Bioleaching is a naturally occurring process that has been harnessed in metal recovery from low grade ores. The heap bioleaching technique involves complex interactions between chemical reactions, microbial processes and transport processes. The need for efficient heap operations has led to the scientific investigation of heap bioleaching and the development of mathematical models for the process. Over time, the focus of heap leach modelling has moved from models that emphasize particle scale processes to models that emph8size bulk scale processes. In many cases however, the particle scale effects in these bulk scale models are quite simplified. This thesis aims to provide a means for the systematic integration of particle (or micro-) scale processes into bulk (or macro-) scale models for heap bioleaching, by the development of an intermediate (or meso-) scale "agglomerate" model. The agglomerate is defined as a unit volume of a heap that comprises a solid phase (a size distribution of ore particles), a liquid phase (stagnant and flowing leaching solution, which contains dissolved solutes, attached and planktonic microbes) and a gas phase (flowing air and air pockets). The processes incorporated into the proposed model include reagent diffusion and ree1ction in a s.ze distribution of ore particles, microbial attachment, detachment and oxidation processes, and the transport of chemical and microbial species to and from the agglomerate. Isothermal agglomerate conditions, and a uniform distribution of reagents in the stagnant liquid phase, are among the modelling assumptions made. The agglomerate model is applied to investigate the meso-scale bioleaching of a theoretical case study ore that contains mainly chalcocite and pyrite, in the presence of iron oxidizing microbes. The numerical implementation of the model is done in the Python programming language. The integrity of the numerical results is confirmed by performing mass balance checks at the end of each simulation.

This research pertains to bioleaching of copper containing ores with particular reference to the copper sulfide mineral chalcopyrite (CuFeS2). While it is focused on heap bioleaching, it has applications to stirred tank bioleaching operations. In the context of bioleaching, microbial extra-cellular polymeric substance (EPS) components are thought to complex chemical oxidants and extend the chemical reaction space available for mineral dissolution reactions, making the microbial-mineral-EPS interface the dominant active zone in terms of microbial oxidation and mineral dissolution. There is a limited understanding of microbial biofilm formation within a bioleach heap. The implication of various microorganisms having a set of defined or optimal conditions under which they colonise and proliferate is quite substantial. Understanding what creates favourable interfacial microenvironments enabling a sessile population to flourish (and thereby decrease lag time) has great implications for minimising costs and maximising productivity. Furthermore, limited work has been conducted on thermophilic microorganisms relevant to bioleaching. These microorganisms are pertinent to successful bioleaching at high temperatures, with work incorporating low grade ores and gangue mineralogy also being scarce. The aim of this research is to provide a thorough investigation into microbial-metal sulfide interfacial environments in situ, using a thermophilic archaeon M. hakonensis, low-grade metal-sulfide ores, a series of temperature regimes, heap-simulating conditions and an in depth extraction and analysis of the EPS produced under varied culturing conditions.

Includes abstract. / Includes bibliographical references (leaves 118-123). / This thesis investigates parameters influencing the concentration of aqueous tin in acidic sulphate solutions containing Fe(III/II) as they arise in the Reduction Releach process at Teck Cominco Trail Operations (TCML). This study documents the impact of initial sulphuric acid and As(V) concentrations, temperature, and lead concentrate reductant amount on tin solubility in acidic Fe(III/II) sulphate solutions as they arise in an intermediate leaching step at TCML. Supporting test work examined the speciation of commercial tin bearing residues involved in the processing of indium and germanium. Analysis of these residues determined the oxidation state of crystalline tin in ZnO fume, Ge Preconcentrate, and Releach residue to be primarily Sn(IV), and associated with zinc, lead, and iron oxides; in addition to lead, iron, and aluminum silicates, and minor amounts of Sn(II) as SnO or SnSO₄. Experimental validation of Sn(II) solubility values in 100 g/L H2SO4, between 30 to 90 °C, compared well with literature and theoretical tin solubility values. Measured tin solubility values ranged between 95 g/L Sn and 99 g/L Sn concentration. The aqueous tin concentration decreased slightly (4 g/L Sn) when the temperature was increased from 30 to 90°C. Measured aqueous tin values for both thesis benchscale test work and commercial Reduction Releach process were all less than 1 g/L Sn. The oxidation rate of Sn(II) between 300 mg/L and 700 mg/L in 100 g/L H₂SO₄ at 20 °C, was first order kinetics with a rate constant ranging between 0.0002 and 0.0003 mg Sn/L∙s, and the REDOX potential (Eh) varied between 550 and 650 mV. The low rate constants may have been due to poor mass transfer. Iodometry could not be used for aqueous tin analysis with other divalent and trivalent cations present in solution and, therefore, inductive coupled plasma analysis was used.

Includes abstract. Includes bibliographical references (leaves 109-116).

Includes bibliographical references (leaves 85-89). / Heap bioleaching is an established metallurgical route for the recovery of copper from low grade sulphide ores and pretreatment of refractory gold bearing sulphides. However, metal recovery is generally low (80 to 85% copper recovery is achieved in about a year) due to the slow heap bioleaching kinetics. It is believed that more metal values can be recovered in a shorter timeframe, if the kinetics of ferrous iron biological oxidation can be accelerated. This requires careful study of the bio-oxidation kinetics under heap-like conditions. Two different experimental methods are commonly used for the study of ferrous iron biological oxidation kinetics, namely batch and continuous culture techniques. However, the continuously changing conditions in batch culture and the slowness and bacterial wash out in continuous culture are significant weaknesses for these experimental methods. This work has evaluated the Redostat™ device for faster and controlled ferrous iron biological oxidation kinetics studies. The Redostat™ device offers controlled conditions as in continuous culture but the speed and concentration range of batch culture.

Includes abstract. / Includes bibliographical references. / Acidic drainage as a result of mining and mineral processing activities is a growing concern. The effects of Acid Rock Drainage (ARD) include environmental pollution in the affected areas and beyond. As South Africa has water challenges, the potential threat of continual depletion of useable water resources through their contamination by ARD and other mining activities may affect economic productivity, as well as quality of life. Currently used ARD remediation measures are variable and costly, not only in South Africa but worldwide. End of pipe approaches such as treatment by neutralisation fail to reduce the risk of ARD generation and provide long term solutions. Further it fails to address the limited resource utilisation of the byproduct materials, currently disposed of as ARD forming wastes. The Department of Chemical Engineering, at UCT, has focused research onto the prevention of ARD generation and minimisation of waste. One approach proposed is the two stage froth flotation process for separating sulphides, responsible for ARD formation, from the remaining tailings, leaving these benign with respect to ARD. Testwork results have proven its technical feasibility using porphyry copper tailings, fine coal and more recently gold tailings. Historically, ultrafine coal was not treated by most collieries in South Africa, but disposed as waste. Oxidation of the pyrite in the coal leads to generation of acidic water. In this project, an economic analysis of the coal two stage flotation process for the mitigation of ARD formation is considered. This project proposes ARD prevention by desulphurisation of sulphide rich waste coal material as an in-process approach which can be incorporated into mineral process flowsheets or as an add-on process for desulphurisation of old workings. The two stage flotation may yield a valuable mineral or coal product, as well as a low volume sulphide rich fraction which can be processed further to yield sulphuric acid or disposed of with containment and a benign tailings fraction which can be used as cover material or disposed conventionally.

Includes abstract. / Includes bibliographical references. / The intrinsic environmental advantages of industrial scale bioprocesses over chemical processes remain a discussion point owing to limited objective analysis. Studies to date are often limited to energy or global warming considerations with little regard for full Life Cycle Assessment (LCA) analyses. This, in part, may be owing to the difficulty in obtaining the material and energy balance inventory required for such assessment at an early stage in process development. However, these studies are important in designing and selecting environmentally beneficial processes for the conversion of renewable resources to commodity and energy products. The overall objective of the thesis is to obtain the data required to perform these LCA analyses. To achieve the overall objective, the thesis presents a methodology to obtain the material and energy balance data estimates required for the LCA of industrial bioprocesses through a generic flowsheet model. The flowsheet was presented as a MS-Excel spreadsheet allowing aerobic or anaerobic production of intra- or extracellular products using batch or continuous microbial processes. A database presented in the model facilitates the use of a variety of carbon, nitrogen, sulphur and phosphorus inputs and provides relevant constants and physical data. Typically downstream processing units were taken into account and included downstream chemical inputs (reacting or inert). The model was built using a stoichiometric approach, first principles and rules of thumb.

Laccases (EC 1.10.3.2) are blue multicopper oxidases that catalyse a single electron oxidation of various phenolic substrates with an associated four-electron reduction of dioxygen to water. The varied uses of laccase as a biocatalyst can be attributed to its ability to produce a free radical from a suitable substrate. Of importance to the pharmaceutical, chemical, and industrial sectors, are the laccase-catalysed reactions providing means for the synthesis of dimeric phenolics showing biological activity, including antioxidant activity. The objective of this research was to investigate the production of value-added compounds, with biological activity, via laccase-catalysed oxidation reactions. Our laboratory has access to several unique and previously unexploited culture collections obtained from extreme environments spanning the globe. Potentially novel strains were screened for the ability to produce laccases: 14 environmental isolates, of which 2 strains were fungi, 7 were streptomycetes, and 5 were non-streptomycetes, representing the rare actinomycete genera Gordonia, Rhodococcus, Mycobacterium, Amycolatopsis, and Micromonospora were screened. This is the first report of laccase production in these species. A screening protocol, using criteria specifically suited to bioprocess development, was developed to investigate variables affecting the production of laccase by the native strains. Variables investigated included different types of media (nutritional variables), pH, temperature, incubation times, aeration and agitation, salt concentrations, and the effect of inducers on laccase production by the native strains. Of the isolates investigated, actinomycete strain Micromonospora sp. 044 30-1 showed the greatest potential for the production of laccase. This strain may be novel and the role of laccase in this strain may be related to sporulation. Various growth requirements were investigated in order to optimise for maximal laccase production by strain 044 30-1. The optimal medium for laccase production was M172F medium, pH 5, supplemented with a high concentration of Cu2+ (8 mM), and 2.0% sodium chloride. Extracellular laccase production was higher than intracellular laccase production. The successful application of a Micromonospora strain in an airlift bioreactor specifically for the synthesis of laccase was demonstrated. The biocatalytic potential of the laccase from Micromonospora sp. 044 30-1 was investigated. Laccases are responsible for the formation of radicals that can react non-enzymatically with each other to form dimers or oligomers linked by C-C or C-O bonds. This study reports on laccasecatalysed oxidative reactions involving, primarily, tyrosol, monoacetyltyrosol, and to a lesser extent, reactions with totarol, 3-hydroxyanthranilic acid, and 8-hydroxyquinoline. This study reports for the first time the isolation and structure determination of novel biocatalysis reaction products, specifically the dimeric products obtained through biocatalytic reaction of monoacetyltyrosol with Trametes versicolor laccase, and Micromonospora sp. 044 30-1 laccase. The biocatalysis reaction products of the laccase-catalysed oxidation of tyrosol and monoacetylated tyrosol showed higher antioxidant activity than the parent compounds, as determined by the 2,2- diphenyl-1-picrylhydrazyl (DPPH) and low density lipoprotein (LDL) assays, showing that the dimeric derivatives of laccase-catalysed reactions with phenolic compounds have enhanced antioxidant capabilities. The biocatalysis products were also evaluated as antimicrobials and showed antimicrobial activity against E. coli, a vancomycin resistant clinical strain of Enterococcus faecium, a clinically relevant strain of Micrococcus, and Mycobacterium aurum, a strain that displays a similar antibiotic susceptibility profile to Mycobacterium tuberculosis, the causative agent of the prevalent disease tuberculosis.

Includes bibliographical references (leaves 132-145).

Includes bibliographical references. / Since this was the first research project into olive wastewaters produced in South Africa, the scope of the project was broad, and recommendations were made for further research in several directions. Most importantly, the development of smallscale treatment systems that could be used on site would be of great benefit to olive and olive oil producers, as they are often remote and do not have access to appropriate treatment facilities. In addition, the combination of unit operations, such as an extraction system and a biological degradation system, would allow for the recovery of a valuable product that would offset the cost of producing a treated effluent.