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Doctoral Degrees (Biological Sciences)

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    Metagenomics assessment of Anthropogenic impact on coral reef-associated microorganisms on the Kenyan Indian Ocean.
    (2020) Wambua, Sammy Musee.; Macdonald, Angus Hector Harold.; De Villiers, Santie.
    The Western Indian Ocean (WIO) is the world’s second richest marine biodiversity hotspot. It is characterized by a diverse range of ecologically and nutritionally rich marine ecosystems that are increasingly under pressure from the impacts of human population growth and coastal development. A comprehensive understanding of variations of marine microbial community composition with environmental conditions is key to understanding and predicting responses to human and climate pressures because microorganisms are the main drivers of biogeographical processes, and they respond and adapt fast to climatic patterns. Also, because unique environments harbour unique microorganisms with unique properties, genomic exploration of marine microorganisms may lead to discovery of novel metabolic processes, and bioactive products with potential for novel biotechnological applications. This project aimed to assess the effect of local anthropogenic impacts on the community structure and the functional potential of microorganisms inhabiting the WIO coral reefs along the Kenyan coast by metagenomics. Reasons for low application of genomics specifically in marine research in the WIO region were examined through literature review and in-depth interviews with scientists in the region. Coral reef seawater and sediment samples were collected, for microbial assessments, along gradients of human impacts and protection regimes. Environmental variables were estimated, and microbial taxonomic and functional diversity analysed by metagenomic approaches. Comparisons were done between sites with differential human impacts, and with oceanic metagenomes from Tara Oceans expedition. Compartmentalised training of marine scientists and lack of collaboration with molecular scientists are key reasons highlighted for poor uptake of genomics in marine research. Significant differences in taxonomic and functional composition were observed between the coral reef and Tara Oceans datasets. Coral reef metagenomes had more diverse and even microbial taxa and gene groups. Tara Oceans metagenomes were enriched with groups of genes of functions in keeping with oligotrophic conditions, and reefs metagenomes with genes for functions related to adaptations to heterogenous environments. E. coli density decreased with increasing degree of protection, but physicochemical and nutrient variables did not differ across coral reefs in the protected coral reefs. Variations in relative abundances of copiotrophic bacteria and coliphages were observed in coral reefs corresponding to magnitude of the neighbouring human impacts. Malindi and Mombasa marine parks, the coral reef sites experiencing degradative human impacts, were significantly enriched with genes for functions suggestive of mitigation of environment perturbations e.g. capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. This study establishes essential baselines for microbiome studies in the WIO region and provides insights to anthropogenic impact on microbial structure and functions, and potential indicators of health status coral reef ecosystems.
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    The micromorphological characterization, histo-phytochemical analysis and bioactivity of Tabernaemontana ventricosa Hochst. ex A. DC. (Apocynaceae)
    (2021) Naidoo, Clarissa Marcelle.; Naidoo , Yougasphree.; Dewir, Yaser Hassan.; Singh, Moganavelli.
    Medicinal plants are universally important due to their healing properties and pharmacological effects. Tabernaemontana ventricosa Hochst. ex A. DC. is a curative plant belonging to the Apocynaceae. The bark, stem, leaves, flowers, and latex of T. ventricosa are frequently used in ethnomedicine to palliate fever, treat wounds, and reduce high blood pressure. Due to the inconsistencies in the interpretation of specialized secretory structures within the Apocynaceae, the current study aimed to distinguish, for the first time, the type and distribution of the laticifers in the embryos, seedlings, and adult plants of T. ventricosa. Various microscopy techniques such as light microscopy, stereomicroscopy, fluorescence microscopy, Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM) were used for anatomical and morphological analysis. The histochemical, phytochemical, and biological activities (antibacterial, antioxidant, and cytotoxicity) were assessed using screening standard protocols. Moreover, Gas Chromatography-Mass Spectrometry (GC-MS) was conducted to identify the chemical composition of leaf, stem, and latex extracted with various solvents. Silver nanoparticles (AgNPs) were synthesized using various leaf, stem, and latex extracts. The AgNPs were characterized using UV-visible spectral analysis, Elemental Dispersive X-ray (EDX) spectroscopy, Fourier-Transform Infrared (FTIR) spectroscopy, Nanoparticle Tracking Analysis (NTA), and various microscopy methods. Additionally, AgNPs were evaluated for their biological activity using antibacterial and cytotoxicity assays. The current study indicated the presence of articulated anastomosing laticifers. The laticifers were found to have originated from ground meristematic and procambium cells and were randomly distributed in all ground and vascular tissue, displaying complex branching conformations. The presence of chemical constituents within the laticifers and latex revealed alkaloids, phenolics, neutral lipids, terpenoids, mucilage, pectin, resin acids, carboxylated polysaccharides, lipophilic and hydrophilic substances, and proteins. The GC-MS analysis revealed α-linolenic acid, pentadecanoic acid, α-d-mannofuranoside, methyl, 13-docosenamide, (Z)-, 9,12-octadecadienoic acid (Z,Z)-, lup-20(29)-en-3-ol, acetate, (3ꞵ), 9,19-cyclolanost-24-en-3-ol, (3ꞵ) and ꞵ-amyrin as significant components of the leaf, stem, and latex extracts. It is suggested that these major compounds are responsible for the considerable antibacterial, antioxidant, and cytotoxic activities of T. ventricosa extracts. Biologically synthesized AgNPs displayed a spherical, ovate, and triangular shape ranging from 4-80 nm across all treatments. The FTIR analysis showed that alcohols, carboxylic acids, phenolics, and alkanes are possibly responsible for the capping of silver (Ag) ions, and the NTA data suggests that synthesized AgNPs fluctuated from stable to unable particles, which was treatment dependent. Due to the outcomes of biologically active compounds produced by this species, further studies are necessary to establish the potential medicinal properties of T. ventricosa.
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    Cathodic water invigoration of deteriorated orthodox seeds – implications on subsequent plant growth.
    (2020) Fatokun, Kayode.; Beckett, Pichard Peter.; Varghese, Boby.; Pammenter, Norman William.
    Orthodox seeds deteriorate even when kept under the best of conditions leading to loss of germination, poor seedling growth. In this study, a novel approach via the use of cathodic water, an electrolysed form of calcium magnesium solution, was used to invigorate fresh and controlled deteriorated seeds of wild (Bolusanthus speciosus (Bolus) Harms, Combretum erythrophyllum (Burch.) Sond., Erythrina caffra Thumb.) and agricultural (Pisum sativum L., Cucurbita pepo L.) species. Other treatment solutions investigated alongside cathodic water were un-electrolysed calcium-magnesium solution and deionized water. Fresh seeds of the test species were controlled deteriorated to 50% germination (P50) at 40°C and 100% relative humidity. Thereafter, the seeds were invigorated with the treatment solutions. Fresh and un-primed controlled deteriorated seeds served as the control. In addition, to study the mechanism of invigoration, the effects of priming on the membrane stability index (MSI), amylase activities, lipid peroxidation products malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE) were investigated. The effects of priming on the reactive oxygen species (ROS) scavenging enzymes superoxide dismutase, and catalase and DNA (concentration and purity). All priming treatments improved germination, emergence, growth parameters and subsequent seedling photosynthesis relative to the unprimed seeds. In general, cathodic water was most effective at invigorating seeds in the all test species. Also, controlled deteriorated seeds benefitted more than the fresh seeds treatments. Analyses of the lipid peroxidation products and antioxidant enzyme activities in invigorated seeds provided support for the hypothesis that the effectiveness of cathodic water in the invigoration of debilitated orthodox seeds derive from its ability to act as a potent antioxidant. This study, which is a novel approach at bringing the concept of electrochemistry into germplasm conservation via the use of cathodic water, has also confirmed the efficacy of cathodic water in invigorating debilitated seeds. This is especially critical for seeds containing traits that may be under the threat of being lost due to various reasons. The current study reinforces the strong potential of cathodic water in the recovery of aged germplasm and improved yield of orthodox seeded species.
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    Influence of human-associated tsetse habitat degradation on tsetse fly (Diptera: Glossinidae) populations and prevalence of infection with trypanosomes in North-Eastern Zambia.
    (2021) Chilongo, Kallinga.; Mukaratirwa, Samson.
    African trypanosomiasis is among the most important parasitic diseases of livestock and humans caused by several species of trypanosomes, and the disease occurs in 36 countries in sub-Saharan Africa. Human African Trypanosomiasis (HAT) causes a considerable public health burden on rural populations, and Animal African Trypanosomiasis (AAT) is an important constraint to livestock production and full utilization of land for agricultural production, such that if not controlled the disease can induce important losses through limiting crop production and access to land, and diminishing income from meat, milk and other livestock products, consequently resulting in poverty. In Zambia, approximately 40% of the country’s land is tsetse-infested and the infestation in the Luangwa valley is among the most important with respect to occurrence of both human and animal trypanosomiais. In affected areas, occurrence of trypanosomiasis in humans and in livestock normally correlates with the prevalence of trypanosome infection in tsetse flies. Laboratory studies have shown that among the major factors that affect such trypanosome infection in tsetse flies, is occurrence of stress in tsetse flies. Occurrence of stress in wild tsetse fly populations is associated with unfavourable environmental conditions for the flies, and this is usually a consequence of tsetse habitat degradation. In many parts of Zambia’s eastern tsetse belt, human-associated degradation of the tsetse habitat has been on the increase over the last decades. This suggests that research to determine the effects of such human-associated tsetse habitat degradation, on tsetse populations and prevalence of trypanosome infection in the tsetse population in the area, could provide some insights into the epidemiology of trypanosomiasis in the area. In this study undertaken in three sites, Mpika, Lundazi and Rufunsa sites, in north-eastern Zambia (in parts of the eastern tsetse belt), the objectives were, to determine and measure (i) variation in size, age and hunger stages in tsetse flies and (ii) variation in prevalence of trypanosome infection in the tsetse flies, with increase in distance away from the edge into the inner parts of tsetse belt, and in relation to the distribution of human settlements; and (iii) to detect, assess and evaluate the contribution and importance of existing agricultural and other forms of ecosystem utilization, to tsetse-habitat degradation in the three sites. Three study sites were selected based on level and pattern of human settlement, i.e. Mpika and Rufunsa sites with human settlement concentrated at or close to the edge of the tsetse belt, and Lundazi site with human settlement evenly distributed from the edge into the innermost parts of the tsetse belt. Samples of two species of tsetse flies found in the sample sites, i.e. Glossina morsitans morsitans and G. pallidipes, were collected and (i) size, age and hunger stage in the tsetse flies were recorded and assessed with reference to distance away from the edge of the tsetse belt; (ii) variation in prevalence of trypanosome infection in the tsetse population in the study sites, with reference to distance away from the edge of the tsetse belt, and in relation to distribution of human settlements; and (ii) key land-use and socioeconomic factors in the human settlements, with reference to human-associated tsetse habitat degradation in the study sites. Trapping of the tsetse flies was done in defined sample points, identified with use of a Global Position System (GPS) unit, in the transect line, with use of the Black-screen fly round (BFR) and Epsilon traps. From the sampled flies, the following were recorded; species of fly, sex, body size, age and hunger stage (as indicators of levels of occurrence of stress), and screening for trypanosome infection using microscopy and the loop-mediated isothermal amplification (LAMP). A semi-structured questionnaire was administered in each of the settlements within our study location, and national land cover maps for the years 2000 and 2010, produced by the country’s Forest Department, were used to estimate vegetation cover change during the period 2000 to 2010 in each of the sites. Regression models were applied to determine and measure the level of association of the distance from the edge into the inner parts of the tsetse belt with; size, age and hunger stages of tsetse samples, and prevalence of trypanosome infection in the tsetse flies. In each settlement, data were collected on key land-use and socio-economic factors that may be linked to human-associated habitat degradation and changes in the vegetation cover during the period 2000 and 2010, was calculated in QGIS. The results showed that in the Mpika and Rufunsa sites, the number of Glossina morsitans morsitans tsetse flies caught increased along with the increase in distance from the edge into the inner parts of the tsetse belt. This was also associated with increase in the body size (p < 0.0001 in both sites), and reduction in the age (p < 0.001 in each site) and the hunger stages (p < 0.0001 in both sites), and reduction in the prevalence of trypanosome infection (p = 0.024 and p = 0.012 in the case of all sub-species of trypanosomes tested for in the Mpika and Rufunsa sites respectively; and p = 0.013 and p = 0.025 in the case of only nannomonas sub-species in the two sites, respectively). The level of vegetation cover change was insignificant in each of the sites, such that it was unlikely to have had any significant impact on the quality of the tsetse habitat in each of the sites. In the Mpika and Rufunsa sites, human activities associated with access to resources might have had significant effect on the distribution of wild mammals that served as tsetse hosts in the area, such that numbers (of wild mammals) were low in locations that were close to the settlements and high in locations that were furthest from the settlements – giving rise to a gradient of increasing levels of availability of tsetse hosts with increase in distance away from the human settlements. This same trend was observed with regard to the distribution of body size of the flies, age, hunger stages, and prevalence of nannomonas and trypanozoon trypanosome infection, in G. m. morsitans in the Mpika and Rufunsa sites. This was indication that (in the Mpika and Rufunsa sites) increase in the levels of availability of tsetse hosts was associated with increase in levels of tsetse wellbeing – in turn associated with increase in levels of tsetse habitat quality. With regard to the findings in the Lundazi site (where human settlement was evenly distributed in transect line), the absence of any such variation (in each of the respective attributes in G. m. morsitans) with distance from the edge of the belt, could be taken as supportive to the reason indicated above as the likely basis for the existence of a gradient of reducing levels of tsetse habitat degradation in the Mpika and Rufunsa sites. In the case of G. pallidipes, the results showed no variation in the respective features in the tsetse flies, with increase in distance from the edge of the tsetse belt, and factors such as the relatively fewer numbers of the species caught, and a large proportion of the transect length not having registered any catch of the species, in each site in the study, likely contributed to this outcome.
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    Concurrent spatiotemporal ecology of African lions and spotted hyenas and the potential for inter- and intraspecific interactions in semi-arid and wetland ecosystems.
    (2022) Barker, Nancy Ann.; Slotow, Robert Hugh.
    Intraguild interactions among apex predators can potentially influence carnivore population densities and distribution, which may have profound effects on trophic processes within ecosystems. Coexisting carnivores are able to mitigate such interactions through behavioural mechanisms that promote spatiotemporal separation. Despite increasing research which highlights the occurrence and prevalence of competitive interactions between African lions (Panthera leo) and spotted hyenas (Crocuta crocuta), studies that incorporate the effects of such interactions on lion and hyena space use patterns are limited. Interactions among sympatric carnivores reveal how predators utilize spatial and temporal partitioning strategies within jointly used areas, and elucidate the spatiotemporal patterns enabling species coexistence between them. Thus, an understanding of how inter- and intragroup interactions drives the movement responses of apex predators has important implications for the structure and function of large carnivore communities, and their conservation. We used remote tracking data to investigate aspects of the ecology and behaviour of lions and spotted hyenas, with an emphasis on the spatiotemporal patterns among coexisting populations. Both lions and spotted hyenas mediated the potential for interference competition through subtle differences in temporal activity, fine-scale habitat use differentiation, and localized reactive-avoidance behaviours. Recursivity to, and duration of time at, locales of high competitor probabilities, were similar among female lions and both sexes of hyenas, but different for male lions. Our findings of lion space-use patterns across arid and mesic environments indicated the seasonal influences of competitive interactions with competitors (spotted hyenas), in that lions selected for, and chose to move through areas with a lower probability of competitors during the dry season. Dyadic interactions among lions and spotted hyenas illuminates how hyenas effectively reduced their potential of interactions with lions by utilizing spatiotemporal partitioning strategies and local reactive avoidance behaviours within shared space use areas. Quantifying the types of movement behaviour between competitors highlights the type of interaction occurring in a dyad and enhances our understanding of the potential effects of interspecific interactions among large carnivore space-use patterns within an apex predator system. Both lions and spotted hyenas exploit different behavioural strategies resulting in fine-scale spatiotemporal segregation among shared space-use areas enabling the two species to co-exist, and show adaptability across heterogeneous and homogeneous environments. Such findings are essential in understanding the behavioural choices made by members of a guild that subsequently affects population dynamics and community structure of multi-species food networks.
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    The secretory scales and medicinal properties of combretum erythrophyllum.
    (2021) Bantho, Sahejna.; Naidoo, Yougasphree.; Yaser , Hassan Dewir.; Singh, Moganavelli.
    Medicinal plants are known to contain phytometabolites that could effectively improve an individual’s state of health. Species of Combretum are highly valued in Africa due to the plethora of their traditional medicinal uses. Combretum erythrophyllum. Burch. Sond., commonly known as the river bushwillow, is known to contain medicinally important phytometabolites. Traditionally, the foliage is used to treat venereal diseases and abdominal pain, whilst the bark is used to alleviate sores, infertility, and labour pains. Although C. erythrophyllum has numerous traditional medicinal uses, there is limited scientific knowledge on the micromorphological structures and the associated exudate. Thus, this study aimed to characterize the micromorphological features of leaf and stembark secretory apparatus of C. erythrophyllum, using light and electron microscopy. Furthermore, a histo-phytochemical analysis was conducted to determine the presence and localization of phytometabolites within the trichomes and exudate. The antioxidant, antibacterial, apoptotic and cytotoxic potential of the leaf and stembark extracts were also evaluated. The micromorphological analysis identified the presence of peltate scales and non- glandular trichomes across surfaces. Peltate scales were comprised of a sunken basal cell, bicellular stalk, and a multicellular head. Head cell count appeared to increase upon leaf maturation. The granulocrine pathway was identified as a possible mode of secretion for C. erythrophyllum due to the extensive presence of vesicles, vacuoles, and electron dense material within the peltate scales. Preliminary histo-phytochemical analyses revealed the presence of carbohydrates, sterols, lipids, phenolic compounds, total proteins, alkaloids, and essential oils. Thin-layer chromatography allowed for the visualization of 36 compound classes while gas chromatography-mass spectrometry showed 266 compounds present. Fourier-transform infrared spectroscopy analysis confirmed the presence of phenols, alkenes, amines, alcohols, and esters among many. The antioxidant ability of the generated extracts were evaluated using the 2,2- diphenyl-1-picryl-hydrazyl-hydrate antioxidant assay and Ferric Reducing Antioxidant Power assay. A positive correlation between % inhibition and extract concentrations, was noted in both. In both instances, the methanol stembark extracts performed the best, (Leaf- 5,2866 and Stembark- 4,2866 μg/mL). Furthermore, the results obtained from the total flavonoid assay correlated with the trend observed through the total phenolic assay, whereby methanolic extracts yielded most promising results. Additionally, this study aimed to generate silver nanoparticles using crude extracts. A novel protocol for the synthesis of silver nanoparticles (AgNPs) using the leaf and stembark extracts of C. erythrophyllum was established. The generated AgNPs were characterized and evaluated for its potential antibacterial activity. Methanolic extracts inhibited the growth of Pseudomonas aeruginosa, Bacillus subtilis, Methicillin Resistant Staphylococcus aureus, and Staphylococcus aureus. Lastly, the generated crude extracts displayed promising results when evaluated for their cytotoxic and apoptotic abilities however upon nanoencapsulation the cytotoxic and apoptotic capabilities increased significantly. In correlation with the above, the AgNPs appeared to intensify the overall inhibition activity. Based on the findings of the study, Combretum erythrophyllum has a reservoir of unexplored allopathic potential which could revolutionize the medicinal world.
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    Alleviating delayed field curing-induced deterioration in rice seeds by cathodic water invigoration: a comparison of seed and seedling responses in two upland rice species and their interspecific hybrid.
    (2021) Bam, Raphael Kwame.; Varghese, Boby.; Naidoo, Sershen.; Pammenter, Norman William.
    Rice constitutes the major source of the world’s food supply. A number of varieties are grown in many parts of the world, all which produce orthodox seeds that are usually stored between growing seasons. As in other crop species, storage-induced loss of seed quality (viability and vigour) is inevitable but considerable research effort has been invested in optimising seed bank storage protocols for rice to ensure acceptably high levels of seed germinability and seedling emergence. However, poor post-harvest practices such as delayed field curing before threshing in developing countries in the humid tropics, such as Ghana, result in curing-induced seed deterioration in the field prior to ex situ storage. Given that many rice growing regions are likely to experience significant levels of climate change, seed processing and storage induced declines in rice seed quality could exacerbate the crop losses incurred by rice farmers in these regions in the future. This motivated the present study which was designed around three aims: 1) to investigate how environmental conditions and the duration of field curing influenced seed macro-structural integrity, susceptibility to microbial infection, and seed germinability and vigour; 2) to identify macro-structural and ultrastructural indicators/ biomarkers of field curing and associated storage-induced stress/ damage; 3) to assess whether the invigoration of field-cured seeds with cathodic water (CW), an established antioxidant-based seed invigoration medium, and deionized water (DW) can alleviate the deteriorative effects of delayed field curing on rice seed cellular integrity, germination and subsequent seedling growth and biomass. The specific objectives of this comparative study, which involved an Asian (Oryza sativa L.) and African (Oryza glaberrima Steud) upland rice species and their interspecific hybrid (O. sativa × O. glaberrima), were as follows: a) to compare the impacts of delayed field curing in wet and dry environments on seed physical, physiological and pathological quality; b) to identify potential ultrastructural biomarkers of seed sensitivity to delayed field curing-induced stress/ damage in embryonic root meristematic cells using transmission electron microscopy (TEM); c) to assess whether CW invigoration alleviates cellular stress/ damage induced by delayed field curing using selected ultrastructural biomarkers of seed sensitivity to such curing-induced stress/ damage; and d) to assess whether invigoration with CW and DW improves seed germinability and emergence, and subsequent plant growth in field cured seeds, relative to non-invigorated (NI) dry seeds. For objective (a), seeds of both species and their interspecific hybrid were grown in Ghana, harvested, field cured in open (wet) and within ventilated rainproof containers (dry) for five weeks. Harvested panicles were sampled from the wet and dry cured environments at weekly intervals for 5 weeks, hand threshed, and depending on the moisture content (MC) at sampling, seed samples were further dried to 12% and stored hermetically at 4°C until used. Sub-samples of both species and the hybrid from the weekly samples were used for seed microflora studies and germination assay. Environmental parameters (temperature and relative humidity) were measured in wet (weather station) and dry (tiny tag data loggers) cured environments. Seed samples of both species and hybrid were taken daily from wet and dry cured environments at 08h00 and 15h00 during the 5 week period, equilibrated overnight at 20°C for seed MC and water activity measurements. Sub-samples of seed samples of both species and hybrid taken daily at 08h00 from the wet and dry cured environments were used to measure percentage of seeds with cracked endosperm. Results revealed that dry field curing delayed endospermic cracking and reduced crack frequency (10% in O. sativa; 40% in O. glaberrima; 36% in the hybrid), enhanced subsequent seed germinability (2%), and reduced subsequent seedling vigour (radicle length, 37%; seedling dry weight, 11%) relative to wet cured seeds across both species and hybrid. However, fungal infection was higher (22%) in dry than wet cured seeds: seeds infected with fungal species (e.g., Aspergillus flavus, Bipolaris oryzae, Curvularia lunata, Fusarium moniliforme and Phoma sp) was higher in dry cured O. sativa (22%) and the hybrid (31%) than the wet cured seeds. Seed germinability and seedling vigour declined with delayed field curing, but the decline was higher in the hybrid than in both species. For objective (b), seeds of both species and their interspecific hybrid field cured for different durations (0, 2 and 5 weeks) and hermetically stored at 4°C for 20 months were removed from storage, equilibrated overnight at 25°C and invigorated with DW for 18 h. Untreated dry (nonimbibed seeds, cured for different durations (0, 2 and 5 weeks) were used as the controls for this study. These controls were used for two reasons: 1) to establish whether ultrastructural abnormalities induced by curing are permanent or can be reversed/ repaired during imbibition; 2) to establish whether seed deterioration during curing leads to imbibitional damage. The severity of ultrastructural lesions related to cellular stress/ damage differed across species and the hybrid and progressed at a rate in agreement with the viability and vigour loss brought about by delayed field curing. These microscopy studies also served to identify useful ultrastructural biomarkers of field curing induced cellular stress/ damage in both rice species and the hybrid. These include marked abnormalities in cell wall and key organelle [nucleus (N), nucleolus (nu), mitochondria (M), lipids, vacuoles, plastids and amyloplasts] ultrastructural integrity with delayed field curing. This study suggests that these biomarkers may serve as useful screening tools for rice breeders looking to identify species/ varieties that produce seeds that are more resistant to field curing-induced deterioration. For objective (c), seeds of both species and their interspecific hybrid were field cured for different durations (0, 2 and 5 weeks), stored hermetically and removed from storage and equilibrated as in the experiment for objective (b). However, in the experiment designed to address this objective, seeds of both species and hybrid cured for different durations (0, 2 and 5 weeks) were invigorated with CW and DW for 18 h before comparing their ability to alleviate the effects of field curing induced cellular stress/ damage in terms of the ultrastructural biomarkers of such stress/ damage identified via objective (b). Seed germinability was significantly higher in CW invigorated 5 week cured seeds of both species and 2 and 5 week cured seeds of the hybrid than DW invigorated seeds suggesting that CW invigoration was more effective in alleviating curing-induced stress/ damage. Ultrastructural studies showed that CW invigoration of cured seeds of both species and hybrid appears to have enhanced the repair of damaged cellular components and/ or reduced the damage that ensues during imbibition in the deteriorated seed. More importantly, seeds subjected to CW invigoration exhibited more prominent signs [e.g., M exhibited elongated profile, homogenous matrix, well-differentiated cristae (Cr), and well-defined outer mitochondrial membrane (OM) and inner mitochondrial membrane (IM), and highly developed Golgi bodies (G)] of repair and germinative metabolism than those imbibed with DW. Interestingly, the degree of mitochondrial and G development in CW invigorated seeds was greater in the hybrid than the two species. The results obtained for these biomarkers indicated that CW invigoration can alleviate the cellular stress/ damaged induced by field curing and also point to superior restorative effects of CW on viability, vigour and cellular integrity and metabolism in cured seeds compared with DW. For objective (d), endosperm integrity (i.e., nature/severity of physical damage to endosperm, caryopsis coat thickness, and presence of seed microflora) of stored (4°C for 20 months) NI seeds of both species and their interspecific was assessed using scanning electron microscopy (SEM). Seeds of both species and the hybrid stored for the same duration as in the SEM studies were also equilibrated overnight at 25°C and invigorated for 18 h in CW and DW before being sown in individual pots under greenhouse conditions. Untreated dry seeds, cured for different durations were used as the controls for this study. The uncured seeds (0 week) of both species and the hybrid did not exhibit macro-structural damage; however, 5 week-cured seeds exhibited deep cracks which exposed the aleurone cells (grains and lipid bodies) and facilitated fungal infection and insect damage which may have contributed to viability and vigour loss in cured seeds. Cathodic water invigoration significantly enhanced seedling emergence (17% in 5 week cured O. sativa; 23% in 5 week cured O. glaberrima; 16 and 19% in 2 and 5 week cured hybrid, respectively) in field cured seeds of both species and the hybrid than DW invigoration. Also, CW invigoration significantly produced taller seedlings in CW invigorated cured (2 and 5 weeks) seeds of both species and the hybrid than DW invigorated seeds. Across both species and hybrid, CW enhanced panicle biomass, although differences between CW and DW were not always significant. The invigorative effect of CW on plant growth from cured seeds was generally not observed in terms of total biomass yield and changes in biomass allocation to stem, leaves, and roots. Overall, the study has deepened our understanding of the physical, pathological, physiological, and ultrastructural lesions that contribute to loss of rice seed quality (seed viability and vigour) during delayed field curing. It has also served to identify a number of seed physiological, ultrastructural, and macro-structural biomarkers/ indicators that can be used by breeders for screening rice varieties for sensitivity/ tolerance to field curing. The results have also provided a basis for many new opportunities for research on alleviating seed processing- and storage - induced deterioration in crop seed quality through seed soaking/ invigoration treatments (particularly those involving CW and other antioxidant-based solutions), which is going to represent an increasingly important research area as the effects of climate change and developmental challenges threaten food security in many parts of the world. However, future studies must screen a larger number of rice genotypes to assess the plasticity of the biomarkers identified to be reliable indicators of curing-induced stress and stress recovery before they are adopted by the seed industry. Additionally, future studies must use biochemical, physiological, molecular, omic and biophysical approaches to fully understand the mechanism(s) of action of CW invigoration in deteriorated rice seed in order to extend this method to other crop species that experience a decline in seed quality during seed processing and or storage.
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    Towards understanding alien floristics within an urban matrix: the case of Durban, South Africa.
    (2021) Appalasamy, Minoli.; Ramdhani, Syd.; Naidoo, Sershen.
    Invasive alien plant species (IAPs) represent a major threat to biodiversity loss and ecosystem functioning globally. Alien species can take advantage of changes in ecosystems brought about by natural and non-natural disturbances and compete with indigenous species for resources. Urban areas are becoming increasingly susceptible to plant invasions due to increasing anthropogenic activity levels as urban human populations increase and changing climatic conditions that favour alien species. If uncontrolled, IAP impacts can bring about the transformation of natural habitats and exclusion of indigenous species. Given the limited financial and human resources available for IAP monitoring and control in developing countries like South Africa, increased efforts to monitor the prevalence of IAPs more efficiently and identify the drivers of invasiveness within cities is urgently needed to prioritise urban green spaces and species for monitoring and control interventions. Frameworks to monitor alien invasions, identify their drivers and impacts and prioritise sites and species for control of alien plants have been limited in the urban context, particularly within developing countries such as South Africa. Where these frameworks have been developed, there are challenges of them not being equally effective at different geographic scales and across different habitats. Furthermore, these frameworks often also suffer the weakness of not capturing the multi-dimensionality of plant invasiveness. This inspired the current study, which aimed to inform the design of an evidence-based framework that aids in prioritising urban green spaces and alien species for monitoring and control interventions by carrying out a set of inter-related investigations that addressed the following research questions: (1) What are the major environmental drivers of alien species (particularly IAPs) distribution? (2) Are alien and indigenous plant functional diversity (FD) and alien-indigenous co-occurrence patterns influenced by non-natural disturbance? (3) What is the influence of non-natural disturbance on the alien and indigenous soil seed bank (SB) floristics? and (4) Can selected seed physical and/or chemical traits be used as potential indicators of IAP persistence in natural SBs? These research questions were addressed using a case study approach: plants occurring within selected natural green spaces in an urban matrix in the rapidly developing city of Durban (eThekwini Metropolitan Area [EMA]), located within the Maputaland-Pondoland-Albany biodiversity hotspot in subtropical KwaZulu-Natal, South Africa. Classical vegetation survey techniques were used to identify and quantify (in terms of richness, density and diversity) aliens within 30 natural green spaces in the study area. Levels of non-natural disturbance were quantified using a scoring matrix, and soil SB samples were collected from each site. Cumulatively, 80 alien plant species were identified, of which 35 are presently categorised as IAPs in the EMA. Once it was established that IAP species richness and density were significantly positively related to disturbance level, selected parameters measured (viz. alien species richness and density) were used to develop an Alien Invasive Index (AII), the utility of which was validated in terms of its ability to discriminate between sites with low and high levels of invasiveness. The findings demonstrate the value of integrating the data generated using vegetation surveys and Geographic Information Systems to monitor and prioritise urban green spaces for alien control interventions. Importantly, the results suggest that the AII could assist in identifying invasive plant hotspots within urban areas. In a related study, alien and indigenous floristic patterns were probed further by comparing alien and indigenous species richness, density, diversity (alpha and functional), and species co-occurrence levels at the 30 sites in relation to non-natural disturbance levels. The ratio of alien to indigenous species was 1:1.5, with Asteraceae being the most dominant family. The relationship between species richness and alpha diversity differed for alien and indigenous species. Alien species were found to have higher FD, except for reproductive mode. Additionally, FD was significantly related to disturbance levels, alien species richness, and alien plant density. Co-occurrence data showed that alien-indigenous species pairs cooccur at high levels in urban spaces. Three notable alien-indigenous pairs (Centella asiatica- Conyza sumatrensis, Centella asiatica-Solanum mauritianum and Bidens pilosa-Commelina erecta) co-occurred at more than 40% of sites, while two alien-alien pairs (Solanum mauritianum-Lantana camara and Conyza sumatrensis-Tagetes minuata) co-occurred at more than 50% of sites. The positive interactions between different alien species identified here contribute to the growing amount of evidence that supports the Invasional Meltdown Hypothesis (IMH). The results also showed that non-natural disturbance might lead to high levels of alien plant species diversity and facilitatory alien-alien and alien-indigenous species interactions. Understanding co-occurrence patterns could help design alien control programmes that focus on reducing alien-alien facilitation. For the study examining alien and indigenous species soil SBs in relation to nonnatural disturbance across the 30 sites, samples collected were processed using a modified seedling emergence method, incubated under greenhouse conditions (with irrigation), and monitored for one year. Germinants were identified and quantified, and comparisons were made between the soil SB and standing vegetation (SV). Cumulatively, 70 species belonging to 20 families were identified within the SB, with a higher presence of indigenous (60%) than alien species (40%). Overall, the SB flora was dominated by graminoids. Of the 70 species found in the SB, 69 were shared with the SV. Irrespective of the disturbance level, indigenous was higher than alien plant density within the SB. The findings of this study have implications for managers of urban green spaces since alien species in SBs could exploit niches created by disturbances, promoting urban invasions. In the final investigation, seeds of five IAPs were buried for two years at an experimental site to mimic seed burial within natural SBs. Additionally, the seeds of these species were characterised in terms of selected morphological and anatomical (seed mass, seed size, seed coat thickness) and chemical traits (estimated lipid content and changes in lipid melting properties). This study was designed to assess whether seed physical and/or chemical traits can be used as potential indicators of IAP persistence in natural SBs. Batches of buried seeds were exhumed every three/six months for viability (germinated seeds + seeds that stained positively following a Tetrazolium Chloride Test). Seed mass, size and coat thickness differed significantly across species, with Canna indica having the biggest and heaviest seeds of all species and the thickest seed coat. Solanum mauritianum had the smallest and lightest seed, with one of the thinnest seed coats. Results showed decreases in viability for four species (Canna indica, Melia azedarach, Senna didymobotrya, and Ricinus communis), while Solanum mauritianum maintained a 100% viability throughout the experimental period. However, while the viability of C. indica, R. communis, and S. didymobotrya was dominated by germinable seeds before burial, as viability declined with an increase in burial time, viability was dominated by seeds that were not germinable but stained positively. Melia azedarach differed slightly, where viability declined with burial time, but the majority of the seeds that were viable remained germinable. The longest ageing rate based on P50 was observed for C. indica (lowest estimated lipid content), while M. azedarach had the shortest ageing rate (highest estimated lipid content). Decreases in germination over time for C. indica, R. communis, M. azedarach, and S. didymobotrya led to changes in either/both enthalpy of melting of the lipid, and the temperature of the lipid melt, which could be related to different seed deterioration mechanisms when buried. This study did not identify significant relationships between the seed physical and/or chemical traits and SB longevity using the traits investigated. This could be explained by the relatively low number of species and traits studied and/or the phenotypic plasticity associated with seed post-harvest physiology in wild species. Nevertheless, the study gave rise to the beginnings of a conceptual continuum of IAP seed bank longevity, which, once populated with data for more species, could supplement the criteria currently used for assessing species invasiveness. As mentioned earlier, alien plant invasions are a major challenge for developing countries, particularly in urban settings. In countries like South Africa, the management of IAPs is complicated by heterogeneous combinations of non-natural disturbances, site-specific levels of disturbance intensity, and diverse vegetation types and associated species richness. The results clearly show that IAPs thrive under high levels of non-natural disturbance in urban green spaces and that alien and indigenous species can co-occur in various vegetation types. The AII was able to identify alien hotspots within the study area and may represent a useful tool for conservation practitioners/land managers. Lantana camara and Solanum mauritianum emerged as the most problematic IAPs currently in the study area. It was also evident that disturbance levels play a role in soil SBs of alien and indigenous species richness and plant density, and some problematic IAPs, notably S. mauritianum, can persist in SBs for long periods due to morphological, anatomical, and chemical traits. The results generated were used to design a multi-disciplinary and multi-dimensional framework that aids in prioritising sites and species for alien plant monitoring and control within urban areas. The methods proposed for assessing the prevalence and drivers of alien plant species and the indicators identified as potential indicators of their impacts in the framework can assist land managers, practitioners, and researchers develop recommendations and actions for alien plant monitoring and control in urban areas. The framework is designed to supplement and aid, and not replace, existing EMA policies/guidelines for alien plant control by preceding their planning and preparation phases. It could also help in developing new approaches to monitoring alien plant species in urban spaces.
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    Micromorphology and biological activities of leaves and stem bark of Diospyros villosa (L.) De Winter.
    (2021) Adu, Oluwatosin Temilade.; Naidoo, Yougashree.; Lin, Johnson.
    Review Article: The genus Diospyros consists of many species which are distributed throughout the world. There is no elaborate information about the holistic importance of the plants. This review aims to delve for more information about the usefulness of the plants for humans. A detailed study of the genus Diospyros with a targeted focus on Diospyros villosa (L.) De Winter plant was carried out information on the plants’ morphology was taken as observed during harvest. Other information with respect to geographical distribution, secretory structures, chemical composition, embedded bioactive constituents and the associated mechanism of action of the bioactive constituents were acquired. The genus Diospyros yields products of medicinal importance throughout the world. This study gives some detailed information about the genus Diospyros as well as the potential use of the species as functional medicinal plants with bioactive compounds. Manuscript 1: This study evaluated the phytochemical constituents, antioxidant and antimicrobial potentials of Diospyros villosa (L.) De Winter leaves and stem bark. The extracts were obtained using different media (methanol, chloroform and hexane). DPPH and FRAP methods were used to investigate the antioxidant potentials of the crude extracts. The antimicrobial potency of Diospyros villosa extracts against five pathogenic bacteria was determined using MIC, MBC and agar well diffusion methods. Flavonoids, alkaloids and phenols were identified in D. villosa extracts. The mean concentrations of methanol extracts Diospyros villosa leaves and stem against DPPH providing 50% inhibition were 9.53 ± 0.25 μg ml-1 and 9.52 ± 0.30 μg ml-1 respectively. The methanolic leaves extracts further showed promising antimicrobial activity against Klebsiella pneumonia, Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus and Staphylococcus aureus with inhibition zones which are almost as high as the control. The antimicrobial methods also demonstrated that the leaves and stem bark extracts had wide antimicrobial abilities. The results revealed that D. villosa leaves and stem bark contain reasonable amount of bioactive compounds. Hence, these compounds may serve as natural antioxidants and antibacterial agents for the treatment of bacterial infections and diseases. Manuscript 2: Nanoparticles are synthesized through wet chemical techniques. Meanwhile, the chemicals used often are toxic and flammable. While considering safe substances, Diospyros villosa leaves and stem bark are both observed to be suitable for the biosynthesis of silver nanoparticles. In this research study, we described a less expensive and environmental-friendly technique for the biosynthesis of silver nanoparticles from silver nitrate (AgNO3) solution and Diospyros villosa extracts. The obtained silver nanoparticles were characterized using the UV-vis absorption spectroscopy, FT-IR, EDX, SEM and TEM, DPPH scavenging ability, ferric reducing antioxidant potential, antimicrobial susceptibility and quorum sensing inhibition tests. The biosynthesized silver nanoparticles showed good antibacterial activity against Escherichia coli, Staphylococcus aureus, Staphylococcus epidermis and Enterococcus faecalis. The D. villosa nanoparticles demonstrated potential antioxidant and quorum sensing inhibition and may thus represent a source of antioxidant as well as quorum sensing inhibition candidate for infection and disease control. Manuscript 3: The structural adaptation, histological compatibility and ecological functions of trichomes in Diospyros villosa, however remain largely unclear. This study aimed to interpret the structure and histochemical analysis of the leaves and stem bark of Diospyros villosa using light and electron microscopy and different histochemical tests as well as to elucidate the composition of the secretory products. Trichome density and length were also determined in three developmental stages of the leaves. The results of histochemical tests also revealed the presence of alkaloids and phenolic compounds which are medicinally important and used to treat multiple ailments. Manuscript 4: Diospyros villosa is traditionally used for processing anti-bacterial properties. Its cytotoxic effects have not been studied before. Therefore, this study aimed to examine the nutritional properties as well the cytotoxic effects of D. villosa. The leaves and stem barks were subjected to three different extraction methods (methanol, chloroform and hexane) and their nanoparticles were synthesized at two different temperatures (room temperature and at 80 ºC). Thereafter, extracts were assessed using the associated AOCC protocols, for their nutritional content (moisture, fibre, proteins, lipid, ash and hydrolysable carbohydrates). Diospyros villosa extracts and their corresponding nanoparticles were then incubated overnight with cancerous and noncancerous cell lines to evaluate their cytotoxic potential.
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    Physiological and biochemical investigations into the reinvigoration of deteriorated Brassica oleracea L. (Cabbage) and Lactuca sativa L. (Lettuce) seeds with antioxidants and inorganic salt solutions.
    (2021) Adetunji, Ademola Emmanuel.; Varghese, Boby.; Naidoo , Sershen.; Pammenter, Norman W.
    This study focused on reinvigorating deteriorated Brassica oleracea L. (cabbage) and Lactuca sativa L. (lettuce) seeds with antioxidants and inorganic (electrolysed and non-electrolysed) salt solutions. All pre-treatment solutions were applied to fresh (control) and controlled deteriorated (CDd) seeds at 75% viability (P75), 50% viability (P50) and 25% viability (P25). The pre-hydration treatments were compared in terms of their effects on seed germination, seedling vigour, electrolyte conductivity (EC), accumulation of lipid peroxidation products, protein carbonylation (PC), antioxidant enzymes and germination enzymes. The study also investigated the effects of invigorating CDd seeds with selected antioxidants on subsequent seedling growth, gas exchange and photochemistry under greenhouse conditions. Controlled deterioration, in general, resulted in the loss of seed vigour and viability but at higher rates in lettuce than cabbage, and increased EC and PC, and lowered antioxidant and germination enzymes activities in both species. However, significant lipid peroxidation was only recorded in lettuce seeds. Antioxidant pre-treatments enhanced viability of CDd seeds of cabbage at P25 and lettuce at P50 and P25, and improved seedling vigour of fresh, P75 and P50 cabbage, and P50 and P25 lettuce seeds. Antioxidant pretreatments reduced EC and lipid peroxidation in lettuce seeds, while PC was reduced in both species. The treatments also elevated antioxidant and germination enzymes activities in P25 cabbage seeds and P50 and P25 lettuce seeds. The inorganic salt pre-treatments did not enhance percentage seedling production in CDd cabbage seeds. However, in CDd lettuce seeds, Cacontaining solutions and electolysed (cathodic water) treatments promoted percentage normal seedling production and enhanced seedling vigour irrespective of pre-treatment solution pH or seed deterioration level. In the greenhouse studies, certain antioxidants promoted seedling vigour and leaf area in both species and enhanced shoot dry weight and gas exchange in lettuce. In summary, CDd lettuce seeds responded better to both types of invigoration (i.e., antioxidants and inorganic salt solutions) than cabbage seeds, while antioxidants appeared to be relatively more beneficial than inorganic salts in both species. The results suggest that the benefits of certain pre-treatment solutions were based on the enhancement of the activities of key antioxidant and germination enzymes, and the efficiency of photosynthesis at the early stages of growth. The results argue for the use of these seed pre-hydration treatments for mitigating poor stand establishment brought about by seed ageing, and as a useful approach to reinvigorating seeds in long-term storage collections for ensuring global food security.
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    Applied carnivore management in a data deficient world: leopard Panthera Pardus as a case study.
    (2016) Ross, Tyzack Pitman.; Slotow, Robert Hugh.; Hunter, Luke Thomas.
    Large carnivores are vital to biodiversity at a global scale, through their role as keystone species, but also present significant challenges for conservation and management due to the lack of basic information on carnivore abundance and distribution, particularly at regional and sub-continental scales. Consequently, large-scale carnivore management decisions are seldom supported by science-based evidence. In this thesis, I use leopards Panthera pardus as a model large carnivore, in Limpopo Province, South Africa, to investigate and address some of the fundamental components that underpin wildlife management and conservation in a landscape dominated by people. Furthermore, I develop practical and scientifically justified methods to facilitate accurate and efficient management of the species at a scale that is meaningful to leopard conservation. I begin by developing a model approach to leopard management, particularly in the context of trophy hunting, using data that are currently available to management authorities, and provide management recommendations to improve leopard population persistence. Next, I focus on the game ranching industry—the primary driver responsible for lethal leopard control—and assess the relationship between game ranchers and free-ranging wildlife. I then explore the evolution of game ranching practices to better understand the concomitant change in game rancher tolerance of free-ranging wildlife, and integrate this mechanistic understanding into the challenges facing conservation policy making more generally. Given the challenges faced by leopards across Limpopo (e.g., high levels of trophy hunting, statesanctioned population control, and illegal killing), I then set out to investigate leopard resource use and landscape connectivity across Limpopo to better understand leopard space use in the region. I present an efficient method of integrating connectivity within wildlife management, and in doing so, identify key conservation priorities. Lastly, given that so little is known about how species respond to hunting, I present a simulation study focused on assessing biological sustainability of leopard hunting. I demonstrate that the sustainable hunting of leopards remains a challenging objective given the high degree of additive anthropogenic mortality (i.e., illegal killing and state-sanctioned problem animal control) and challenges associated with accurately aging leopards in the field. The findings presented in this thesis provide valuable information and novel guidance that could benefit the management and conservation of leopards across the region, and further afield.
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    Structural, chemical and physiological investigations of bilirubin found in seed arils of strelitzia nicolai.
    (2017) Dwarka, Depika.; Baijnath, Himansu.; Thaver, Veneesha.; Naidu, Mickey.
    In 2009, a team of researchers from the Florida International U niversity discovered bilirubin which is an animal compound in the se ed arils of Strelitzia nicolai , commonly known as the White Bird of Paradise plant. Bilirubin is an endogenous yellowish compound that is formed following the standard catabolic pathway by the breakdown of haem. This catabolism is an essential practice in the human body as it allows for the elimination of waste products. Bilirubin is formed in humans some vertebrates and invertebrates. Previously thought to be a toxic compound if accumulated, recent ad vancements in medical sciences show bilirubin as an eff ective antioxidant. This study describes novel protocols to reveal new insights into the presence of the only animal pigment found in S. nicolai arils, the potential advantages of bilirubin found in a plant and its therapeutic value indications. In vitro a nd in vivo experim ents using the aril extract was conducted in order to assess the antioxidant , anti cancer and toxicity dosage of S. nicolai aril extract. In vitro studies showed that S. nicolai aril extract caused apoptosis in 52% of Hela cancer cell lin es. These results indicate that S. nicolai aril s extract possess conceivable chemo preventive properties. In vivo results in a rat model showe d no acute toxicity nonetheless, t hese results were inconclusive as a lengthier chronic study needs to be conducte d in order to completely rule out toxicity. An ultrastructure study of the seed arils was embarked in order to integrate supplementary knowledge The developing seeds were grouped in five stages according to seed maturity and aril colour. The arils were an alysed using light and electron microscopy. The Hall’s staining which is generally used on human tissue was modified to detect bilirubin on the surface of the aril tissue. Light microscopic results showed that as the aril matures it undergoes an atypical c olour change from opaque to yellow and finally a deep orange. This colour change might be attributed to the accumulation of bilirubin in the aril tissue. This hypothesis was further justified by cryo SEM and TEM which shows the trend of an accretion of a p igment as the aril matures. In addition, the inclination of aril maturity in S. nicolai follows an analogous prototypical pathway to that of bilirubin catabolism in humans. This study consequently highlights the potential use of S. nicolai aril extract co ntaining bilirubin and also attempts to relate aril structure with impending function.
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    The role of secondary metabolites in protecting lichens from climate change induced stress.
    (2022) Ndhlovu, Nqobile Truelove.; Beckett, Richard Peter.
    Lichen secondary metabolites play a great diversity of roles in lichen biology by acting as UV screens, antimicrobials, herbivore deterrents or allelopathic compounds. The main aim of the work described in this thesis was to test the potential roles of secondary metabolites in the tolerance of lichens (twelve species) to a variety of abiotic stresses. The first stress considered was that of tolerance to high levels of photosynthetically active radiation (PAR). Photosynthetic organisms possess a great diversity of mechanisms to protect themselves from the potentially stressful effects of high PAR. In addition to non-photochemical quenching and antioxidant mechanisms, it has been suggested that lichens use secondary metabolites for photoprotection. A few studies have shown that even faintly pigmented or unpigmented lichen substances can reduce photoinhibition. Here, the acetone rinsing technique was used to harmlessly remove secondary metabolites from all lichen thalli and then the chlorophyll fluorescence technique was used to measure their tolerance to photoinhibition in desiccated and hydrated states. Results showed that colorless lichen substances can increase the tolerance of lichen photobionts to photoinhibition when thalli are hydrated, apparently by increasing reflectance. Interestingly, substances can also photoprotect lichens in the dry state, while having no effect on reflectance. The acetone rinsing technique was also used to compare the relative importance of lichen substances in photoprotection in sun and shade collections of four species of Afromontane lichens. Results showed that lichens collected from sunny microhabitats have higher tolerance to photoinhibition than those from shaded locations. Furthermore, removal of lichen substances increases sensitivity to photoinhibition much more in sun than shade collections. Results further emphasized the importance of lichen secondary metabolites in photoprotection. This study also considered whether melanins, a pigmented secondary metabolite can cause problems with using fluorimetry techniques for e.g., to measure NPQ. A dissecting technique was used to remove the lower cortices and medullas of two lichen species so that NPQ could be measured from the underside of the thallus with an imaging PAM. Results confirmed that NPQ can be satisfactorily assessed with a standard fluorimeter by taking measurement from above using intact thalli. However, interestingly, photobionts from the bottom of the photobiont layer tended to have slightly lower rates of photosynthetic activity and lower NPQ than those at the top, i.e., display mild “shade” characteristics. The results presented in the final chapter looked at the protective role of secondary metabolites against desiccation-induced stress. It was hypothesized that secondary metabolites may act as antioxidants that protect lichens from desiccation-induced stress. Unfortunately, the findings of this part of the work did not present a consistent story, but rather indicated that according to species, the secondary metabolites can act as antioxidants or prooxidants. Nevertheless, taken together, the work presented in this thesis clearly shows that lichen secondary metabolites, whether pigmented or unpigmented, play important roles in photobiont photoprotection.
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    Aligning elephant conservation with societal aspirations.
    (2022) Van de Water, Antoinette.; Slotow, Robert Hugh.
    Protection of biodiversity and social development often seem at odds in the world of today. The aim of this thesis is to show that it does not need to be that way. Most global social compacts focus on either economic development, or biodiversity conservation. Few prioritise the needs, values and rights of local people living in or near conservationsensitive areas. If biodiversity and human well-being goals are to be realised simultaneously, we must find ways to increase land use for conservation purposes, while respecting the values and needs of local people and future generations. In an effort to contribute to this aim, this thesis explores and analyses how elephants are valued and perceived by a wide range of stakeholders; it investigates why narrow conservation approaches fail; and it uses the research outcomes to develop an alternative roadmap for conservation, one that realises beneficial outcomes for elephants, people and the environment. Through literature review, participatory workshops, questionnaires, interviews and reports provided by reserves and provincial government, I developed: (1) the TUSKER framework to reconcile integrity of nature with human well-being, (2) the pluralist elephant valuation system to incorporate all values of elephants that I have been able to uncover and provide insight into trade-offs associated with conservation decisions, (3) a theory of change for human-elephant coexistence and building common ground, and (4) a One Well-being framework to holistically assess and rank the consequences of elephant management interventions at different scales of animal, human and environmental well-being. The frameworks can be used in strategies that promote animal well-being and range expansion, while simultaneously empowering local communities and enhancing local economies. They may be employed by policymakers and managers to work towards ‘living-in-harmony’ conservation schemes, in which elephants and other iconic species do not represent a threat to humans but a chance for development and joy. Through ‘Living in harmony’, ‘convivial conservation’, and the incorporation of African philosophy Ubuntu (a philosophy that recognises moral values such as justice, dignity and rights), we will move towards a more ethical, just, and sustainable world.
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    The role of nutritional status of soils from grassland and savanna ecosystems on the biochemical and physiological responses of Vigna unguiculata L. (Walp)
    (2022) Makaure, Brenda Tsungai.; Magadlela, Anathi.; Aremu, Adeyemi Oladapo.
    Most arable soils in sub–Saharan Africa savanna and grassland ecosystems are acidic and nutrient deficient with nitrogen and phosphorus being the most limiting and this poses a huge threat to agricultural productivity. To overcome soil nutrient deficiency and increase crop yields, farmers have resorted to high inputs of synthetic fertilizers, which are expensive and may cause environmental degradation. Use of legumes is an important alternative as they help enhance soil nutrition through biological nitrogen fixation. Vigna unguiculata L. (Walp), a highly nutritious legume crop that could be incorporated in small scale cropping systems to improve soil nutrition. However, there is limited information on the physiological and biochemical strategies enabling the growth of V. unguiculata under acidic and nutrient stress conditions. In this study it was hypothesized that symbiotic association between V. unguiculata and rhizospheric microbes affects the growth, nutrient assimilation and phytochemicals of the grain legume grown in nutrient stressed soils. Firstly, this study evaluated the physicochemical properties, microbial composition and soil enzymes activities of soils from four geographically distinct regions of KwaZulu-Natal representing savanna and grassland ecosystems. Secondly, the study investigated how the tripartite symbiosis of V. unguiculata, arbuscular mycorrhizal fungi and nodulating bacteria affect phosphorus and nitrogen nutrition, and the growth of V. unguiculata grown under acidic and nutrient stress conditions. Then, the study investigated how four V. unguiculata varieties regulated their phenolic acids and antioxidants to enhance their growth in acidic and nutrient stressed soils conditions. The four soil types were acidic with low mineral nutrients, with Bergville being the most acidic. The soils were significantly different in their physicochemical and microbial composition. Most bacterial strains identified in the soils belonged to genera Lysinibacillus, and Bacillus while the most identified fungal strains belonged to Fusarium and Trichoderma genera. There were variations in soil lignin degrading, C, N and P cycling enzyme activities. The identified soil enzymes included β-D Phosphatase, L-asparaginase, β-glucosaminidase, β-cellobioside, catalase and lacasse. The availability of this rich pool of soil microbes and soil enzymes is a great opportunity as these can be used to regulate nutrient cycling and enhance nutrient availability for crop production in the savanna and grassland ecosystems. Four V. unguiculata varieties (IT18, Batch white, Brown mix, Dr Saunders) were grown in these acidic and nutrient poor soils. These V. unguiculata varieties were nodulated by several bacterial strains including those of genera Bradyrhizobium, Rhizobium, Bacillus and Paenibacillus. The V. unguiculata fixed more than 60% of its total nitrogen from the atmosphere across all soil treatments. Interestingly, V. unguiculata plants which were nodulated by non-rhizobial bacteria strains effectively fixed significantly high amounts of atmospheric nitrogen. Vigna unguiculata also developed symbiotic association with arbuscular mycorrhizal fungi (AMF) as evidenced by high root mycorrhizal fungi colonization ranging from 58-100%. Variations were observed on growth kinetics, nutrient assimilation and utilization among the four V. unguiculata varieties. Vigna unguiculata was able to switch N source preferences utilizing both soil and atmospheric nitrogen. These findings revealed that V. unguiculata has the capacity to adapt to nutrient poor ecosystems by establishing symbiotic interaction with naturally occurring soil bacteria and AMF and through its ability to switch N source preferences; by using soil N and atmospheric N2 through biological nitrogen fixation. There were variations in the response of the four V. unguiculata varieties to different levels of soil acidity and nutrient stress with regards to phenolic acid concentration and antioxidant capacities. The most abundant phenolic acids were vanillic acid and protocatechuic acid and these constituted 22.59% and 17.22% respectively of the total phenolic acids in the plants. More so, there were differences in correlations between the phenolic acids and plant biomass, plant nutrition, soil nutrition and AMF infection. There was negative correlation between phenolic acids protocatechuic acid and syringic acid, and concentration of plant nutrients N and P. Varieties IT18 and Batch white had relatively lower concentrations of phenolic acids but these had the highest plant biomass. These results confirm that low phenolic acid concentrations have stimulatory effects on growth and nutrient uptake by plants while high concentrations may inhibit plant growth and development. There were variations among the V. unguiculata varieties with respect to oxygen radical absorbance capacity (ORAC) across the four soil types. Overall, the study demonstrated that V. unguiculata is adaptable to acidic and nutrient poor ecosystems as it has the capacity to regulate its phenolic acids which enhance nutrient uptake, promote legume-microbe symbiosis, and help scavenge radical oxidative species due to their antioxidant properties.
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    Ecology of some mammals in relation to conservation management in Giant's Castle Game Reserve.
    (1982) Rowe-Rowe, David Treloar.; Meester, Jurgens Anthonie Janse.
    Abstract available in PDF.
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    Impacts of anthropogenic disturbance on persistence patterns of forest mammals in an urban-forest mosaic of eThekwini Municipality, Durban, South Africa.
    (2018) Zungu, Manqoba Moses.; Downs, Colleen Thelma.; Kalle, Riddhika Vinod.; Tharmalingam, Ramesh.
    The burgeoning human population size and the consequent land development pressures to meet its various needs has led to an unparalleled increase in the rates at which natural environments are converted for anthropogenic purposes. Among the major drivers of landscape modification by humans, urbanisation is arguably the most damaging, persistent and rapidly expanding across the globe. With the expansion of urbanisation, an increasing proportion of global biodiversity will be affected. The Ethekwini Municipality Area (EMA) is an urbanised landscape with high levels of biodiversity in South Africa. However, this area has a relatively large human population (~3.5 million), most of which is poor. Furthermore, it is located within a region (KwaZulu-Natal) undergoing rapid landscape changes. High development pressures, unauthorised development practices, conflicting governance systems and the preponderance of development priorities over environmental concerns has subjected most of the EMA to human activity. Considering these pressures, it is important to understand how wildlife adapt and persist in this human dominated landscape in order to guide conservation action. The aim of this study was to assess the impacts of anthropogenic disturbance on persistence patterns of forest mammals (excluding bats) in an urban-forest mosaic in the EMA, Durban, South Africa. The objectives were to: (1) determine factors affecting the occupancy of forest mammals; (2) determine the effects of landscape context on mammalian richness; (3) determine the effects of patch attributes and species’ ecological and life-history traits on nestedness patterns and (4) determine the effects of anthropogenic disturbance and abiotic factors on activity patterns and temporal niche overlap of mammals. Between May–September 2016 and December 2016–April 2017, mammalian surveys were conducted in forest patches within the study area using remote-triggered camera traps. Furthermore, data on vegetation structure at each camera trap location was recorded in order to better understand the habitat requirements of species. The results showed varying responses of mammals to landscape and habitat structural variables. The blue duiker (Philantomba monticola), bushbuck (Tragelaphus scriptus), bushpig (Potamochoerus larvatus), and Cape porcupine (Hystrix africaeustralis) were negatively affected by the loss and degradation of forest habitat and the increase in matrix development intensity whereas the large-spotted genet (Genetta tigrina) and vervet monkey (Chlorocebus pygerythrus) were relatively unaffected by such changes. Among habitat variables, an intact undergrowth and a high density of large trees were found to be important for the occurrence of many species found in this area as they provide sufficient breeding, roosting and browsing resources for specialist species that respond negatively to urban development. The results also demonstrated the importance of habitat area and its spatial configuration to the occurrence and persistence of mammals in this area. Patches that supported a high diversity of mammals were significantly larger, closer together, more contiguous and less separated by roads and urban development than patches that supported fewer species. The mammalian assemblage in the EMA was found to be significantly nested, with nestedness patterns related to patch size and isolation. This suggested that both the ability of species to persist on patches of various sizes and the ability to move to patches with different degrees of isolation affects the distribution and abundance of mammals in this area. Ecological specialists were found to be under more severe threat from further loss of forest habitat, which will likely threaten the long-term ecosystem functioning of forest habitat. When the activity patterns of species in the EMA were compared with activity patterns of the same species occurring in a less-disturbed landscape (Isimangaliso Wetland Park), no significant shifts in activity patterns were observed for most species except for common duiker (Sylvicapra grimmia), vervet monkey and Cape porcupine. Furthermore, there was only partial support for higher temporal overlap in activity patterns of ecologically similar species in the highly-disturbed EMA. Overall, the results presented in this thesis have provided insights into the persistence abilities of mammal species found in the EMA. The results have also provided basic ecological information on poorly known taxa, which will advance our understanding of their ecology locally and regionally. To ensure the continued persistence of mammals in the EMA, conservation efforts should prioritise the prevention of further loss of habitat, particularly large tracts of contiguous habitat. Furthermore, measures aimed at improving matrix permeability (e.g. stepping stones or corridors) should be promoted. This will help in reducing the negative effects of roads, which will ultimately increase landscape connectivity. Nevertheless, this is a metropolitan area with high development pressures, which are expected to increase even further in the future given the rapid population growth rate and the need to provide basic services to the people. Therefore, town planners, land owners, ecologists, and other decision makers need to consider the whole landscape, including the matrix, in the planning phase of future development projects in this area in order to minimise potentially negative effects on biodiversity.
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    A revision of the taxonomy and phylogenetic background of the South African genus Kazimierzus Plisko, 2006 (Oligochaeta: Kazimierzidae)
    (2018) Nxele, Thembeka Clara.; Zishiri, Oliver Tendayi.; Plisko, Jadwiga Danuta.; Mwabvu, Tarombera.
    Species identity and distribution information is important in conservation and monitoring of biodiversity. Megadrile fauna is very diverse in Southern Africa with most of the fauna demonstrating high levels of endemism, closely related species often separated by subtle morphological characters. Natural and various fertile biotopes of South Africa have a diverse terrestrial megadrile fauna, but to date, taxonomic and systematic studies of most taxa are incomplete. Such studies are vital as they contribute to the understanding of evolutionary processes and also provide information for conservation. To date, South African indigenous megadrile accredited to three strict indigenous families, Microchaetidae (s.str.), Tritogeniidae and Kazimierzidae, differ morphologically and differ also in their geographical distribution. The representatives of Kazimierzus, the only genus in Kazimierzidae, are known from the Western and South-Western Atlantic coast of South Africa, the area known for endemism in other invertebrate fauna and often associated with diverse flora. Considering these factors Kazimierzus was selected for the present study. The selected 25 Kazimierzus species occur in specific biotopes, their distribution is highly restricted to selected places, and most of them do not overlap. The study aimed to employ integrative taxonomy (morphology and molecular) to carry out a taxonomic revision of this genus and the objectives were1. to evaluate the validity of described species and provide an identification key to all species of Kazimierzus; 2. to determine the distribution of the genus Kazimierzus, in order to provide reliable data on species diversity, geographical distribution in Southern Africa and factors contributing to their distribution limits; this information is vital for conservation planning because earthworms can be used as bio-indicators of soil ecosystem health and 3. to investigate phylogenetic relationships within the genus. Kazimierzus was originally accredited to the family Microchaetidae (s. lato). Family Kazimierzidae was erected to accommodate Kazimierzus species because their morphology and anatomy were found to be different from the Microchaetidae (s. str) and also their geographic distribution confirmed separation from the other families. Four new species were described and a key to all species of Kazimierzus was constructed. DNA was extracted from twelve species and mitochondrial gene fragments (COI) were amplified and sequenced. Bayesian and maximum likelihood were used to determine phylogenetic relationships among species. The results validated the twelve species known currently. Cryptic diversity was observed in K. occidualis with genetic divergence greater than 12 % among populations. Kazimierzus franciscus and K. ljungstroemi have a low genetic variability suggesting close relatedness or probably conspecificity. A group of specimens from Clanwilliam are morphologically identical to K. sophieae but are genetically distinct and may belong to an undescribed taxon. These observations highlighted the importance of integrative taxonomy in earthworms in order to present reliable taxonomic and biogeographic data. A species distribution model was used to predict the distribution patterns of K. hamerae. Potentially new habitats were predicted along the Atlantic Ocean, in the southern part, as well as, in the north-western part of Namibia. The occurrence in Namibia was tested in the south, unfortunately no Kazimierzus specimens were found in the region where sampling was done. In addition, the model demonstrated that precipitation in the driest month is the most relevant predictor in spatial distribution patterns of K. hamerae. Because of the increasing awareness of the importance of earthworms in South Africa, indigenous earthworm species are given English common names. As such, all the species of Kazimierzus were given English common names. It is hoped that using common names may facilitate and increase the use of earthworms in conservation planning and environmental impact assessments. More farmers are showing interest in soil biology and it is hoped that, by giving earthworms English names, their importance and use will increase in the agricultural sector.
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    A genetic approach to the biodiversity of shallow water alcyonacea in South Africa.
    (2018) Etsebeth, Kerry-Lee.; Macdonald, Angus Hector Harold.
    The cnidarian order Alcyonacea (Octocorallia) represents a diverse group of marine invertebrates that are dominant taxa on shallow and deep reefs. These organisms constitute sensitive indicators of climate change and have bioprospecting potential. In South Africa, alcyonacean soft corals form the dominant faunal component of the high latitude marginal reefs on the east coast, an understudied region of interest that forms some of the southernmost distribution limits for key taxa in this order. Globally, soft corals are understudied whereby systematic, ecological, and biochemical studies are challenged by inconclusive taxonomy. This is in contrast to the growing understanding of the necessity for genetics in the systematics of Scleractinia, where large scale reclassification has been successful in reconstructing more accurate phylogenies of the order. The knowledge deficit in the systematics and evolution of Alcyonacea is paralleled in South African taxa. An integrative assessment using morphological classification in combination with phylogenetics of Alcyonacea is the most promising approach to assess their biodiversity in South Africa. Accordingly, the aims of these studies were to advance the taxonomic knowledge of soft corals in South Africa; assess species richness and provide a national checklist; and investigate evolutionary relationships between taxa. In so doing, this thesis also aimed to support the global taxonomy of Alcyonacea. Particular attention was given to Alcyonacea that dominate the reef biota in the UNESCO world heritage site, the iSimangaliso Wetland Park (iSWP). Three genetic markers, cytochrome c oxidase I (COI), bacterial MutS homolog (MutS) and nuclear 28S ribosomal RNA (28S rRNA) were used to determine genus and species boundaries in the closely related Alcyoniidae genera; Cladiella, Aldersladum and Klyxum. The use of these genes corroborated taxonomic analyses and demonstrated that morphologically aberrant members of the genus Cladiella should be reassigned to another as yet undescribed genus. The undescribed genus, Beta6, is characterised by an absence of platelet sclerites in the polyp region, features that demonstrate major distinctions from the genera Cladiella, Aldersladum and Klyxum. The species richness of 67 Sinularia specimens in the iSWP was estimated 6 Beta was selected as a placeholder name until the full taxonomic descriptions of this new genus and any of its associated species are published. using DNA barcoding (MutS and concatenated MutS+28S respectively). Phylogenetics and species delimitation methods were used to infer identifications for 63% of the specimens in the study, including a new record for Sinularia grandilobata. In addition, 16 putative species of Sinularia were discovered that are considered potentially undescribed or new records that require further taxonomic investigation by an octocoral expert. Furthermore, S. brassica exhibited two distinct morphotypes that were genetically differentiated and indicative of two distinct species. Taxonomic boundaries were investigated using integrative taxonomic approaches for 239 specimens of Alcyonacea from the iSWP. Specimens were assigned to ~61 putative species that were inferred from phylogenies, divergence estimates, colony photographs and sclerite characters for taxa in this study. Molecular evidence supported the reassignment of non-S. brassica congeners of Sinularia to an undescribed genus due to significant large scale polyphyly. Furthermore, this study reported new records for three genera; Scleronephthya, Paraplexaura, and Chironephthya and an undescribed species of Lobophytum. The results of this study, in conjunction with previously published records, contributed towards revised species estimates for the iSWP that increased from 37 to 81 species (with 12% endemism), 11 to 47 genera and 4 to 17 families. An updated checklist of the Alcyonacea across South Africa was compiled using records from chapters 2 to 4 in this thesis and published records. Two hundred and twenty-six different species from among 89 genera and within 25 families of Alcyonacea were reported. Seventy-five of these species are endemic to South Africa (33%). This represents a substantial increase from the last published estimates in South Africa of 130 species of Alcyonacea. This body of research represents a significant advancement in the knowledge of the biodiversity of an important group of marine invertebrates in South Africa. It provides resolution within some problematic identification assignations (Cladiella, Sinularia brassica). Sinularia, Beta and the Lobophytum-Sarcophyton complex require further taxonomic work for a better perspective on the diversity of this complex, marginal and neglected aspect of South Africa’s marine heritage.