low root phosphite concentrations, could have led to the observed results. These findings are discussed in detail in Chapter 2. The second aim of the experimental work was to investigate whether reduced phosphonate sensitivity in P. nicotianae was associated with a fitness cost. To this end, the least- and most sensitive isolates from Chapter 2, were compared in vitro and in planta for various measures of fitness. This yielded very little evidence of a fitness cost. However, as these isolates were still comparatively sensitive to phosphonates, the possibility of fitness costs in less sensitive isolates cannot be excluded. Other factors could also have contributed to the observed results. This is discussed fully in Chapter 3. Finally, this thesis is concluded with a summary of the overall findings of this study and possible implications thereof. Suggestions are also made for bettering similar future studies.
Disentangling shifts in the soil microbiome of potatoes infected with Rhizoctonia solani AG 3-PT in two contrasting regions of South Africa
Gush, Sasha-Lee (University of Pretoria, 2024-05-28)
Potato (Solanum tuberosum L.) is a widely consumed and economically important vegetable crop that ensures food security to many communities worldwide. The fungus Rhizoctonia solani AG 3-PT is one of the most devastating pathogens causing several potato diseases in South Africa and globally. The removal of various fungicides from the market and strict regulations on the use of synthetic chemicals makes disease management difficult. Therefore, alternative and environmentally safe control measures, such as biological control agents (BCAs), are being considered to improve the soil and plant health of important crops. Next-Generation Sequencing (NGS) methods, such as amplicon sequencing, enable detailed structural characterisations and possible interactions of the soil microbial communities as a whole, without the need for microbial culturing. The objective of this study was to investigate the changes in soil fungal and bacterial communities in response to R. solani AG 3-PT infection for the identification of key microbial indicators that show potential disease-suppressive activity. To identify key microbial indicators of disease suppression against R. solani AG 3-PT, a greenhouse pot trial experiment was conducted using soil from two contrasting potato production regions in South Africa, namely the KwaZulu-Natal and the Sandveld. High-throughput sequencing of fungal ITS and bacterial 16S rRNA was used to characterize the fungal and bacterial community composition in the soils, respectively, with and without artificial inoculation with R. solani AG 3-PT. Results indicated that the R. solani AG 3-PT caused dysbiosis in the potato soil microbiome in both soils, leading to a shift in the fungal and bacterial community composition. However, soil microbial extracellular enzyme activities revealed that only the KwaZulu-Natal soil exhibited potential functional changes. Furthermore, the results from the disease assessment showed that the KwaZulu-Natal soil showed an overall lower disease index as compared to the Sandveld soil. These findings highlight the fact that the KwaZulu-Natal soil demonstrates a more robust soil microbiome with the potential to suppress R. solani AG 3-PT as compared to the Sandveld soil. Differentially abundant fungal and bacterial taxa in R. solani AG 3-PT inoculated soils suggest a promising potential for disease-suppressive microbial indicators against the pathogen. Network analysis further provided insight into the presence of key microbial taxa involved in the microbial community shifts, which could support their role in the suppression of R. solani AG 3-PT. The utilization of high-throughput amplicon sequencing and advanced bioinformatic methods in this study, shed light on the intricate shifts in the soil microbiome upon R. solani AG 3-PT infection of potatoes. Moreover, this study provides a comprehensive framework for identifying potential disease-suppressive microbes and/or microbial groups against R. solani AG 3-PT that can facilitate future studies investigating potential biocontrol agents. The identification of these key microbial indicators against Rhizoctonia diseases will contribute to the development of environmentally sustainable potato production systems, which are particularly important considering the implementation of the European Green Deal.
The Erythroxylaceae of southern Africa : a metabolomical, genetic and chemotaxonomical evaluation
Alberts, Paul Sewes Frederick (University of Pretoria, 2024-06-01)
The Erythroxylaceae family consists of trees and shrubs sub-divided into four genera, some of which can produce highly valued, or precursors to, medicinal compounds, including atropine, cocaine, tropacocaine and tigloidine, amongst others. Selected species within the Erythroxylum and Nectaropetalum genera are endemic to southern Africa, showing great pharmaceutical potential based on literature reports and their traditional uses. Discrepancies from specific reports regarding the presence of tropane alkaloids initiated a GC-MS-based phytochemical investigation of E. delagoense, E. emarginatum and E. pictum. Results from these investigations showed the presence of atropine, tropacocaine, and the precursors, tropinone and methylecgonine, in selected South African Erythroxylum species, providing clarity to these discrepancies. Moreover, the species with the most pharmaceutical potential based on its tropane alkaloid content, E. emarginatum, was further investigated using plant tissue culture-based tropane alkaloid precursor feeding strategies to determine the potential of upregulating these tropanes in vitro. These experiments, conducted on leaf callus cultures of E. emarginatum revealed the upregulation of tropine, a precursor to tropacocaine and atropine, when tropinone was introduced into the culture media. Morphologically differentiating between the three Erythroxylum species and the two Nectaropetalum species (N. capense and N. zuluense) has proven troublesome. Thus, alternative chemical- (NMR and GC-MS) and molecular (DNA barcoding)-based identification strategies were investigated. These analyses provided species-level resolution on a chemical and molecular basis. The shared morphological characteristics, phytochemical profiles and phylogenetic relatedness to Neotropical cocaine-producing varieties, initiated investigations into the final steps of cocaine biosynthesis in these Old-World species. Results from the comparative Sanger sequencing analyses and enzyme-ligand docking simulations revealed the presence of a highly mutated cocaine synthase gene, the penultimate cocaine biosynthesis enzyme, in all five investigated species. This provided evidence for their inability to biosynthesise cocaine and the first evidence of an evolutionary-related cocaine synthase gene from these Old-World species. The collective results from this PhD thesis emphasise the pharmaceutical potential of the South African coca plants while broadening our understanding of the effect of biosynthetic pathway evolution.
Environmental drivers of Drakensberg grass species distributions at broad and fine scales
McMillan, Bridgette (University of Pretoria, 2023-12)
The Poaceae is an ecologically and economically important plant family worldwide, as grasses are diverse and abundant in many regions and key to a range of ecosystem services. Numerous factors may influence the distribution of grass species, but the relative influence of these factors remains mostly unknown, both at coarse- and fine-scales. The Maloti-Drakensberg Mountain Range is a rugged and topographically complex environment that supports high levels of biodiversity, and is dominated by grassland vegetation. These montane grasslands contain a high diversity of grass species, which, in turn, support many human communities that rely on the region for livestock grazing. In Chapter 1, I (a) identify which environmental variables are related to the distribution of these grass species across broad-scales, (b) test if the different taxonomic, morphological and functional groupings of the grass species differ in the variables related to their distributions, and (c) predict how climate change will impact the distribution of these species. I show that mean temperature of the coldest quarter and precipitation of the wettest quarter were the most important predictors on average for 43 common grass species’ distributions. There were significant differences in the importance of the variables that were included in the final models between grasses that differ in photosynthetic pathways (C3 vs C4) and life forms (perennial vs annual). Future climatic conditions are predicted to reduce the area of suitable habitat for most of the species, with many of the species shifting their distribution ranges to higher elevations. In Chapter 2, I (a) determine which factors are related to the fine-scale cover and occurrence patterns of ten dominant grasses, and (b) determine if the factors influencing these grass species cover and occurrence patterns change with elevation in the Maloti-Drakensberg grasslands. I show that mesotopography and soil depth (both of which are non-climatic environmental variables) were consistently important predictors of the grass species distributions. The importance of the predictors changed with elevation, where at the highest elevation site mesotopography and rock cover were the most important predictors, the mid-elevation site indicated that soil depth was important and the lowest elevation site highlighting soil depth and soil moisture as important predictors. This study highlights the intricate relationships between environmental factors, grass species distributions and their various physiological and ecological classifications. The broad-scale study results emphasized the importance of climatic variables (including measures of temperature and precipitation), in contrast to the fine-scale study where the importance of the non-climatic variables (mesotopography and soil depth) was highlighted. Therefore, this study emphasises the imperative for further research into understanding the intricacies and complexities of the relationships between species distributions and the environment, allowing for the facilitation of well-informed conservations efforts.
Evaluation of the aerial application of micronutrients and adjuvants to citrus orchards
Strydom, Johannes Petrus (University of Pretoria, 2024-03-28)
Large farming operations make use of conventional tractor sprayers that spray high volumes of water. This is done to increase coverage and uptake of the active ingredient that is sprayed. However, time is of the essence to make applications at critical phenological growth stages of the citrus trees in order to make the micronutrient application as effective as possible. Due to the need for timeous applications, large farms make use of aerial applications that are more time efficient with lower volumes of water used. Thus, a trial was initiated in collaboration with Villa Crop Protection and the Citrus Research International (CRI) to evaluate the aerial application of micronutrients, and to test the value of an added adjuvant (Masterlock®) to improve application efficacy and nutrient uptake. An experimental citrus orchard of McClean Valencia’s was selected at Letaba Estates in the Limpopo province, and foliar Zinc (MAX-IN™ ZINC) and Boron (MAX-IN™ BORON) products were applied, as well as a patented product Masterlock®. The MAX-IN™ range consists of a surfactant and humectant to increase leaf uptake of the micronutrient, Masterlock® enhances droplet distribution throughout the canopy, as well as increasing the uptake of applied compounds through the leaf surface. The trial was carried out over two years, with micronutrient applications conducted in September of 2019 and 2020. Leaf analyses to quantify total B and Zn concentrations were conducted on leaf samples before application and two weeks after application. Droplet deposition was quantified by using two methods: 1. Water sensitive paper and 2. Dropsight. Deposition measured throughout the canopy to ascertain the efficacy of Masterlock® to improve distribution and wetting levels of the spray mixture. Fruit set was determined for both seasons as well as fruit size and brix for the 2019 season. The aerial application of micronutrients significantly increased the total foliar nutrient concentration in the leaf. Micronutrients can be used to maintain the micronutrient nutrition status of trees throughout the growing season if multiple aerial or conventional applications aremade. Compared to the producer’s prescribed programme, where products were applied at a much lower concentration, the MAX-IN™ products, applied at a higher concentration were not more effective at increasing the foliar total B and Zn concentration when applied either aerially or conventionally. Both the MAX-IN™ product range and the farm practice were able to iv increase total Zn and B concentrations inside the leaf within the prescribed norms. Masterlock® significantly increased the droplet deposition and total wetted surface area throughout the tree canopy for aerial applications compared to the treatment were no Masterlock® was included. The better distribution throughout the canopy can be explained by an increase in deposition onto the leaf surface. This study conclusively established that aerial application of foliar nutrients such as B and Zn are effective in citrus and can be used successfully. Masterlock® an adjuvant that consist of drift control characteristics and a surfactant will significantly improve the deposition of the spray mixture of aerially applied nutrient mixtures.
Reversing the effect of skin aging using Elegia tectorum (L.F) Moline & H.P. Linder
Radebe, Princess Gugulethu (University of Pretoria, 2021-02-18)
Skin aging is associated with the degradation of the extracellular matrix through increased activity of enzymes such as elastase, collagenase and hyaluronidase. The aim of this study was to investigate the ability of a South African wetland plant, Elegia tectorum to reduce the formation of wrinkles on the skin through the inhibition of elastase and KIAA1199 protein. Elastase inhibition assay was used to screen the plant extracts of E.tectorum made from ethanol, hexane, dichloromethane, ethyl acetate, water, acetone and methanol. The methanolic and ethanolic extracts showed highest anti-elastase activity with an inhibitory concentration (IC50) of 10.93±4.98 and 13.495±1.53 µg/ml respectively. The ethanolic extract, which is a suitable solvent in product development, was selected for further testing. In vitro cytotoxicity was investigated on human colorectal adenocarcinoma cell line (HT-29), the ethanolic extract was found to be not toxic at the highest tested concentration (IC50>400 µg/ml). Furthermore, at non-toxic concentrations (15, 60, and 240 µg/ml), E.tectorum was able to significantly inhibit the KIAA1199 protein. The mutagenic potential of the extract was investigated using Salmonella typhimurium TA98, and was found to be a non-mutagen. Molecular docking was conducted to predict the binding affinity and binding mode of the compounds, identified through GC-MS, to the active site of elastase. Five compounds had the closest docking score to the reference ligand which had a score of -11.64, octadecanoic acid, 9,12,15-octadecatrienoic acid (Z,Z,Z), n-hexanoic acid, 3-(5-methylfuryl)-n-furamidopropionamide, and hexanedioic acid bis(2-ethylhexyl) ester. The docking scores were -6.92, -6.39, -6.20, -5.21, -5.02 respectively. Bio-assay guided fractionation column chromatography was conducted and none of the six pooled fractions were able inhibit elastase, indicating a potential-synergistic activity with two or more compounds within the crude extract. Stability testing of the formulation containing the extract and extract was conducted and parameters such as odour, colour, pH, and viscosity were investigated. The results indicated that the product is stable for a period of two years when stored at temperatures below 40 ºC and away from direct sunlight. In vivo irritancy studies revealed that the plant extract, when applied neat, showed mild irritancy. Elegia tectorum was able to inhibit elastase enzyme and KIAA1199 protein. It is a good candidate as an anti-wrinkle product as it is a non-mutagen, is stable and is a mild irritant. Therefore, this plant has a potential to result in an antiaging product.

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