College of Agriculture, Engineering and Science

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A framework for modelling the interactions between biochemical reactions and inorganic ionic reactions in aqueous systems.
(2022) Brouckaert, Christopher John.; Lokhat, David.
Bio‐processes interact with the aqueous environment in which they take place. Integrated bio‐process and three‐phase (aqueous–gas–solid) multiple strong and weak acid/base system models are being developed for a range of wastewater treatment applications, including anaerobic digestion, biological sulphate reduction, autotrophic denitrification, biological desulphurization and plant‐wide wastewater treatment systems. In order to model, measure and control such integrated systems, a thorough understanding of the interaction between the bio‐processes and aqueous‐phase multiple strong and weak acid/bases is required. This thesis is based on a series of five papers that were published in Water SA during 2021 and 2022. Chapter 2 (Part 1 of the series) sets out a conceptual framework and a methodology for deriving bioprocess stoichiometric equations. It also introduces the relationship between alkalinity changes in bioprocesses and the underlying reaction stoichiometry, which is a key theme of the series. Chapter 3 (part 2 of the series) presents the stoichiometric equations of the major biological processes and shows how their structure can be analysed to provide insight into how bioprocesses interact with the aqueous environment. Such insight is essential for confident, effective and reliable use of model development protocols and algorithms. Where aqueous ionic chemistry is combined with biological chemistry in a bioprocess model, it is advantageous to deal with the very fast ionic reactions in an equilibrium sub‐model. Chapter 4 (part 5 of the series) presents details of how of such an equilibrium speciation sub‐model can be implemented, based on well‐known open‐source aqueous chemistry models. Specific characteristics of the speciation calculations which can be exploited to reduce the computational burden are highlighted. The approach is illustrated using the ionic equilibrium sub‐model of a plant‐wide wastewater treatment model as an example. Provided that the correct measurements are made that can quantify the material content of the bioprocess products (outputs), the material content of the bioprocess reactants (inputs) can be determined from the bioprocess products via stoichiometry. The links between the modelling and measurement frameworks, which use summary measures such as chemical oxygen demand (COD) and alkalinity, are described in parts 3 and 4 of the series, which are included as appendices to the thesis. An additional paper, presenting case study on modelling an auto‐thermal aerobic bio‐reactor, is included as a third appendix, as it demonstrates the application of some of the principles developed in the series of papers.
Developing integrated climate change adaptation strategies using the water-energy-food nexus approach: a case study of the Buffalo River catchment, South Africa.
(2023) Dlamini, Nosipho.; Senzanje, Aidan.; Mabhaudhi, Tafadzwanashe.
South Africa’s climate has high spatial and temporal variability. Literature on historical rainfall patterns shows substantial declines in rainfall across the country, except in south-western South Africa, which displays increasing trends. Under the Representative Concentration Pathways (RCPs) 4.5 and 8.5 scenarios, statistically downscaled rainfall projections show different patterns across South Africa throughout the 21st century. Literature indicates that this uncertainty will majorly impact South Africa’s surface water availability as its main input variable is rainfall; hence, all possible outcomes need to be planned for. Planning should include the energy and food production sectors as they primarily depend on the water sector. The Buffalo River catchment, situated in the northern parts of KwaZulu-Natal, South Africa, is a high rainfall receiving area, with a mean annual precipitation of 802 mm. Despite its abundant rainfall, the catchment has had its fair share of droughts, significantly impacting livelihoods and socio-economic activities. Recent reports indicate that the Buffalo River catchment’s surface water storage facilities are insufficient to meet the population’s demands by 2050. A detailed water resources assessment is required to confirm and quantify the possible alterations that climate change could cause to the catchment’s hydrology before any actions can be taken, especially regarding increasing the water storage capacity of the catchment. As such, this study aims to investigate and assess the impacts of climate change on the Buffalo River catchment’s surface water availability and reliability of water resources in meeting projected water demands, with a specific focus on agricultural and energy generation water demands. Furthermore, the study aims to develop integrated water resources adaptation strategies to increase water, energy and food security within the catchment. Due to its transdisciplinary nature, the Water-Energy-Food (WEF) nexus methodology was used as an analytical tool to carry out the research’s objectives. The study was based on the null hypotheses of climate change not varying surface water availability and reliability, and that the optimized CC water management strategies will not yield any improvements in merging potential gaps between water supply and demands. Study findings indicate that the Buffalo River catchment is anticipated to receive increases in precipitation magnitude and fluctuations throughout the 21st century. However, the increases in surface water availability that result from the anticipated rainfall increases are insufficient and unreliable to meet the rise in demands for water within the catchment, more so the irrigation demands. Through investigating the catchment’s already-existing proposed climate change policy interventions for water resources management, the study found that they were centred around boosting domestic water provisions whilst only meeting <3% of projected demands by the energy and agricultural sector. As such, by optimizing these policy plans using the WEF nexus’ Climate, Land-Use and Water Strategies (CLEWS) framework’s analytical tools, integrated climate change adaptation strategies were formulated, which were modelled to significantly improve the water storage capacity of the catchment, as well as water allocations and distribution among water users. The study concluded that the Buffalo River catchment’s surface water availability is expected to increase under climate change, however, current water storage capacity is not reliable to meet water demands throughout the 21st century. Lastly, the study also concluded that the catchment does possess immense potential for improved surface water availability to merge the gap between its water supplies and demands. Thus, the null hypotheses stipulated in this research are rejected. For discussions, policymaking and general research related to these improvements in water resources management in the Buffalo River catchment, the climate change adaptation strategies established in this research are recommended. Also, based on model evaluation statistics, the WEF nexus was successful in examining the interrelations among WEF resources, and is recommended for future studies to examine long-term integrated demand-supply strategies for WEF sectors.
Evaluation of soil moisture estimates from satellite based and reanalysis products over two network regions.
(2022) Naidoo, Kivana.; Chetty, Kershani Tinisha.; Gokool, Shaeden.
The soil is an important variable of the hydrological cycle. It plays a key role in the distribution of water and energy fluxes between the surface and atmosphere. Soil moisture data can be used to develop early warning systems for flood and drought monitoring, improve weather and climate forecasting and provide an indication of crop water requirements. Therefore, the regular monitoring of this variable can prove to be beneficial to various management applications. One of the main issues associated with estimating soil moisture is to adequately account for its spatial and temporal variability as it is influenced by factors such as climate, topography, soil properties and land cover. There are different methods available to derive soil moisture estimations such as in-situ, remote sensing and modelling-based approaches. In-situ methods generally produce reliable soil moisture estimates, however, are only suitable for small scale studies. Alternatively, remote sensing and modelled reanalysis methods can provide soil moisture estimates over a large spatial extent, however, they are generally limited by their coarse spatial resolutions and may not be suitable for localised applications. Therefore, the aim of this study was to implement and evaluate a downscaling technique across two regions (South Africa and USA) to ultimately produce finer scale soil moisture and address the scale mismatch between in-situ methods and coarse resolution products. This procedure was facilitated by two data processing platforms, Google Earth Engine (GEE) and R, which showed significant potential for data processing and analysis. Additionally, satellite-based and reanalysis products were also evaluated to determine which of these methods are more suitable for soil moisture estimation. The soil moisture products and the downscaled products were validated against the CRNS instrument, which was particularly chosen for its performance at an intermediate spatial resolution. The SMAP_25 km product performed best at the Two Streams site and was selected for downscaling, whilst the CFSV2 product performed best at the Mead CSP3 and York Benny catchments and was chosen to be downscaled at both these sites. The results from the study indicated that the downscaled products for the Two Streams and Mead CSP3 sites performed better than the original products when compared to the CRNS data. The data acquired for the York Benny site revealed that the downscaled product performed similarly to the CFSV2 product. Therefore, downscaling does not always result in an improved outcome. However, from the results acquired for the Two Streams and Mead CSP3 study sites, it is evident that downscaling shows significant potential in producing better soil moisture estimates, which could be used to improve planning and management operations for various purposes.
Isolation and characterization of bacteriophages from wastewater as potential biocontrol agents for Escherichia coli.
(2022) Ntuli, Nontando Percevierance.; Schmidt, Stefan.
Host-specific lytic bacteriophages have regained momentum as an alternative treatment option to control and eliminate pathogenic bacteria. This study aimed to isolate, characterize and evaluate the potential application of Escherichia coli phages as a biocontrol agent in wastewater. In this study, four lytic Escherichia coli phages were isolated from wastewater for biocontrol purposes, using the double-layer method with E. coli (ATCC-25922) as a host. The phage morphology was characterized using transmission electron microscopy, with further parameters such as host range, phage stability at different temperatures, and pH values analyzed additionally. The genome of two selected phages (NPS and NPM) was sequenced, and the capacity of the phage isolate NPM to eliminate E. coli from artificial wastewater was evaluated and compared to conventional chlorination. All the four phage isolates showed typical T4 phage appearance with isometric capsids and contractile tails of different sizes, matching the family Myoviridae in the order Caudovirales. They exhibited a narrow host range limited to E. coli isolates, with two exceptions: phage NPS and NPM additionally lysed Salmonella Typhimurium (ATCC-14028). The four phage isolates were even able to lyse MDR (multidrug-resistant) E. coli isolates, such as the strain FP29. The four phages had burst sizes ranging from 70-115 per host cell and a latency period of 10- 20 minutes. All the four bacteriophages were stable at pH 5-9 but completely inactivated at pH 12. Exposure to 60°C for 10 minutes reduced phage titers by 1.5- log, while exposure to 80°C for 10 minutes completely inactivated all four phage isolates. The two genomes (NPS and NPM) were 99% identical and had similar sizes (169 536 bp), but phage NPS differed from phage NPM in view of its host range and plaque morphology. Another difference observed at the genome level was a shift of coding sequences between phage NPS and NPM. Phage isolate NPM achieved a 3.5- log reduction of E. coli cells present in artificial wastewater at an MOI of 0.1 in 120 minutes. A 90-minute chlorine treatment achieved a log reduction in the same range, highlighting that phages have the potential as environmentally friendly biocontrol agents in wastewater treatment.
Monitoring the efficacy of a lowland instream barrier on the lower uThukela River and the importance of river connectivity.
(2023) Van Zyl, Bradley Bruce.; Downs, Colleen Thelma.
Freshwater is the key to life on earth, with rivers being the pathway that allows it to run from mountains to the ocean, performing many important functions along its way. Humans rely on the many ecosystem services that freshwater provides, such as water quantity provision for domestic, industrial, and agricultural processes, food supply, water purification, and recreation and tourism, to name a few. Water-scarce countries, such as South Africa, are particularly vulnerable to water shortage issues and require many water supply solutions, like dams, weirs, and transfer schemes, to harvest the available rainfall. The uThukela River in KwaZulu-Natal is not only an important resource within its catchment but also to external catchments through inter-basin water transfer schemes, including that of the Thukela-Vaal transfer, which feeds the economically important hub of South Africa, the Gauteng Province. The lower uThukela River is a highly stressed system, with synergistic effects from multiple stressors relating to water quality, water quantity, habitat alterations, and wildlife disturbance affecting it. Additionally, the Lower Thukela Bulk Water Supply Scheme (LTBWSS) weir was recently constructed in its lower reaches, approximately 20 km upstream of the uThukela Mouth to the Indian Ocean, to provide bulk water to surrounding local municipalities. Due to the rich diversity of fish species in the region, particularly those with marine, estuarine, and freshwater migratory patterns, a fishway was incorporated into the design of the weir to facilitate fish movements over the weir. This study evaluated the impact that the LTBWSS weir has on fish community structures in the region and additionally assessed the efficacy of the fishway in allowing fish movements through it. Various sites were selected upstream, downstream, and on the tributary Mandeni ii Stream to assess environmental variables driving fish community structures, with passive and active sampling methods used to assess the fishway's functionality. Fish collection occurred at three sites upstream of the LTBWSS weir, four sites downstream of it on the uThukela River, and two sites on the Mandeni Stream. Abiotic variables relating to water quality, velocity, depth, and habitat were collected along with fish to determine which environmental variables were driving the fish communities at these sites. Multivariate analyses indicated that available substrate and cover, the average depth, and temperature were drivers of the fish communities in the study. Upstream sites showed lower species richness compared with downstream sites, with fish communities largely made of freshwater species and few euryhaline species. Additionally, individual species showed different responses to different environmental variables. Furthermore, since the construction of the LTBWSS, the loss of previously highly abundant cichlid species has occurred in the region. This is likely because of the synergistic effects of stressors created by it, such as the disruption of fine sediment transport, water abstraction, and pollution. Passive assessment of the fishway's efficacy in catering for migratory species used PIT telemetry. Budget constraints only allowed the installation of a single PIT antenna at the upstream entrance of the fishway, which was able to assess the upstream migration of fish from downstream. The results found that only eight individuals representing three species managed to navigate the fishway during the study successfully. This included Oreochromis mossambicus, Labeo molybdinus, and Clarias gariepinus. Active sampling involved electrofishing three key locations in the fishway on a monthly basis. Results showed that small-size classes of fish largely dominated the fishway and that the downstream entrance had the highest abundances and species richness. Further research on the role of the fishway in maintaining river connectivity is recommended. iii The outcomes of this study showed the importance that water resource managers have in maintaining the resource for humans and the environment. Knowing individual species' responses to environmental variables allows their populations to be better managed. Additionally, the outcomes of this study showed the importance of river connectivity past a barrier and highlighted the need for effective fish passage solutions in South Africa. It emphasised the need to better understand the migratory requirements of local fish to build better fish passage structures. Major stressors to be addressed include the impacts caused by barriers relating to flow releases, migration blocks, and habitat alteration upstream and downstream of them. Furthermore, the proper management of fish passage structures is essential to their functionality, which includes regular monitoring of the fishway for issues such as debris blockages and swiftly finding solutions to them to ensure that no undue delays or stress may occur for migratory fish.
The evaluation of the health status of Clarias gariepinus from the Inanda and Nagle dams in KwaZulu-Natal, South Africa.
(2021) Mdluli, Siphosakhe.; Lebepe, Jefferey.; Vosloo, Dalene.
The uMgeni River is one of the most polluted freshwater ecosystems in KwaZulu-Natal. This river is home to about 48 fish species. The study aims to determine the effects of water quality on the health of Clarias gariepinus from the Nagle and Inanda dams. Water variables were measured in situ using a YSI meter. Water and sediment samples were collected at three sites in each dam. Fish were collected and euthanized by severing the spinal cord. Different fish biometrics were measured. Fish tissues were preserved based on the analysis to be carried out. Neutral to alkaline water pH was recorded at both dams. Although the Inanda Dam exhibited higher total nitrogen concentration, both dams were mesotrophic, whereas the phosphate concentration at the Inanda Dam was eutrophic. Generally, the Nagle Dam showed good quality water compared to the Inanda Dam. The Inanda Dam fish population showed a relatively higher prevalence of alterations in the gills and liver than fish from the Nagle Dam. The degree of alterations showed some variability within each population, however, there was no significant difference (p>0.05) between the two populations. Both populations exhibited organ indexes less than 20, hence, moderate alterations. Fish ovaries and testis showed slight alterations at both dams. Acetylcholinesterase (AChE) brain activity recorded no significant difference in between the dams (p>0.05). Male populations recorded no significant difference in vitellogenin (VTG) induction between the dams (p>0.05). Despite, AChE activity and VTG induction showing no significant difference between the two populations, there was a great variability within each population. The lowest AChE activity as well as the highest VTG level were observed in the Inanda Dam fish populations. Both histopathologic and biochemical biomarkers are signs of increased pollution effect at the Inanda Dam. Nevertheless, it is evident that the uMgeni River system which is supposed to be providing sanctuary to aquatic biota is becoming deteriorated. These findings provide baseline data or a point of reference for future studies as it is the first of its kind in this river system.
The use of zebrafish to assess water quality and remediation efforts.
(2023) Zondi, Thandolwethu Beauty.; Hewer, Raymond.
Although wastewater effluents continue to be significant polluters of aquatic ecosystems in developing countries with limited water resources, little is known about the ecotoxicity induced by these effluents on fish throughout their early life stages. Several wastewater treatment plants (WWTPs) in South Africa (SA) do not adequately meet the minimal wastewater treatment requirements established by the country's Department of Water and Sanitation (DWS). Moreover, contaminants of emerging concern (CECs) originating from synthetic or natural sources, are widely distributed in aquatic environments of SA. This includes a broad range of natural and chemical compounds, such as aspirin (44243 ng/L), Fluoroquinolones (27100 ng/L), Atenolol (25900 ng/L), Nalidixic acid (25234 ng/L) and Ciprofloxacin (20514 ng/L). In addition to chemical compounds, endocrine disrupting chemicals, pharmaceuticals and personal care products are also distributed in the water systems. In the process of wastewater treatment, agents such as flocculants, coagulants, chemical precipitants (e.g., calcium hydroxide or sodium hydroxide) and chlorine disinfectants are utilized in wastewater treatment settings. However, research to understand the adverse effects that can be caused by these agents on aquatic organisms is still ongoing in SA. In order to bridge this knowledge gap, advanced techniques could be employed to help reveal adverse effects of wastewater as well as any shortcomings of current water remediation techniques. Using an appropriate aquatic model organism with highly conserved physiological pathways present in higher vertebrates (including humans), a rich behavioural repertoire, and occurrence in a variety of habitats would be a novel approach. To this effect, this study employed zebrafish with the aim to monitor six distinct wastewater samples from various regions of SA and to assess the effectiveness of currently used water remediation techniques such as chlorination. Two wastewater effluents, namely, Southern Works Final Effluents (SWFE) and Jacob’s Incoming (JB) alerted potential toxicity during chemical characterization with suboptimal pH (SWFE = 9.02 ± 0.16 and JB = 5.65 ± 0.02) and total alkalinity of zero (0 mg/L) detected for both effluents. The lethal toxicity of these effluents was seen by the elevation of mortality rate up to 77 ± 2.89 % and 100 ± 0.00 %, respectively for SWFE and JB at 40 %, with corresponding LC50 values of 17.77 % and 16.46 %. The zebrafish jaw and face, heart, brain, fins, notochord, somite and tail were significantly deformed (p < 0.05) post-exposure to these effluents, as revealed by morphological scores upon the analysis of the zebrafish’s body structure. Moreover, there was a delay in development due to the aforementioned effluents, unsuccessful hatching, craniofacial abnormalities, pericardial and yolk sac oedema, notochord abnormality somite defects and spinal cord curvature. In addition, locomotor activity of zebrafish was inhibited following observation of distance travelled, frozen moments, acceleration rates, swimming trajectories and exploration rate. Surprisingly, safety of these wastewaters was restored by chemical precipitation revealing non-lethal pH ranges of 6.02 - 8.02 and 6.65 - 7.65 for SWFE and JB, reducing the mortality rate to non-significant levels (p > 0.05) compared to the control. Also, sodium bicarbonate (NaHCO3) at 120 mg/L was found effective at supplementing the wastewater total alkalinity. In contrast, Amanzimtoti water before and after chlorination (TB and TA), Incoming Badulla (IB) and Chatsworth Incoming (CI) exhibited no consistent lethality effects on zebrafish and induced no apparent stress as demonstrated by insignificant expression (p > 0.05) of the stress protein: heat shock protein 70 (HSP70). However, the insignificant mortality v rate (p > 0.05) in the water tested before (TB) and after (TA) chlorination appeared to be the same (~25 %) indicating that chlorination is not enough at completely remediating wastewater. Our study is a pioneer in evaluating the ecotoxicological impact of wastewater effluents from localized regions of a developing country like South Africa in relation to the adjustment of water quality parameters for the neutralization of contaminants. To better understand emerging contaminants released as effluents in SA's water bodies and their interactions with aquatic organisms at the adult stage, more studies needs to be developed.

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