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The expression and evaluation of CrpeNPV gp37 as a formulation additive for enhanced infectivity with CrleGV-SA and improved Thaumatotibia leucotreta control
Get PDFThaumatotibia leucotreta (Meyrick) (Lepidoptera: Tortricidae) is a significant pest native to Africa, causing damage to citrus and posing a threat to the export of fresh citrus in South Africa. Classified as a phytosanitary risk by several South African export markets, this pest necessitates effective control measures. Baculoviruses emerge as promising biological control agents against T. leucotreta due to their inherent safety and eco-friendly characteristics. Among these, Cryptophlebia leucotreta Granulovirus (CrleGV-SA) and Cryptophlebia peltastica Nucleopolyhedrovirus (CrpeNPV) stand out, both causing larval mortality upon infecting T. leucotreta. CrleGV-SA has been formulated into the products Cryptogran™, CryptoMax™ and Cryptex®, while CrpeNPV has been formulated into the product Multimax™. Both viruses are used in integrated pest management programmes to reduce fruit damage in agricultural fields, with CrleGV-SA having been employed against T. leucotreta for nearly 20 years in South Africa. However, these control options are limited by factors such as virulence and the slow speed of kill. This limitation can be addressed by exploiting potential synergistic relationships between baculoviruses infecting the same host. Previous studies have demonstrated that the truncated CpGV gp37 can enhance the infectivity of NPVs on other lepidopteran pests, such as Spodoptera exigua (Hübner). Although the mechanism behind this phenomenon remains unclear, it presents an opportunity to enhance the effectiveness of baculovirus-based management strategies. Notably, the genome of CrpeNPV encodes gp37, while CrleGV-SA lacks this gene. The potential interaction between CrleGV-SA and CrpeNPV gp37 remains unexplored. Therefore, investigating whether they exhibit synergistic or antagonistic effects is essential for optimising baculovirus-based management of T. leucotreta. This study aims to express CrpeNPV gp37 in a bacterial system and then evaluate its effect on larval mortality when combined with CrleGV-SA in laboratory bioassays. The initial step involved extracting genomic DNA (gDNA) from occlusion bodies (OBs) of CrpeNPV. A modified Quick DNA Miniprep plus kit was utilised, which entailed pre-treatment with Na2CO3 followed by neutralisation with Tris-HCI before gDNA extraction using the kit. Subsequently, the concentration of the gDNA was estimated using a Nanodrop spectrophotometer. Oligonucleotides targeting the CrpeNPV gp37 gene were designed for PCR amplification, with the gDNA serving as a template. The gp37 amplicon was identified through agarose gel electrophoresis and then gel purified in preparation for cloning. Secondly, the purified PCR product was cloned into the intermediate vector pJET1.2/blunt and then subcloned into the bacterial expression vector pCA528 through DNA ligation. The construction of recombinant plasmids (pJET-gp37 and pCA-gp37) was conducted and verified using Colony PCR, plasmid extraction, restriction enzyme analysis, and Sanger sequencing. Thirdly, the recombinant protein (6×His-SUMO-gp37) was expressed and purified using Nickel affinity chromatography and analysed through SDS-PAGE and Western blot techniques. The expression of 6×His-SUMO-gp37 was carried out at both 25 °C and 18 °C. A time course induction study was conducted, inducing transformed cells for 0-, 3-, 5-, and 24-hours post induction (hpi). SDS-PAGE and Western blotting of samples collected at various time points revealed that 6×His-SUMO-gp37, approximately 42 kDa in size, was visible from 3 hpi, with maximal expression at 24 hpi. Solubility analysis of 6×His-SUMO-gp37 was performed at both temperatures, showing solubility at 18 °C but predominantly present in the insoluble fraction. The soluble protein was purified under native conditions, while the insoluble protein was purified under denaturing conditions. Despite being unable to elute 6×His-SUMO-gp37 under native conditions, successful elution was achieved under denaturing conditions, confirmed via Western blot analysis. No further experiments were conducted on the eluted 6×His-SUMO-gp37 under denaturing conditions. Lastly, a preliminary surface dose bioassay was conducted to evaluate the efficacy of pelleted bacteria expressing 6×His-SUMO-gp37 in combination with CrleGV-SA against T. leucotreta neonates. Two lethal concentration doses of CrleGV-SA were prepared: a low concentration (2.96×104 OBs/mL) capable of killing 40 % of the T. leucotreta population, and a high concentration (2.96×105 OBs/mL) capable of killing 90 % of the population. The target protein, 6×His-SUMO-gp37, and the control, pCA528, were obtained by lysing the cells, centrifuging the samples, and collecting the insoluble fractions in pellet form. These fractions were then resuspended in PBS and used as treatments in combination with the prepared CrleGV-SA concentration doses. The concentration of the pellets was estimated using a Nanodrop spectrophotometer by measuring the absorbance at 280 nm. The bioassay results revealed that the combination of 100 μg/mL of pelleted bacteria expressing 6×His-SUMO-gp37 with CrleGV-SA had no effect on T. leucotreta larval mortality compared to CrleGV-SA alone. A one-way ANOVA was performed to assess differences among the virus treatment groups, concluding that no statistically significant differences were observed among the groups. The experiments in this study provided valuable insights for future research, particularly in exploring the use of a protein-virus combination as a novel method for pest control.Thesis (MSc) -- Faculty of Science, Biochemistry, Microbiology & Bioinformatics, 202
Decolonizing Journalism Education in South Africa
No full textThe British, French, and Portuguese regimes colonized most African countries. This colonization took away African languages, cultures, religions, and practices, only to replace them with colonial traditions. Decolonization debates are now rife in South Africa: decolonizing higher education, the economy, the law, and the justice system. All these debates and attempts are made to achieve equity and justice in the country. To contribute to these debates, this chapter examines how journalism education can be decolonized in South Africa from a sociolinguistic perspective. To achieve its aim, the chapter will review course descriptions of journalism curriculums at three universities in South Africa that offer journalism education and possible ways to decolonize the curriculums from the sociolinguistics perspectives. The chapter has concluded that sociolinguistics is critical in decolonizing journalism education. Journalism is a verbal medium; it uses language to communicate. Hence, it is essential for journalism curriculums in South Africa to teach students that language and identity can influence journalism practice to reflect its context and speak to its people in a language and forms that they understand
Black Twitter and Digital Counterpublics in South Africa
Get PDFThe growth of technology has made the Internet an essential tool in so-ciety. Scholars have argued that the Internet supports a more delibera-tive democracy. However, scholars have also raised concerns about the role of the Internet in political matters. While scholars agree that the Internet has facilitated broader public discussion, in many regards, its ‘virtual public sphere’still mirrors existing social structures. Twitter has become a common social media platform for many South Africans. This has led to a virtual community of Twitter users engaged in real-time dis-courses primarily related to Black South Africans. Black Twitter in South Africa is used for social, political, and economic motivations. This study argues for the practice of Black Twitter as a digital counterpublic in South Africa. The aim is to spotlight how black people in South Africa have used Black Twitter as a digital counterpublic for the marginalized groups within South Africa. The research will investigate the potential challenges and opportunities associated with Black Twitter functioning as a digital counterpublic. Utilizing digital ethnography, the study gath-ered a dataset of tweets from Black Twitter in 2022, focusing on those addressing social, political, and economic issues. More than 700,000 tweets were identified under these specific thematic hashtags
Biotic resistance towards Hydrellia egeriae, a biological control agent for the aquatic weed Egeria densa, in South Africa
Get PDFEgeria densa is a submerged aquatic weed that can grow into dense monocultures in rivers and dams in South Africa, which negatively affects ecosystem functioning and services. The biological control agent Hydrellia egeriae Rodrigues-Júnior (Diptera: Ephydridae) was first released against Egeria densa Planchon (Hydrocharitaceae) in South Africa in 2018. Biotic resistance in an introduced range can have negative impacts on the ability of a biological control agent to establish and exert top-down pressure. Dipteran and lepidopteran species that are used as biological control agents are often susceptible to higher levels of parasitism in their introduced range than biological control agents from other insect orders. In addition, ecological analogues that are present in South Africa, make H. egeriae particularly vulnerable to biotic resistance. Considering this, post-release surveys were conducted to investigate if native parasitoids will extend their host range to include H. egeriae. Chaenusa seminervata van Achterberg, C. anervata van Achterberg (Braconidae: Alysiinae: Dacnusini) and Ademon lagarosiphonae van Achterberg (Braconidae: Opiinae) were reared from field-collected H. egeriae pupae, within a year of its release. These braconid parasitoids were previously recorded from a native herbivore, Hydrellia lagarosiphon Deeming (Diptera: Ephydridae)
A Feasibility Study on the Efficacy of Functional Near-Infrared Spectrometry (fNIRS) to Measure Prefrontal Activation in Paediatric HIV
Get PDFHuman immunodeficiency virus (HIV) infection is associated with disturbed neurotransmission and aberrant cortical networks. Although advances in the imaging of brain microarchitecture following neuroHIV has added to our knowledge of structural and functional changes associated with HIV, no data exists on paediatric HIV using optical neuroimaging techniques. This study investigated the feasibility of optical neuroimaging in paediatric HIV using functional near-infrared spectrometry (fNIRS). We measured prefrontal brain activation while participants executed a sustained attention task. We specifically tested whether patients living with HIV and study controls could perform the study protocol and whether we could measure the typical fNIRS haemodynamic response associated with neuronal activity. Eighteen participants (10 HIV participants, mean age: 13.9, SD = 1.66 years; 8 controls, mean age: 14.8, SD = 1.28 years), matched for sex, grade, and socio-economic status, were included in the study. All participants completed the Stroop colour word test (SCWT). Oxygenated haemoglobin concentration and the deoxygenated haemoglobin signal were recorded from the dorsolateral prefrontal cortex and the frontopolar area (FA) using fNIRS. The control group performed significantly better in terms of reaction time on the congruent and incongruent condition (congruent: t (16) = −3.36, : incongruent: ). A pooled group analysis of the sample indicated significant activation in the DLPF and FA to the congruent condition of the SCWT (). Although cortical activation was noted in the DLPF and the FA in each of the groups when analysed independently, this neural activation did not reach statistical significance. The results show promise that fNIRS techniques are feasible for assessing prefrontal cortical activity in paediatric HIV. Future studies should seek to reduce the signal-to-noise ratio and consider inter-individual variability when measuring prefrontal activation in paediatric samples
Spatiotemporal variations in the occurrence of Campylobacter species in the Bloukrans and Swartkops rivers, Eastern Cape, South Africa
No full textAn increase in the incidence of Campylobacter species in rivers raises concerns on the safety of river water for humans who get exposed to river water. This study examines the spatiotemporal dynamics of Campylobacter species in the Bloukrans and Swartkops rivers, analysing patterns of its occurrence in relation to meteorological conditions, physicochemical parameters, seasons, and sampling sites. Physico-chemical parameters and meteorological conditions were measured during water sampling from various sites along the rivers over a year, while Polymerase Chain Reaction (PCR) was utilised to detect Campylobacter genus-specific genes and selected antibiotic-resistant genes
No grief without joy
No full textHow does grief unfold and refold after the death of a loved one? How does it bend and diffract through the prism of loss? What are the possibilities of feeling or even love in the wake of bereavement? These questions linger as I listen to Lise Morrison's No grief without joy, released in July 2023 on Sawyer Editions. The debut portrait album comprises five works written between 2016 and 2019 in a time of feverish artistic growth while she was studying composition at the Royal Conservatoire in The Hague. Yet, as Morrison writes in the liner notes, this was also a ‘period that echoes, in part, the grief after [her] mother's passing at the end of 2015’
Sediment and associated phosphorus dynamics in meandering floodplain wetlands in the Tsitsa River catchment
Get PDFA key function of floodplain wetlands systems is their ability to remove and store sediments and associated particulates (such as nutrients, organic carbon, and contaminants) from water, thus improving water quality for downstream ecosystems and water users. Increases in sediment and nutrient inputs to drainage networks pose a serious challenge to integrated resource management. These issues can be partly mitigated through natural buffering solutions along drainage networks, such as preserving essential wetland systems like floodplains. However, their trapping efficiency and storage timescales are uncertain. Although a large body of international knowledge and literature has advanced our understanding of river-floodplain systems and the ecosystem services that they provide, the factors determining their likelihood and effectiveness in supplying those regulatory ecosystem services have not been extensively and scientifically tested in floodplain systems in South Africa. This research aimed to describe and quantify the regulatory ecosystem services related to sediment and phosphorus buffering dynamics of two meandering floodplain systems in the Eastern Cape, South Africa. The study examined the geomorphology, sedimentology, and historical rates of sediment and associated phosphorus accumulation and release in the two floodplain systems. These systems varied in their morphometric features, size, catchment location, and predominant land use, providing a diverse range of characteristics. A comparative analysis was conducted between the two systems to understand the influence of local and catchment-scale factors. Time-averaged suspended sediment samples from the two wetlands were used to compare suspended sediment and associated total phosphorous fluxes over annual scales. Although both floodplains were net depositional during the study period, contemporary suspended sediment mass balance calculations suggested that the relatively larger Minnehaha floodplain system (~1.5 km²) situated in a significantly smaller catchment (~40 km²) had notably higher sediment and associated phosphorus trapping efficiencies of 44 % and 49 % respectively, compared to 16 % and 8 % for the relatively small Gatberg floodplain system (~0.3 km2) situated in a much larger catchment (~135 km²). This variability is attributed to the interaction between annual rainfall regimes, sediment supply, sediment composition, relative wetland size to catchment area and wetland geomorphic character. To test the hypothesis that the suspended sediments and associated total phosphorus were retained by the adjacent floodplain system and to determine which parts of the two floodplains were most effective for retaining suspended sediments and phosphorus, concurrent measurements of sediment accretion were made at 6 sites in different geomorphic features in each of the floodplains. This was achieved using Cesium-137 and Lead-210 (Hereinafter referred to as ¹³⁷Cs and ²¹⁰Pb) dating techniques. In-field observations suggested that all geomorphic units are still active and are frequently inundated during overbank flood flows. The average overbank sediment deposition and total phosphorus accumulation rates were 9376.9 g-sediment m¯² yr¯¹, 0.8 g-TP m¯² yr¯¹ for the Gatberg floodplain and 11802.8 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Minnehaha floodplain. Deposition rates were temporally and spatially highly variable and dependent on the sediment supply, microtopographic relief, sinuosity, distance from the channel, the mode of inundation, and the extent of retention pondage. Overall, high average deposition rates were associated closest to the channel within the proximal floodplain zone (9712.1 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Gatberg floodplain; 13541.1 g-sediment m¯² yr¯¹, 1.0 g-TP m¯² yr¯¹ for the Minnehaha floodplain) where the highest D₅₀ particle sizes (25.4 μm for the Gatberg and 32.8 μm for the Minnehaha) and percentage sand fractions (15 % and 21 %, respectively) were found. This may reflect the coarse nature of the sediment and the frequent connectivity to the channel, suggesting rapid accumulation is linked to a larger particle size which was deposited more readily in this zone. In the Gatberg system, the backswamp zone had one of the highest sedimentation rates and second highest phosphorus accumulation rates (13806.8 g-sediment m¯² yr¯¹, 0.9 g-TP m¯² yr¯¹). This was attributed to the additional coarse sediment inputs from the uncapped gravel forestry road that runs adjacent to the floodplain margin. In contrast, the backswamp zone within the Minnehaha River floodplain system had the lowest sedimentation rates (2005.9 g-sediment m¯² yr¯¹, 0.1 g-TP m¯² yr¯¹, which is what would be expected for the zone furthest away from the channel. In both floodplains, oxbows were important fine-sediment and phosphorus retention features (7126.0 g-sediment m¯² yr¯¹, 0.6 g-TP m¯² yr¯¹ for the Gatberg floodplain; 10101.0 g-sediment m¯² yr¯¹, 1.1 g-TP m¯² yr¯¹). Phosphorus distribution patterns were mainly attributed to variations in organic matter content and iron concentrations in fine-grained sediment deposits, while particle size distributions were less important. Using a mass balance approach the trapping efficiencies of the two floodplain systems were estimated. The average trapping efficiency for the Gatberg River floodplain accounts for 16 % of the suspended sediment yield (1317.5 tonnes-sediment yr¯¹) and 8 % of the suspended sediment-associated total phosphorus yield (0.093 tonnes-TP yr¯¹). Deposition on the Minnehaha floodplain accounts for an average of 44 % (1073.6 tonnes-sediment yr¯¹) and 49 % of the suspended sediment-associated total phosphorus yield (0.098 tonnes-TP yr¯¹). Within the Gatberg and Minnehaha River floodplain systems, the sediment sinks (oxbow and backswamp geomorphic zones) accounted for 13 % and 6 % (1070.6 tonnes-sediment yr¯¹ and 0.069 tonnes-TP yr¯¹); and 28 % and 33 % (683.2 tonnes-sediment yr¯¹ and 0.066 tonnes-TP yr¯¹), respectively, of the mean proportion of the total sediment and associated phosphorus yield. The zone of potential exchange (the proximal floodplain geomorphic zone) within the Gatberg floodplain system was calculated to trap 3 % (247.1 tonnes-yr¯¹) of the mean proportion of the total sediment yield and 2 % (0.023-tonnes yr¯¹) of the mean proportion of the total associated-phosphorus yield. Within the Minnehaha floodplain, this zone was estimated to trap 16 % (390.4 tonnes-sediment yr¯¹ and 0.032 tonnes-TP yr¯¹) of the mean proportion of both the total sediment and associated total phosphorus yield. These results indicate the importance of the distal floodplain reaches and oxbows as sediment and phosphorus storage hotspots. While floodplains mainly result from the accumulation of sediment, they're often modified and altered by erosion processes. Channel erosion and avulsions (e.g. meander bend cutoff events) are natural dynamic processes and form two of the principal processes of meandering river migration. During two wet seasons, both Gatberg and Minnehaha River floodplain areas experienced a mix of deposition and erosion, with slightly higher erosion observed in the Gatberg River reach. Channel bed scouring was prevalent in most cross-sections, suggesting limited sediment accumulation within the main channel beds. Volumetric estimates of sediment loss from meander migration were calculated by analysing cross-sectional data from 2019 and 2021 surveys to determine median and maximum eroded volumes, which were then converted to mass and scaled to tonnes per year for each river's eroded meander bends. The eroded sediment volumes were estimated as 520 tonnes yr¯¹ for the Gatberg and 360 tonnes yr¯¹ for the Minnehaha. The time sequence analysis using historical aerial images (between 1958, 1966, 1993, and 2015) revealed a few channel planform changes due to meander bend cutoff events in both river reaches. These events influence river morphology, increasing local channel slope, reducing sinuosity, and limiting floodplain access while impacting sediment and phosphorus flux. In the Gatberg system, changes in land use, such as increased road density from commercial forestry activities, likely drove channel straightening to accommodate higher sediment and bed loads. In the Minnehaha system, agricultural practices and livestock tracks likely increased sediment loads and hillslope-channel connectivity, driving channel changes. The results from the geochronology of two nested oxbows on the Gatberg floodplain estimated lateral migration rates of ~0.03 m yr¯¹. The floodplain reworking rates of the Gatberg River floodplain are low compared to other systems in humid regions around the world, although, the Gatberg system compares well with migration rates of rivers in dryland regions. This study highlights the potential for floodplains undergoing regular flooding to be effective natural buffers along the sediment and phosphorus cascade in dryland landscapes. It enhances our comprehension of how sediment accumulates over time on floodplains within South African river systems, shedding light on both spatial and temporal patterns. These insights can contribute to better methodologies for evaluating the services provided by floodplain wetlands. These results can inform management decisions by offering a deeper understanding and allowing for the quantification of the cost-benefit of floodplain restoration and preservation actions in South Africa.Thesis (PhD) -- Faculty of Science, Faculty of Science, Geography, 202
Context-related drivers, occurrence and human exposure to antibiotic resistant Campylobacter in selected river systems in the Eastern Cape, South Africa
Get PDFThe increasing prevalence of antibiotic-resistant Campylobacter species in river systems is a growing public health concern globally. This challenge presents the need to understand the drivers influencing the occurrence of these antibiotic-resistant strains to inform effective mitigation strategies. Identifying local anthropogenic pressures/activities will enable tailored intervention and ensure that management efforts are targeted and effective in mitigating actual risks faced by local water resources. In particular, the occurrence of antibiotic-resistant Campylobacter in river systems causes concerns regarding potential human exposure. Campylobacter species are regularly implicated in both animal and human diarrhoea, and have gained recognition as one of the main causes of waterborne diseases. This study investigated context-related drivers to the presence of antibiotic-resistant Campylobacter, its occurrence, and the risk of human exposure in the Bloukrans and Swartkops rivers in the Eastern Cape, South Africa. The study utilised a questionnaire survey and focus group discussions to identify context-related sources and drivers of antibiotic-resistant bacteria and genes in the Bloukrans and Swartkops rivers. Additionally, physico-chemical analysis of water samples was done, and polymerase chain reaction (PCR) was employed to investigate occurrences of Campylobacter in both rivers, as well as the presence of virulent and antibiotic-resistant genes. Two control sites, one for each river, and a total of nine other sampling sites were selected for this study, four along the Bloukrans River and five along the Swartkops River. Water samples were collected from all eleven sites over a period of one year, covering all the seasons (winter, spring, summer and autumn). Exposure assessment was investigated by conducting propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) to quantify the concentration of viable Campylobacter and its antibiotic-resistance genes (ARGs) in the river water. The calculated concentration of viable Campylobacter and ARGs was then used to estimate human exposure dose of antibiotic-resistant Campylobacter via unintentional ingestion during swimming in the Bloukrans or Swartkops rivers. The questionnaire surveys and focus group discussions identified the factors of socio-demographic characteristics of the study catchments, lack of knowledge regarding antibiotic resistance, inappropriate antibiotic and disposal practices as well as anthropogenic activities (improper solid waste management, discharge of poorly treated wastewater, poor animal husbandry practices, urban run-off and storm water, industrial effluent and agricultural run-off) as context-related sources and drivers contributing to the emergence and of continuing occurrence antibiotic-resistant bacteria and genes in the Bloukrans and Swartkops rivers. The results obtained in this study suggest that the physiochemical properties of the water in the Bloukrans and Swartkops rivers are conducive for Campylobacter survival. The prevalence of Campylobacter was high at sites that recorded high turbidity, low dissolved oxygen and high conductivity. This study also highlighted the widespread and continual presence of Campylobacter spp. in the Bloukrans and Swartkops rivers, which are potentially antibiotic-resistant. The prevalence of Campylobacter was 60% virulence genes were detected at 15% (cadF), 10% (htrB), 10% (clpP), 5% (ciaB) and 5% (ctdC) for water samples from the Bloukrans River. Campylobacter was detected in 58% of water samples from the Swartkops River, while cadF, htrB, ciaB, clpP and ctdB were detected at 24%, 0%, 9.5%, 14.8% and 4.8%, respectively. Of the Campylobacter-positive water samples, the virulence genes cmeA, cmeB and cmeC were detected in 20%, 65% and 10% of the water samples from Bloukrans River, respectively. Similarly, the genes cmeA, cmeB and cmeC were detected at 14.3%, 52% and 9.5%, respectively, for the Swartkops River. Tetracycline resistance genes (tetO) were detected in 70% and 76% of the water samples collected from the Bloukrans and Swartkops rivers, respectively. It was also observed that the sampling site had a significant effect on the detection of Campylobacter for both rivers (p < 0.05). The prevalence of Campylobacter was higher for sites impacted by anthropogenic activities. The results show that sampling season had no significant effect on the occurrence of Campylobacter for both rivers. The analysis through PMA-qPCR revealed that the mean concentrations of the Campylobacter 16S rRNA gene from viable cells ranged from 2.1 × 104 to 1.75 × 105 copies/ml for the Bloukrans River, and from 0 (no detection) to 1.11 × 104 copies/ml (viable concentration) for the Swartkops River. The concentration of tetO from viable cells ranged from 4.75 × 101 to 2.71 × 103 copies/ml and 115.96 to 325.12 copies/ml, for the Bloukrans and Swartkops Rivers, respectively. Similarly, the concentration of cmeB genes from viable cells ranged from 7.8 × 101 to 2.76 × 104 copies/ml for the Bloukrans River and from 1.71 × 101 to 7.39 × 103 copies/ml for the Swartkops River. We utilized the calculated concentrations of viable Campylobacter 16S rRNA genes and ARGs to estimate the human intake burden of viable Campylobacter 16S rRNA copies per one-hour of swimming to range from 9.9 × 101 – 3.7 × 106 copies/h across the two rivers. The human intake burden of Campylobacter ARGs ranged from 3.6 × 102 – 5.8 × 105 copies/h for cmeB, and 9.98 × 102 – 5.7 × 104 copies/h for tetO. This study highlighted the intricate interplay of socio-demographic characteristics in the study catchments, such as insufficient awareness of antibiotic resistance, inappropriate antibiotic disposal practices and anthropogenic activities, which all contribute to the prevalence of antibiotic-resistant Campylobacter in the Bloukrans and Swartkops rivers, emphasizing the need for targeted interventions to address these specific influences. There is a potential risk of Campylobacter infections associated with human exposure to the rivers. This work contributes towards the body of knowledge in closing the current research gap on possible human exposure to antibiotic-resistant Campylobacter, and in general, exposure to ARBs through freshwater sources. The findings have practical implications for designing targeted interventions to mitigate these risks, to enhance the overall environmental and public health management in the region.Thesis (PhD) -- Faculty of Science, Institute for Water Research, 202
Taxonomy- and trait-based responses of chironomid assemblage structure to pollution in selected urban rivers, Eastern Cape, South Africa
Get PDFUrbanisation, occasioned by an increasing human population and the proliferation of industries, is a major threat to freshwater resources and has been implicated as a cause of stream water quality deterioration, habitat degradation, and the loss of aquatic biodiversity. Pollution of freshwater systems resulting from urban-related activities severely alters stream ecosystem structure and function. To effectively protect and sustainably manage freshwater resources, it is important to develop biomonitoring tools which are both sensitive to changes in water quality conditions and can provide an understanding of the mechanisms by which urban pollution impacts freshwater ecosystems. In South Africa, the macroinvertebrate-based South African Scoring System version 5 (SASS5) is routinely used for water quality assessment. This tool is developed at the family level of taxonomic resolution, with the exception of a few taxa. This raises the question as to whether a species-level taxonomic approach, complemented with a trait-based approach could add additional value. This question was addressed comparatively by developing and applying a taxonomy- and trait-based approach using the taxonomically and functionally diverse Chironomidae family. Fifteen sites across three urban river systems (Buffalo, Bloukrans and Swartkops River systems) in the Eastern Cape Province of South Africa were purposefully selected for this study. Based on the predominant land use within the catchment of the sites and water quality variables, the study sites were grouped into five site categories. The least-impacted sites (REF) had 78.53% mean forested area, 5.98% mean urban area and 13.49% mean agricultural land. Sites that received diffuse pollution but were upstream from the effluent discharge point of wastewater treatment works (DP) had 59.07% mean forested area, 32.53% mean urban area and 6.20% mean agricultural land. Sites that received point source pollution from wastewater treatment works (PP) had 63.66% mean forested area, 26.26% mean urban area and 7.39% mean agricultural land. Sites further downstream from the wastewater treatment works that received impacts from both point source and diffuse pollution (AG) had 65.95% mean forested area, 18.24% mean urban area and 12.5% mean agricultural land. Sites selected for exploring the potential system recovery of the study rivers (RECV) had 77.21% mean forested area, 9.12% mean urban area and 10.7% mean agricultural land. Macroinvertebrates and physicochemical variables were sampled at sites in the Bloukrans and Buffalo rivers over four sampling events (spring, summer, winter, and autumn) between November 2021 and June 2022 using the SASS5 protocol. Historical chironomid and physicochemical data from the Swartkops River collected between 2009 and 2012 were also used in this study. The SASS5 family-level biotic index classified the water quality condition at the least impacted site (REF) of the Swartkops River as minimally impaired 80% of the time, compared to the chironomid-based multimetric index (CUMMI), which indicated that the water quality condition at this site was near-natural 50% of the time. The chironomid-based multimetric index and the SASS5 were divergent in their classification of water quality conditions at the DP and AG sites but were 100% in agreement regarding water quality conditions at the PP site as critically/severely modified. The SASS5 scores classified the water quality condition at the AG site as critically/severely modified 100% of the time, whereas the CUMMI index classified the water quality condition at this site as critically/severely modified 90% of the time but moderately modified 10% of the time. The results indicate that species-level and family-level indices tend to be in agreement for heavily impacted sites, but the same was not true for least or moderately impacted sites. Traits such as the possession of tracheal gills, very large body size, burrowing, whole-body undulation, construction of rigid tubes, possession of three tracheae, completion of lifecycle in more than one year, production of more than 1000 eggs per egg mass, preferences for fine detritus, and bivoltinism were deemed tolerant of urban pollution. Traits such as cuticular respiration, medium body size, predator feeding mode, completion of lifecycle within one year, and a preference for stone biotope were deemed sensitive to urban pollution. An approach was developed to classify chironomids into those that are potentially vulnerable and those that are resilient to urban pollution. The abundances of vulnerable species correlated positively with increasing dissolved oxygen and negatively with increasing turbidity, electrical conductivity, nitrite-nitrogen, ammonium-nitrogen, and orthophosphate-phosphorus. The relative abundance of the highly vulnerable species and that of the highly tolerant species responded significantly to urban pollution and differentiated between the site categories. The relative abundance of the highly vulnerable species was significantly different between the DP and PP site categories. The richness of vulnerable and highly vulnerable species was significantly different between the REF sites and the impacted site categories (DP, PP, and AG). These results indicated that the developed approach successfully predicted chironomid responses to urban pollution. Overall, the study makes important contributions to the field of freshwater biomonitoring. First, the study highlighted that species-level identification is necessary to differentiate sites which may be considered moderately impacted. Both family and species-level tools were sensitive to water quality conditions for least impacted and highly impacted sites, but the differences between the family-level and species-level indices were pronounced for sites considered moderately impacted. Second, a trait-based approach provided a mechanism for developing predictive tools, and in the case of this study, the potential resilience or vulnerability of chironomids was reliably predicted.Thesis (PhD) -- Faculty of Science, Institute for Water Research, 202