Browsing by Author "Engelbrecht, Adriaan"

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    Characterization of bacterial species in Steinkopf a communal farming area in South Africa: A closer look at pathogenesis
    (University of the Western Cape, 2019) Foster, Jodene; Engelbrecht, Adriaan; Du Plessis, Morné; Taioe, Oriel Moeti
    The human population in sub-Saharan Africa has been increasing due to decreases in mortality rates and increases in average human age; in turn increasing poverty and pressure placed on agriculture and agricultural production. However, livestock production in South Africa, and globally, is declining due to disease and parasite prevalence, lack of feed, poor breeding, marketing management, change in nutrition in both livestock and humans, rapid urbanization, encroachment on wildlife and unfavourable climatic conditions brought about by global change. One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic disease. Zoonotic diseases are sicknesses transmissible from animals to humans, resulting from direct contact or environmental reservoirs. Previous studies have identified small-scale farmers as the group most prevalent to contracting zoonotic diseases, especially those working in a communal dispensation. Therefore, this study focused on the communal farming area of Steinkopf in the semi-arid Namaqualand region of South Africa. Steinkopf is one of the largest Act 9 areas, with communal land tenure and a mixed farming system, sheep and goats, on about 759 ha. Steinkopf is divided into two rainfall regions, the Succulent Karoo (winter rainfall region) and the Nama Karoo (summer rainfall region). This study aims to identify and characterise the bacterial microbial communities found in the topsoil layer and faecal matter (dung) within the winter and summer rainfall regions of Steinkopf communal rangeland using Next-generation sequencing. Further, the aim is to assess whether pathogenic bacteria are present within the rangeland and what their potential impact on the local farming community might be if present. A high-throughput sequencing technique (Next-generation sequencing) was used to amplify 16S rRNA targeting the V3-V4 hypervariable regions. The phylotypes produced were 37 phyla, 353 families and 634 genera of which the most abundant bacterial phyla were Planctomycetes, Firmicutes and Bacteroidetes and the most abundant genera were Gemmata, Akkermansia and Arthrobacter. Alpha diversity indices showed a variation in species diversity, evenness and richness between soil and dung samples, it shows a higher species richness, evenness and unique OTUs detected in summer soil samples and at natural water holes. Through these analysis soil samples were regarded as superior to dung samples within this particular environment and for this particular study. Natural water holes were identified as a safer option when compared to man-made water holes as there are natural systems in place that combat the spread and growth of harmful bacterial microbes. It was found that seasonality has a great impact on the development and growth of environmental bacterial microbiota and that the current randomness of grazing routes and migrations within the Steinkopf communal rangeland is not a detriment but instead acts as a benefits to environmental and livestock health. Furthermore, a total of three pathogenic bacteria were identified however, they occurred at relatively low abundances. It can thus be concluded that this study thoroughly describes the usefulness of using a high-throughput sequencing technique such as Next-generation sequencing when amplifying a small sample size in order to achieve a large volume of information; and that currently the Steinkopf communal rangeland is not subjected to or at risk of a potential zoonotic threat.
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    Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH)
    (BMC, 2018) Matthee, Conrad A.; Engelbrecht, Adriaan; Matthee, Sonja
    BACKGROUND: The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist. RESULTS: To test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (±0.00) and a low level of population differentiation (mtDNA Fst= 0.56, p < 0.05; nuDNA Fst = 0.33, P < 0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (±0.03) and comparatively higher levels of population differentiation (mtDNA Fst = 0.87, P < 0.05; nuDNA Fst = 0.48, P < 0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA Fst= 0.53, P < 0. 05; nuDNA Fst= 0.12, P < 0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA Fst of 0.79 (P < 0.05) while R. dilectus populations are less structured with a mtDNA Fst= 0.18 (P < 0.05). CONCLUSION: These findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species.
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    Implications of potential biome boundary shifts for small mammal assemblages in the arid zone
    (University of the Western Cape, 2019) Piers, Laetitia; Engelbrecht, Adriaan
    Desertification deteriorates the landscape functionality of rangelands, affecting the resilience of biome boundaries which have a cascade effect not only in vegetation composition and characteristics but also in animal communities. The balance between plants and small mammals are essential in maintaining the functionality (i.e. nutrient cycling, soil stability, and water infiltration) of rangeland which includes the arid Steinkopf communal rangeland. However, the landscape functionality of rangelands has not been extensively studied, especially in communal areas where desertification is a serious concern since many people farm with livestock to survive. The aim of this study was to assess landscape functionality along an arid biome boundary and its relationship to small mammal assemblages. This study further aimed to provide a local landscape perspective of the current desertification process and projected expansion of the Desert Biome into more mesic biomes in South Africa. Three replicates for three Desert Biome, ecotone and Succulent Karoo Biome sites (27 sites in total) were selected to assess landscape functionality and survey small mammal assemblages over a one-year period. The change in landscape functionality between the three areas was assessed to determine the resilience of the biome boundary to desertification. For each small mammal survey, 216 live Sherman traps were set up during the summer and winter seasons to account for breeding, mortality, and possible migration. With the data, the body condition index, population density, and diversity were quantified.
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    Investigating the diet selection and genetic variation of small ruminants in a dryland pastoral system in South Africa
    (University of the Western Cape, 2019) Schroeder, Amy; Engelbrecht, Adriaan; Samuels, Igshaan; Cupido, Clement
    Small ruminants found in pastoral dryland systems face many challenges regarding constant environmental and climate changes. These variable environments are home to many pastoralists who use the natural resources to sustain their livestock. Due to the prevailing environmental changes, these pastoralists require various adaptation strategies for the survival of their small ruminants. Adaptation is vital for all pastoralists globally, especially those living in semi-arid to arid regions as these areas are badly impacted by climate change. Farming with small ruminants that are able to constantly adapt to variable environments are a long-term and low cost resource strategy for farmers in these areas. Drought is a recurring challenge that farmers in dryland systems have to cope with and small ruminants are forced to adapt to food and water available to them as drought affects their survival, reproduction and production. This is because drought affects the environment directly as rainfall has an impact on all forage and water resources found in drylands. Thus available forage and the utilisation of this resource by small ruminants is essential for sheep and goat farmers who depend on these animals for their livelihoods. This thesis sets out to establish sheep and goat breeds found in a dryland pastoral system in South Africa focussing on their genetic differences and their diet selection during a drought period. The study was carried out in the 582 634 ha Steinkopf communal area located in the semi-arid to arid region of Namaqualand in South Africa. The dominant land use in this area is livestock farming where farmers utilise two biomes for grazing. Using mitochondrial DNA, genetic differences were investigated in small ruminants found in Steinkopf. The small ruminants that were studied were the Boer goats, Swakara sheep (Karakul) and cross-bred sheep. These were the most commonly farmed small ruminants in this area. Genetic differences and diversity found within the small ruminants in this area supports their ability to adapt to drought and changing environments. Diet selection of these small ruminants were assessed using direct forage observation during this drought period in both the Succulent and Nama Karoo biomes. Findings of the study indicate that small ruminants during a drought period will largely forage on what is available to them. Boer goats changed their diets from browser to grazers in the different biomes while sheep remained grazers in both biomes. This suggests that these animals are well adapted to changing forage availability and will adjust their feeding behaviours accordingly. Succulent plant species were utilised by all small ruminants and this can be regarded as new knowledge for small ruminants in dryland systems. Succulent species play a role in the diets of small ruminants in the Steinkopf rangeland and these animals have adapted traits that allow them to eat plants that contain high levels of phenolics and tannins, which show their high adaptability to this area. This study also revealed that indigenous and locally bred sheep in this area are crucial resources for livestock farming in this area. Swakara sheep in this area showed a low level of genetic variation while cross-bred sheep and the Boer goat had significant variation. With a long tradition of breeding small ruminants in the Steinkopf communal area that suit changing conditions, livestock keepers have accumulated detailed knowledge of their animals. Recommendations from this study were to do further studies regarding genetic variation within the cross-bred sheep as this information will be useful for breeding programs in dryland areas and it will add to the small ruminant genetics in South Africa. Because this study was conducted in a drought period, I recommend that diet selection should be observed during a regular wet and dry period as this would indicate how these animals adapt to what forage is available to them. These studies can act as management strategies for herders as it can provide information on how to use the natural resources sustainably.
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    Investigating the relationship between novel farming practices and zoonotic disease transmission at the wildlife/livestock interface: A case study at a commercial farm and conservancy in Beaufort West, South Africa
    (University of the Western Cape, 2022) Badrodien, Yameen; Engelbrecht, Adriaan
    In recent years, the intensification of agricultural activities in South Africa, has led to many of the sectors farmers adopting novel farming practices as a means of promoting economic productivity. One such practice, is the expansion of traditional livestock systems to include unconventional forms of stock such as wildlife. Despite the economic benefits of this approach, the threat of disease re/emergence remains a major obstacle, as both wild and domesticated animals are known reservoirs to a variety of disease-causing agents. Whilst many studies have directed their attention toward the surveillance of emerging pathogens within animal populations, less attention has been directed towards monitoring pathogens within environmental disease reservoirs (i.e., soil), which may be affected by these novel farming practices.
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    Phylogeography and co-evolution of ectoparasitic mites that live on the rodent host species Lemniscomys rosalia (Rodentia: Muridea)
    (University of the Western Cape, 2022) Meissenheimer, Keenan Keith; Engelbrecht, Adriaan
    Lemniscomys rosalia is a widespread, possibly cryptic species of murid grass mouse. Cytogenetic evidence points towards cryptic speciation in L. rosalia as the eastern African karyotype (2N = 54; FNA = 62) differs from the southern African karyotype (2N = 48; FNA = 62). Further resolution through phylogeographic analysis is necessary to corroborate this hypothesis; however, there is little to no molecular data on L. rosalia. The present study sought to determine the phylogeographic patterns found in southern African populations of L. rosalia using mitochondrial and nuclear markers. Parasites are commonly used to complement the genealogy of their host species since both species may undergo co-phylogeny.
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    Revealing the factors that promote divergence in the Bladder Grasshopper Bullacris unicolor (Orthoptera; Pneumoroidea)
    (University of the Western Cape, 2019) Sathyan, Rekha; Couldridge, Vanessa; Engelbrecht, Adriaan
    Variation in sympatric and allopatric populations is believed to be a precursor to eventual speciation. The dispersion of genes from one gene pool into another is prevented by various processes, including the founder effect, sexual selection, ecological differences and random genetic divergence. Examining patterns of intraspecific variation in phenotypic and genotypic traits may thus provide valuable insights into the processes that govern species origination. Bladder grasshoppers (Orthoptera; Pneumoroidea) are an ideal model system to investigate patterns of geographic and ecological divergence due to their high host plant specificity, low dispersal and distinctive acoustic signals. This dissertation investigates intraspecific diversification in the bladder grasshopper Bullacris unicolor (Orthoptera: Pneumoroidea). Recent research on this species has shown significant intra- and inter-population variation in male advertisement calls and morphological characters. However, the exact cause of this variation has remained unclear. Furthermore, a previous study showed that the calls of B. unicolor from one particular population are highly differentiated from other populations, possibly due to the effects of anthropogenic noise. Here we aim to examine the drivers of diversity within Bullacris unicolor by embracing a multidisciplinary approach that encompasses the effects of environmental factors, genetics, anthropogenic noise and host plant associated divergence.
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    Species recognition and reproductive isolation in Malawi cichlid fishes, Metriaclima estherae and M. callainos (Teleostei: Cichlidae)
    (University of the Western Cape, 2019) Nyalungu, Nonhlanhla Precotia; Couldridge, Vanessa; Engelbrecht, Adriaan
    Cichlids are one of the most diverse groups of fishes in the world. The highest concentration of cichlids is found in Lake Malawi, where over 1500 species are recorded to occur, which are dominated by the haplochromine tribe. Several authors proposed that sexual selection has been a major contributor in the high rate of speciation of haplochromine cichlids. However, sexual selection alone may not be sufficient to fully explain high speciation rates among cichlids. Many closely related cichlids in Lake Malawi differ only in coloration, yet occur in sympatry. It is still not fully understood how they remain reproductively isolated. Previous studies suggest that visual cues are primarily used for reproductive isolation and species recognition. In the current study, visual, chemical and acoustic cues were investigated to observe how they may potentially influence species recognition and reproductive isolation between two closely related species, Metriaclima estherae and M. callainos, as well as between alternate colour morphs of M. estherae.
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    A survey on external (Ixodidae) and gastrointestinal parasites of small ruminants on an arid communal rangeland in South Africa
    (University of Western Cape, 2020) Govender, Saloshnie Simone; Engelbrecht, Adriaan; Samuels, Mogamat Igshaan; Cupido1, Clement
    Parasites pose a major constraint on livestock farming. Its impacts are represented as transmission of disease to humans and economic costs for prevention and treatment as well as loss in terms of; livestock mortality and, lowered productivity. Although the impacts of parasitic loads can be decreased through proper management, extensive management systems are depended on external factors such as rainfall and forage availability, which, in its absence, promote malnutrition and therefore parasite susceptibility.
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    Towards an unravelling of the taxonomy of Chrysaora (Scyphozoa; Semaeostomeae; Pelagiidae) from around South Africa
    (University of the Western Cape, 2017) Ras, Verena; Gibbons, Mark J; Engelbrecht, Adriaan
    Historically, two species of Chrysaora are known from the Benguela Current Ecosystem: C.fulgida (Reynaud 1830) and C. africana (Vanhöffen 1902). However a third morphotype is now seen, which bears a resemblance to both. Thus a complete qualitative and quantitative analysis of the morphometric and meristic data of these three species was conducted, along with an in depth study into the cnidome as a potential tool of identification. These findings are supplemented by a genetic analysis using cytochrome c oxidase subunit I and internal transcribed spacer 1 gene markers. Three species were unambiguously identified. The genetics and morphology showed considerable divergence, with some of the features used to separate them including: tentacle number and shape, colouration and shape of the oral arm, shape of the gastrovascular pouches and the number and shape of the marginal lappets. Although the mtDNA indicated clear separation of the three Chrysaora, the nucDNA displayed some ambiguity. The cnidome showed considerable divergence and succeeded in separating these species, while the rhopalia of the three species also showed distinct differences in the lengths of the rhopalal canals and basal stems. Much of the confusion surrounding jellyfish taxonomy has been the result of observations made on predominantly preserved specimens that are in subpar quality, a hinderence which this study endeavored to overcome.