A diverse and abundant nematode fauna is known to exist in South Africa with plant parasitic nematodes being the most representative. Seven genera belonging to the family Belonolaimidae Whitehead, 1960 are known to occur in South Africa, including Histotylenchus Siddiqi, 1971, a small genus only found in Africa and India. Nematodes belonging to the family Belonolaimidae are obligatory, primarily migratory ectoparasites of roots. These nematodes are found in cultivated soils and natural veld and are usually seen as mild plant parasites. Histotylenchus is represented by three species from South Africa, namely Histotylenchus hedys Kleynhans, 1975, Histotylenchus histoides Siddiqi, 1971 and Histotylenchus mohalei Kleynhans, 1992. Diagnostic characters of Histotylenchus include a lip region confluent with body contour or offset, asymmetrical stylet conus with an angular lumen, a large metacorpus valve, genital tracts about equal, lateral fields with four lines usually areolated, spicules tapering distally with distinct vela and gubernaculum proximally recurved with titillae. The aim of this study was to review all existing literature concerning the genus Histotylenchus in Africa, and to examine and describe the species from this genus collected in South Africa, which are deposited in the National Collection of Nematodes, Biosystematics Programme, Agricultural Research Council, Plant Protection Research Institute, Pretoria, South Africa. Results showed that a total of 44% of the fixed material examined was not suitable for this morphological study as a result of the separation of the cuticle from the body. This phenomenon is reported from this genus for the first time. Histotylenchus hedys and Histotylenchus mohalei were re-described from material of the National Collection of Nematodes, while Histotylenchus histoides was re-described from type material of the Rothamsted Nematode Collection housed at the Food and Environment Research Agency (Fera), York, United Kingdom; and CABI Bioscience, Egham, United Kingdom. A new species, Histotylenchus niveus sp. n., was described from material collected in the Witsand Nature Reserve, Northern Cape, South Africa. Additionally, two species Histotylenchus sp. 1 and Histotylenchus sp. 2 were described during this study and could possibly be new to science. However, additional material needs to be collected to verify these results. The present study revealed that further research into the genus is necessary, especially since the current information is limited and incomplete.

In the Qwa-Qwa and Thaba Nâchu regions of the Free State Province, South Africa, resource limited farmers that produce wheat are mainly situated in temporary crop environments. They are drastically affected by crop losses that occur during years of serious Russian wheat aphid (Diuraphis noxia) (Kurdjumov) and oat aphid (Rhopalosiphum padi) (Linnaeus) infestations. Therefore the main objective of this study was to identify simple alternate control methods to be used by small-scale farmers for the control of these aphids. The focus was on minimizing the numbers of the immigrating individuals. That must happen before they arrive in the crop habitat and decrease the possibility of the pest population reaching damaging levels when the crop is still in its susceptible phase for insect damage. Plant derived semiochemicals, which could modify insect behaviour, were considered as an option to be used since this could be extracted from plants, and were demonstrated to be successful in other countries. These semiochemicals are also known to attract natural enemies of these insects. It was therefore decided to test two types of extracts (an aqueous and a light mineral oil) which could be easily prepared from four plant species, namely Wild wormwood Artemisia afra (Jacq. ex Willd.), Big thorn apple Datura stramonium (Linnaeus), Khaki bush Tagetes minuta (Linnaeus) and Wild garlic Tulbachia violacea (Harv.). The plants were chosen due to their availability in the wheat production regions and their possible insect repelling properties known from other species in the same genera. The behavioural response of alate aphids D. noxia and R. padi and two parasitoids, Aphelinus hordei (Kurdjumov) and Diaeretiella rapae (McIntosh) to these extracts was tested in olfactometer trials in the laboratory. The aphid D. noxia showed the highest repellence to the aqueous extract of A. afra and the oil extract of T. violacea. Aphid R. padi was also best repelled by the aqueous extract of A. afra and the oil extract of D. stramonium. The parasitoid A. hordei was strongly attracted to the aqueous extracts of A. afra and T. minuta. Diaeretiella rapae on the other hand, was also highly attracted to the aqueous extract of T. minuta, but T. violacea oil extract had a very strong effect on the parasitoid and would be recommended to farmers. Artemisia afra and T. violacea are perennials and available as green material for extraction purposes in the winter when wheat is planted. The other two plants are annuals and not available in winter. The A. afra aqueous extract will repel both aphid species when sprayed early in the wheat growing season when wheat is still small and aphids are flying into the wheat. This extract will also attract A. hordei and this could enhance the biological control of D. noxia. The T. violacea oil extract could also be used to repel D. noxia. It could also be used to attract the parasitoid D. rapae later in the season and enhance the biological control of both aphid species. Thus there are potential alternate simple aphid control methods available for small-scale farmers. These methods should be refined and farmers trained to use them effectively.

Theileria parva (T. parva) is transmitted from carrier buffalo to cattle causing Corridor disease in cattle. The 989/990 conventional Polymerase Chain Reaction (PCR) assay used for the detection of T. parva is labour-intensive and has the potential for contamination due to the need for post-amplification handling. Real-time PCR offers a way of addressing these limitations. This thesis describes the development of a TaqMan assay for the detection of T. parva and a comparison between this real-time assay with the real-time Hybridization probe assay and the conventional PCR assay for the diagnosis of T. parva. Theileria general forward and reverse primers and a T. parva TaqMan probe specific for the recognition of a conservative region of the T. parva 18S rRNA gene was designed. The TaqMan PCR assay could detect T. parva DNA at a 2x10-5% parasitaemia with a 93% certainty. The primer pairs and probe only cross-reacted with Theileria sp. (buffalo) and no amplification with other Theileria species, bacteria or related haemoparasites was observed. Theileria sp. (buffalo) is genetically closely related to T. parva. However, its biology and disease relations are not known. The TaqMan probe assay detected 87% of all positive samples for evidence of the diagnostic sensitivity and 100% of all negative samples tested negative for the diagnostic specificity assay. These results were compared with those obtained from 989/990 conventional PCR and BioPAD Hybridization probe PCR which targeted the same gene. The Hybridization probe PCR appeared to be more sensitive than the TaqMan probe PCR or conventional PCR assay. With the specificity test, the Hybridization probe PCR proved to be more specific than the other two assays. All three tests gave similar results for the diagnostic specificity. The TaqMan probe assay with its high sensitivity, wide range of detection ability and simplicity is particularly useful in the detection of T. parva. However, further studies are required to improve the specificity of the TaqMan PCR assay in order to eliminate the detection of Theileria sp. (buffalo).

The exactness of species descriptions in taxonomy, taking only morphology into account, has long been debated over. This is evident in the systematics of parasitic copepods that are mostly based on morphological characteristics. The gap in molecular information of the class Copepoda leaves a hole in the understanding of crustacean systematics and their ecological importance. Due to work done in China by a group of Chinese scientists on the genus Ergasilus (Family Ergasilidae). molecular studies on genera of this family from Africa were used to do the same analysis. Although only some representatives of the family is a threat to the fish populations of Africa, the availability of samples and information on morphological traits make this family a good starting point in the use of molecular work on the parasitic copepods of Africa. The focus of this study is the phylogeny of southern African ergasilids, based on the morphological characteristics coupled with the 28S rDNA sequences, with specifically designed primers (used in the Chinese study). The family Lernaeidae (using the genus Lernaea), closely related to the genus Ergasilus, was used as the out-group. Using the morphological analysis four new species of Ergasilus from southern Africa were found, i.e. Ergasilus sp. A from Synodontis leopardinus Pellegrin, 1914; Ergasilus sp. B from Rhabdalestes maunensis (Fowler, 1935); Ergasilus sp. C from Micropterus punctulatus Rafinesque, 1819 and Ergasilus sp. D from Petrotilapia tridentiger Trewavas, 1935. The molecular study proved to be a challenge and only results for Ergasilus sp. A could be obtained and were used in a tree-building analysis with the sequences from the Chinese study.

The Seekoeivlei Nature Reserve wetland is a designated Ramsar site, situated on the north-eastern boundary of the Free State Province. Field trips were made on three occasions between October 2011 and May 2012. A total of 43 genera belonging to 20 families and 7 orders were identified from the three localities. Of the three sites sampled, Bird Lookout point showed the highest species richness (S = 16) and species diversity in terms of the Shannon-Wiener diversity index (Hâ = 2.18) and Hills diversity index (Hills N1 = 8.78) during the summer survey. It was found that all localities were dominated by plant parasitic nematodes with the exception of Bird Lookout during the winter survey and Mamba Pool during the summer survey, which was dominated by predators and omnivores, respectively. The Maturity Index (MI) value was highest at the Hippo Pool during the preliminary collection (MI = 14.22) and lowest at the Mamba Pool on all three collections. Key genera found at the site included Tobrilus Andrássy, 1959, Eutobrilus Tsalolikhin, 1981; Brevitobrilus Andrássy, 1959 and Chronogaster Cobb, 1913. Tobrilus sp. 1 is characterised by a vulva at mid body (49%), the tail long and cylindrical (216-295 μm) with a spinneret present. Eutobrilus sp. 1 is characterised by labial sensillae papilli form, cephalic setae just over one third labial region diameter, vulva placement at midbody, tail elongate tapering, 6.5 anal body widths long. Brevitobrilus sp. 1 is characterised by body length (1019-1792 μm female; 1123-1526 μm male), labial sensillae papilliform, cephalic setae one third of labial region diameter, vulva at 46% body length, tail five anal body widths long and spinneret present. Males characterised by six supplements with largest distance between S5 and S6, spicule 21 μm, tail three anal body widths long and subterminal setae present. Chronogaster sp. 1. is recognised by female habitus being straight to completely ventrally curved and male habitus being ventrally curved, J-shaped, lip region not annulated, cephalic setae as long or longer than lip region diameter, cylindroid pharynx with denticulated valve in basal bulb, female reproductive system monodelphic-prodelphic, vulva at (45.3%) body lengths from anterior end, male tail conoid, spicule slender, with fifteen dissimilar supplements. Descriptions, measurements and illustrations including light microscope micrographs are provided for the four species.

Includes bibliographical references (leaves 94-107). / The Australian river red gum (Eucalyptus camaldulensis Denhardt) (Myrtaceae) is regarded in South Africa as a valuable general-purpose utility and ornamental tree, as well as an essential source of nectar and pollen to sustain the honeybees which are crucial for pollinating the economically important fruit crops in mainly the Western Cape Province. Despite its utility value, it is regarded as invasive in South Africa, the major concern being the large amounts of water it consumes when growing along watercourses. River red gum is therefore the subject of conflicts in interests between government agencies that target it for control actions, and farmers and beekeepers who utilize it. As a contribution towards resolving this conflict in interests, a research project was initiated to investigate the potential use of host-specific insects that might reduce the number of viable seeds produced by E camaldulensis. The aim was to reduce its invasive potential while retaining its general utilizability for all concerned. From the start, the need for introduced agents from Australia was weighed against the presence of two species of chalcidoid wasps, both regarded as gall inducers, in the seed capsules of E camaldulensis in South Africa. The current study was motivated by the need for information on the biology of these two species and the effect they were having on seed production in their host plant. As it progressed, three more chalcidoid species, all undescribed at that time and probably of Australian origin, were found to be emerging from the seed capsules of E camaldulensis collected in several parts of South Africa, and these became part of the investigation.

Urbanisation and associated anthropogenic activity release large quantities of metallic elements and metalloids into the environment. Due to their toxicity, environmental persistence and bioaccumulative nature, these chemical pollutants threaten wildlife and human health. As urbanisation increases and top predators are forced to utilise more urban spaces, they will likely be exposed to more toxic heavy metals and metalloids. As secondary and tertiary consumers, terrestrial carnivores may be at increased risk of metal exposure through biomagnification effects. Relatively little is known about this emerging threat to terrestrial carnivores persisting in human-transformed landscapes, especially in the Global South. To better understand the extent of this issue, I quantified the level of metallic element and metalloid exposure in a sentinel top predator, the caracal (Caracal caracal), inhabiting the rapidly-urbanising, primarily coastal metropole of the Greater City of Cape Town, South Africa. Whole blood samples (n = 67) from GPS-collared (n = 25) and opportunistically sampled (n = 31) individuals were collected. Using Redundancy Analysis (RDA) and mixed-effect models, I explored the relative influence of caracal demography, landscape use, and diet on levels of individual exposure to 11 metallic elements and metalloids: Aluminium (Al), Arsenic (As), Cadmium (Cd), Chromium (Cr), Cobalt (Co), Copper (Cu), Mercury (Hg), Manganese (Mn), Lead (Pb), Selenium (Se), and Zinc (Zn). Mean metal concentrations (including Al, Cd, Co, Cu, Hg, Mn, Pb, Se and Zn) were generally found to be below toxic thresholds, however, As and Cr are present at potentially sublethal levels in certain individuals. The results suggest that increased use of human-transformed landscapes in home ranges (particularly urban areas, roads, and vineyards) was significantly associated with increased caracal exposure to Al (P < 0.05), Co (P = 0.05) and Pb (P = 0.07). Home ranges closer to the coast (RDA, P < 0.05) and feeding within aquatic food webs (marine and wetland-adapted prey) were associated with higher blood levels of Hg (P < 0.05), Se (P < 0.01) and As (P < 0.05). Further, increased predation on seabirds and aquatic birds likely facilitates the transfer of metals from aquatic to terrestrial food webs. Overall, these findings highlight the importance of urbanisation and anthropogenic activity as major environmental sources of metal exposure in terrestrial wildlife, including more natural areas through long-distance transport of pollutants. Further, they contribute towards a growing global evidence base suggesting cities act as ecological traps for wildlife, threatening their long-term health and persistence in these landscapes. Therefore, it is crucial that cities work to reduce the large quantities of chemical pollutants released into their surrounding environment. In Cape Town, this effort could be focused on the urban edge, waste management, water treatments, roads and agricultural areas. Future research into a possible ecological trap for urban-adapted carnivores should focus on assessing metal exposure at different trophic levels and investigating the potential physiological responses of exposure in species. I argue that the caracal is a valuable sentinel for assessing metal exposure and should be used in tandem with other small and mediumsized carnivores and aquatic bird species in local and national pollutant monitoring programmes to mitigate further exposure and promote carnivore conservation in human landscapes. A charismatic species, with a well-established local platform of research and science communication, the caracal is centrally positioned to help promote greater public awareness and engagement in issues concerning environmental pollutant contamination and monitoring.

Buffalo-adapted Theileria parva causes Corridor disease in cattle. Strict control measures therefore apply to the movement of buffalo in South Africa and include mandatory testing of buffalo for the presence of T. parva. The official test is a real-time hybridization PCR assay that amplifies the V4 hypervariable region of the 18S rRNA gene of T. parva, T. sp. (buffalo) and T. sp. (bougasvlei). The effect that mixed T. parva and T. sp. (buffalo)-like infections have on accurate T. parva diagnosis was investigated. In-vitro mixed infection simulations indicated PCR signal suppression at 100 to 1000-fold T. sp. (buffalo) excess at low T. parva parasitaemia. Suppression of PCR signal was found in field buffalo with mixed infections. The T. parva-positive status of these cases was confirmed by selective suppression of T. sp. (buffalo) amplification using a locked nucleic acid clamp and independent assays based on the p67, p104 and Tpr genes. Conventional and SYBR® Green touch-down PCR methods were developed for each protein coding gene and buffalo from the endemic Kruger National Park were screened. The protein gene assays compared well with the negative and T. parva positive samples diagnosed on the current real-time assay however, they did detect additional positive samples diagnosed as negative on the real-time hybridization. These samples were all T. sp. (buffalo) positive. This confirmed the suppressive effect on PCR signal due to template competition in the current real-time PCR assay. Some positive samples were not detected by the protein genes, possibly due to sequence variation in the primer regions. These independent markers proved useful as supplementary assays in the accurate diagnosis of T. parva infections where mixed infections occur in the buffalo host. The development of the Hybrid II assay, a real-time hybridization PCR method, which compared well with the official hybridization assay in terms of specificity and sensitivity revolutionized the diagnosis of the disease for the main reason that it is not influenced by mixed infections of T. sp. (buffalo)-like parasites and is as such a significant improvement on the current hybridization assay. While the incidence of mixed infections in the Corridor disease endemic region of South Africa is significant, little information is available on the specific distribution and prevalence of T. sp. (buffalo) and T. sp. (bougasvlei). Specific real-time PCR assays were developed and a total of 1211 samples known to harbor these parasites were screened. Both parasites are widely distributed in southern Africa and the incidence of mixed infections with T. parva within the endemic region is similar (~25-50%). However, a significant discrepancy exists with regard to mixed infections of T. sp. (buffalo) and T. sp. (bougasvlei) (~10%). Evidence for speciation between T. sp. (buffalo) and T. sp. (bougasvlei) is supported by phylogenetic analysis of the COI gene, and their designation as different species. This suggests mutual exclusion of parasites and the possibility of hybrid sterility in cases of mixed infections.

African animal trypanosomiasis (AAT) is a disease caused by haemoparasites of the genus Trypanosoma and its vectors are tsetse flies of the genus Glossina which are endemic to the African continent. In South Africa the disease is restricted to the north eastern parts of KwaZulu-Natal Province and it is transmitted to susceptible vertebrate hosts by Glossina brevipalpis and G. austeni. The current study aimed at determining the prevalence, genetic diversity and the phylogenetic position of the South African trypanosome species in the north eastern KwaZulu-Natal as well as determining preferred feeding host by tsetse flies from their blood meal. A total of 296 blood samples were collected from the north eastern parts of KwaZulu-Natal Province whereby 137 were from cattle; 101; 9; 49 were from goats, sheep and dogs respectively and 376 tsetse flies (375 G. brevipalpis and 1 G. austeni) were also collected. PCR with universal KIN primers was used to detect the trypanosome parasites in both blood and tsetse flies. From 137 cattle samples 23.4% (32/137) were positive for the presence of trypanosome infections whilst none were positive for sheep, goat and dog samples. A total of 15.4% (54/375) G. brevipalpis tested positive for trypanosomes. Detected trypanosome species with KIN primers were Trypanosoma congolense (Savannah) and T. theileri for blood samples and for tsetse flies T. congolense (Savannah and Kilifi) types were detected. Nested PCR targeting 18S rRNA gene detected T. congolense (Savannah) and T. theileri species. The sequences from this gene revealed great genetic diversity within these Trypanosoma species. Amplification of gGAPDH gene detected T. congolense (Savannah) and T. brucei brucei species when subjected to BLAST. Sequences obtained from this gene also revealed great genetic diversity and showed that the detected trypanosomes are different genotypes from the known species in other countries outside South Africa. Phylogenetic analysis revealed that South African Trypanosoma species were more genetically related to east African trypanosomes however, they formed isolated clusters with each other indicating that indeed they are different genotypes from the trypanosome species on the NCBI database. Blood meal analysis showed that G. brevipalpis preferred to feed on small mammals, birds and humans in the absence of livestock or other large wild reservoir hosts. This study showed that there are active trypanosomes circulating amongst livestock and tsetse flies in KwaZulu-Natal Province as well as the prevalence of T. theileri and T. b. brucei which were never documented in previous studies. Further research is needed to investigate the pathogenicity of these detected Trypanosoma parasites in domestic animals.

The use of urban wastewater for agriculture crop production is receiving renewed attention in most parts of the world due to the increasing scarcity of water. Water scarcity has placed pressure on the ability of households to meet their basic needs as the intermittent supply of water has created a demand for other sources of water, such as wastewater for irrigation, which can either be expensive or dangerous to public health. In this regard it might seem obvious to view wastewater as a major source of water for Bulawayo, Zimbabwe, particularly for irrigation. The general objective of the study was to characterise and determine treated domestic wastewater parameters that are of agricultural, public health and environmental importance for use in urban agriculture irrigation in Bulawayo. The study critically assessed the wastewater quality being used for urban agriculture in relation to its characteristics, the possible impacts on environment health and also quantifying the socio economic factors that can be derived from its use and, based on this assessment, to formulate a strategy for sustainable treated domestic wastewater use for irrigation. Data collection for this study was conducted in Bulawayo urban area and the gum plantation from 2005 - 2010. Extensive wastewater quality analysis was carried out and results of effluent analysis of key parameters, nitrogen and phosphorous were found to be 11.5 mg/l ± 4.4 and 13.5 mg/l ±14.9 respectively, which were within the World Health Organisation (WHO) (2006) acceptable range. These results aided to confirm that the treated domestic wastewater is of acceptable quality and hence has potential to be used for irrigating crops such as maize, beans and vegetables (chomolier) with minimal risk. Effluent heavy metals concentration in the form of Cadmium (Cd) and lead (Pb) measured values of 0.027 mg/l ± 0.01 and 0.45 mg/l respectively and were within the acceptable levels according to the WHO guidelines and Zimbabwe National Water Authority (ZINWA) standards. Heavy metal soil content was also observed to be within the acceptable limits with both Cd and Pb showing strong correlation with soil pH (r2= 1). Vegetable tissue analysis did not detect any significant levels of Cd and Pb in vegetable samples including Chomolier (not detected),maize (not detected), and beans (not detected), which then confirmed the conclusion that the treated domestic wastewater has potential for agricultural irrigation provided the quality of the effluent would not change drastically from the observed status which was measured over five years. With regard to social acceptance and economic benefits, the study revealed that acceptance for use of treated domestic wastewater and consumption of produce from its use was high amongst the farmers with 88.9% of respondents acknowledging no problem in using the treated domestic wastewater. Estimation of financial benefits were derived using the conventional market based approach which then revealed that an income of about US$1000 per plot/year is feasible if a proper management system is put in place. Findings of this study confirm that use of treated domestic wastewater for urban irrigation can improve livelihoods of the resource limited farmers despite the health challenges associated with its use. Majority of the famers reported that use of treated domestic wastewater for agriculture has contributed significantly to their socio- economic lifestyles by making extra income to cover school fees (44.6%), medication (9.85%) and food (99.1%). Apart from the financial benefits observed, calculations using the FAO formula for nutrient contribution, the study indicated that the treated domestic wastewater which was used contributed approximately 92 kg/ha/year, 108 kg/ha/year and 281.6 kg/ha/year of nitrogen, phosphorus and potassium respectively hence improving soil fertility of the sandy loam soils found at the farming area. Evaluation of the findings in relation to the recommended guidelines and standards of Food and Agricultural Organisation (FAO)/WHO and ZINWA suggests that the treated domestic wastewater used at the gum plantation is suitable for crop irrigation specifically for the following crops: chomolier, maize and beans that were investigated over time. In addition the benefits of using the treated domestic wastewater were noted to have the potential to enhance proper management of wastewater irrigation as proposed in the strategy as it proved to be a reliable water resource. Adherence to the strategy that is proposed in this thesis of involving stakeholders, addressing policy and legal issues, supporting research and outreach, marketing and periodic monitoring of effluent, soil and plant quality parameters will ensure successful, safe, long-term wastewater irrigation that will balance human and environmental needs.