The present study attempts to find an alternate computational tool to model the complex physical interactions within the molten salt FLiNaK in a way that is both efficient and accurate. Additionally, this study seeks to describe the effects of several different types of impurities on the FLiNaK salt system. This study selects two different polarizable force fields, the AMOEBA polarizable approach and the polarizable ion model, to determine the density and the structure of the impure FLiNaK salt mixtures at typical operating temperatures in molten salt reactors (between 500-900 °C). This study conducts ab initio molecular dynamics (AIMD) simulations and classical molecular dynamics (CMD) for these salt mixtures to determine the correct parameter set for these two force fields. This study also uses an optimizer to minimize the difference between the forces calculated with AIMD and CMD simulation data. The AMOEBA polarizable approach is able to predict density for FLiNaK; however, it is unable to reliably predict other thermophysical properties due to the instability of its CMD simulations. The polarizable ion model is able to reliably determine density and salt structure for pure and impure FLiNaK mixtures. This model can be further used to determine other thermophysical properties. The polarizable ion model predicted densities for four impure salt mixtures: FLiNaK-MoF3, FLiNaK-UF3, FLiNaK-CsF, and FLiNaK-ZrF4. The predicted densities at 700 °C given in kg/m3 are 1929.94, 2454.15, 1650.67, and 1961.87, respectively with an error compared to the additive density model of -2.51%, -5.79%, -17.15%, and -1.67%, respectively. This study presents the radial distribution function and density correlation functions for each salt mixture. This study also presents a discussion of the shortcomings of the AMOEBA polarizable approach, as well as further work that may be done with these tools.

Amoebozoa is the eukaryotic supergroup sister to Obazoa, the lineage that contains the animals (including us humans) and Fungi. Amoebozoa is extraordinarily diverse, encompassing important model organisms and significant pathogens. Although amoebozoans are integral to global nutrient cycles and present in nearly all environments, they remain vastly understudied. Here we have isolated a naked eukaryotic amoeba with filose subpseudopodia, and a simple life cycle consisting of a trophic amoeba and a cyst stage. Using a wholistic approach including light, electron, fluorescence microscopy and SSU rDNA, we find that this amoeboid organism fails to match any previously described eukaryote genus. Our isolate amoebae are most similar to some variosean amoebae which also possess acutely pointed filose subpseudopodia. Maximum likelihood and Bayesian tree of the SSU-rDNA gene places our isolate in Variosea of Amoebozoa as a novel lineage with high statistical support closely related to the highly diverse protosteloid amoebae Protostelium. This novel variosean is herein named “Hodorica filosa” n. g. n. sp. We present a robust phylogeny of Amoebozoa based on a broad representative set of taxa in a phylogenomic framework (325 genes). By sampling 61 taxa using culture-based and single-cell transcriptomics, our analyses show two major clades of Amoebozoa, Discosea and Tevosa. Overall, the main macroevolutionary patterns in Amoebozoa appear to result from the parallel losses of homologous characters of a multiphase life cycle that included flagella, sex, and sporocarps rather than independent acquisition of convergent features Integrins are transmembrane receptors that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological processes and are key elements that are associated animal multicellularity. The IMAC was thought to be specific to animals. Over the last decade however, the IMAC complexes were discovered throughout Obazoa. We show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Co-option of an ancient protein complex was key to the emergence of animal multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.

Electronic band structure in the solid and its relation to the energy gap of the monomer is all about studying how intermolecular interactions change electronic structure. In experimental studies this results in broader absorption bands and by extension a lowering of the LUMO and raising of HOMO energy to the conduction and valence band edges respectively. This electronic change involves splitting of the molecular energy levels into bands of non-degenerate energies and can be calculated either quantum mechanically (QM) or by classical force field models through the change in ionization potential (IP) and electron affinity (EA), called the apparent polarization energy, and its relation to HOMO and LUMO through Koopman’s and Janak’s theorem. The study of the formation of a ‘band’ like structure is important in regimes and systems where conventional quantum mechanical (QM) methods become infeasible. Specifically, when systems are non-periodic and plane wave approximations fail, such as in amorphous structures, or in regimes between where the plane wave bulk approximation and the gas phase single molecule QM methods where the scaling of conventional gas phase atomic orbital methods becomes exorbitantly costly and the plane wave approximation fails for open systems. Therefore, the objective of this work is to highlight the changing optoelectronic properties of molecular solids within this regime using both density functional theory and molecular mechanics. The scalability of DFT limits it to multimer systems, leaving the larger nanoscale materials to be studied using molecular mechanics. Here we have utilized a variety of dispersion sensitive functionals in order to characterize the intermolecular interactions and splitting energies in small multimers of some of the smallest oligoacene species, benzene and anthracene. Benzene and anthracene nanoclusters from 0.8 to 5.0 nm in radius have had their changes in electronic band energy calculated due to polarization using the AMOEBA force field and bulk values have also been extrapolated. AMOEBA’s explicit polarization terms allow for direct handling of the polarization energy, control of nanocluster size and shape in a regime that QM methods cannot probe efficiently, and the ability to specify the position of charge carriers in order to examine specific electronic surface behavior. Using differing DFT methods the change in the HOMO and LUMO energy from the single molecule state to multimers of the size of 10 and 12 units for anthracene and benzene respectively. The HOMO band of benzene was raised by ~0.3 eV and LUMO lowered by 0.35 eV. In anthracene the HOMO was lowered by ~0.1 eV and the LUMO by ~0.15 eV. These values remain within 0.1 eV across all dispersion functionals. Using Ren’s parameterization procedure and MP2 for the AMOEBA force field he apparent polarization was calculated. The extrapolated values for the change in the HOMO and LUMO of benzene from single molecule to bulk were 1.42 eV and 0.49 eV respectively. For anthracene the crystalline bulk changes the HOMO and LUMO by 1.34 eV and 1.16 eV respectively. The regression for bulk extrapolation also predicts that benzene clusters of 12 units will be 0.77 eV for HOMO and -0.41 eV for LUMO. Similarly for an anthracene cluster made up of 10 molecular units the apparent polarization is predicted through linear regression to be 0.58 eV for HOMO and 0.53 eV for LUMO.

Les virus géants d'amibes( Acanthamoeba) sont des virus à ADN double brin . Ces virus géants ont été isolés depuis 2008 essentiellement à partir de prélèvements d'eaux et sols) collectés dans diverses régions géographiques à travers le monde, ou à partir de prélèvements humains (selle, liquide broncho-alvéolaire et sang). Ils sont repartis en 4 familles virales dont les plus représentées sont les familles Mimiviridae et Marseilleviridae avec pour membres fondateurs respectifs Mimivirus et Marseillevirus et comptent à ce jour respectivement 44 et 20 isolats. Les virus géants d'amibes sont ubiquitaires dans notre biosphère, et les êtres humains y sont potentiellement exposés. Au cours de cette Thèse, nous avons premièrement écrit une revue de la littérature décrivant les outils de mise en évidence des virus géants d'amibes chez l'homme incluant la sérologie, la culture, la PCR ou l'hybridation de sondes fluorescentes in situ. Deuxièmement, nous avons conçu et évalué 5 systèmes de PCR en temps réel détectant les membres des groupes de mimivirus d'amibes, leurs virophages et les marseillevirus. Nous avons participé à un 3ème travail décrivant les différentes procédures d'isolement sur amibes utilisées jusqu'à présent dans notre laboratoire . Enfin, dans un 4ème travail préliminaire, nous avons recherché par PCR la présence des mimivirus et marseillevirus dans 701 plasmas de patients infectés par HIV-1.Au total, nos travaux ont décrit les mises au point, performances et limites des tests de PCR pour l'étude des virus géants, et ont contribué aux outils et fourni des éléments pour l'étude de l'implication des virus géants d'amibes en pathologie humaine. / The giant viruses of amoebas( Acanthamoeba) are double stranded DNA viruses. These giant viruses have been isolated essentially from water and soil samples collected in various geographic regions around the world or from human samples (stool, blood and bronchoalveolar fluid). These giant viruses are divided into four viral families among which those comprising the largest number of representatives are the Mimiviridae and Marseilleviridae families, whose respective founders are Mimivirus and Marseillevirus and comprise 44 and 20 representative members, respectively. Giant viruses of amoeba are ubiquitous in our biosphere, which means that humans can be exposed to them. In this Thesis, we initially wrote a review of the literature describing the tools to detect the present of these giant viruses in humans, including serology, culture isolation, PCR and fluorescence in situ hybridization (FISH). Secondly, we designed and evaluated the performance of five real-time PCR systems targeting the members of the 3 groups of mimiviruses of amoeba, their virophages and the marseilleviruses. We were involved in a third work that described the different isolation procedures on amoebae used so far in our laboratory for giant viruses. Finally, in a fourth preliminary work, we looked by PCR for the presence of mimiviruses and marseilleviruses DNA in 701 plasma from patients infected with HIV-1. In summary, our work described the developed PCR assays for the study of giant viruses, and their performance and limitations, and it contributed to the tools and evidence for the study of the involvement of the giant amoeba virus in human pathology.

Il a été bien documenté que les différentes canalisations des unités de soins dentaires contiennent un épais biofilm. Ce biofilm est constitué entre autres de bactéries, mais aussi d’amibes. Certaines amibes ont un potentiel pathogène et peuvent causer des infections graves. Deux cas d’infections amibiennes et possiblement reliées aux unités dentaires ont retenu notre attention et sont à l’origine du présent projet. L’identification morphologique des amibes afin de déterminer si elles présentent un potentiel pathogène ou non est une tâche ardue, même pour les protozoologistes chevronnés. Nous avons donc utilisé la réaction de polymérase en chaîne (PCR) pour identifier les amibes. Des nouvelles amorces ont été élaborées pour détecter les amibes des genres Acanthamoeba ainsi que Naegleria. Des échantillons d’eau et de terre ont été prélevés dans l’environnement, et des échantillons d’eau et de biofilm ont été prélevés dans les unités dentaires. Une partie de chaque échantillon a été mise en culture selon une méthode améliorée pour une identification morphologique, et l’autre partie a été soumise à un PCR direct. Des Acanthamoebae et/ou des Naegleriae ont été détectées dans 100% des échantillons, mais les espèces varient d’un échantillon à l’autre. Des amibes à potentiel pathogènes sont détectables dans les unités dentaires ainsi que dans l’environnement, et celles-ci pourraient représenter un risque pour la santé de certains individus. / It has been well documented that the various tubing of a dental unit are covered with a thick biofilm. This biofilm mostly consists of bacteria, but amoebae can be found within the biofilm as well. Some amoebae are potential pathogens and may cause serious infections. Two cases of amoebic infections that were possibly linked with dental units drew our attention and stimulated our researches. Morphologic identification of amoebae in order to determine their possible pathogenicity requires much expertise, and is even difficult for proficient protozoologists. Therefore, the use of PCR is essential to detect potentially pathogenic amoebae with subjectivity. We elaborated new primers for the detection of Acanthamoeba spp. and Naegleria spp. Samples of water and dirt were taken in the environment, and samples of water and biofilm were taken in dental units. A part of each samples was cultivated for morphological identification, when a second part was utilized for PCR identification. Acanthamoebae and/or Naegleriae were detected in 100% of our samples, but the species varied from one sample to another. Potentially pathogenic amoebae were detected in dental units and in the environment, which could represent a health risk for some individuals.

With recent advances and cost reductions in next generation sequencing (NGS), the amount of genetic sequence data is increasing rapidly. However, before patient specific genetic information reaches its full potential to advance clinical diagnostics, the immense degree of genetic heterogeneity that contributes to human disease must be more fully understood. For example, although large numbers of genetic variations are discovered during clinical use of NGS, annotating and understanding the impact of such coding variations on protein phenotype remains a bottleneck (i.e. what is the molecular mechanism behind deafness phenotypes). Fortunately, computational methods are emerging that can be used to efficiently study protein coding variants, and thereby overcome the bottleneck brought on by rapid adoption of clinical sequencing. To study proteins via physics-based computational algorithms, high-quality 3D structural models are essential. These protein models can be obtained using a variety of numerical optimization methods that operate on physics-based potential energy functions. Accurate protein structures serve as input to downstream variation analysis algorithms. In this work, we applied a novel amino acid side-chain optimization algorithm, which operated on an advanced model of atomic interactions (i.e. the AMOEBA polarizable force field), to a set of 164 protein structural models implicated in deafness. The resulting models were evaluated with the MolProbity structure validation tool. MolProbity “scores” were originally calibrated to predict the quality of X-ray diffraction data used to generate a given protein model (i.e. a 1.0 Å or lower MolProbity score indicates a protein model from high quality data, while a score of 4.0 Å or higher reflects relatively poor data). In this work, the side-chain optimization algorithm improved mean MolProbity score from 2.65 Å (42nd percentile) to nearly atomic resolution at 1.41 Å (95th percentile). However, side-chain optimization with the AMOEBA many-body potential function is computationally expensive. Thus, a second contribution of this work is a parallelization scheme that utilizes nVidia graphical processing units (GPUs) to accelerate the side-chain repacking algorithm. With the use of one GPU, our side-chain optimization algorithm achieved a 25 times speed-up compared to using two Intel Xeon E5-2680v4 central processing units (CPUs). We expect the GPU acceleration scheme to lessen demand on computing resources dedicated to protein structure optimization efforts and thereby dramatically expand the number of protein structures available to aid in interpretation of missense variations associated with deafness.

Cette thèse est centrée sur l’analyse du rôle de l’adhésion cellule-substrat et des facteurs de détectionde Quorum sur la migration amibienne de Dictyostelium . Des outils pour automatiser les enregistrementsde vidéoomicroscopie et l’analyse d’image ont été développés afin de travailler avec de trèsgrands échantillons de cellules et de quantifier la migration cellulaire. Un dispositif microfluidique dedétachement cellulaire sous flux hydrodynamique combiné une platine motorisée a permis une étude statistique de l’adhésion mais aussi de la dynamique de détachement. L’analyse de la migration de Dictyostelium en milieu non nutritif met en évidence le rôle de la densité sur la différentiation des celluleset leur capacité de migration. Nous observons la présence d’une vitesse maximale de migrationaprès 6h de carence. Nous montrons que l’adhésion sur verre est deux fois plus faible en milieu carenc´equ’en milieu nutritif. Les exp´eriences de migration en milieu nutritif ont révélé la présence d’un facteur de détection de densité sécrété par les cellules et régulant leur migration aléatoire. Le coefficient de diffusion, la persistance du mouvement et la morphologie des cellules varient en fonction de la concentrationde ce facteur. Ce facteur ne modifie pas l’adhésion cellulaire mais uniquement la dynamique de d´etachement. Enfin, le protocole d’analyse développé nous a permis de faire une étude comparative de la migration en faisant varier d’autres paramètres tel que la surface ou la composition chimique du milieu expérimental. Ce travail se conclue en exposant le possible rôle de l’adhésion sur la migrationchez Dictyostelium en milieu nutritif. / This thesis focuses on the analysis of the role of adhesion between substrate and cell and factors of Quorum sensing on the migration of Dictyostelium amoeba. Tools to automate the recordings of videomicroscopy and image analysis have been developed to work with very large samples of cells and toquantify cell migration. A microfluidic device for cell detachment in hydrodynamic flow combined witha motorized stage has allowed a statistical study of adhesion but also the dynamics of detachment. The analysis of the migration of Dictyostelium in non nutritive medium highlights the role of density on celldifferentiation and migration capacity. We observe the presence of a maximum speed of migration after6 hours of starvation. We show that the adhesion to glass is twice as low in deprivation buffer as inthe nutrient medium. The experiences of migration in growth medium revealed the presence of a factorof detection of density secreted by the cells and regulating their random migration. The diffusion coefficient, the persistence of the movement and morphology of cells vary depending on the concentrationof this factor. This factor does not affect cell adhesion but only the dynamics of detachment. Finally, the testing protocol developed allowed us to make a comparative study of migration by varying otherparameters such as surface or the chemical composition of experimental medium. This work concludesby outlining the possible role of adhesion to the migration of Dictyostelium in nutrient medium.

Il a été bien documenté que les différentes canalisations des unités de soins dentaires contiennent un épais biofilm. Ce biofilm est constitué entre autres de bactéries, mais aussi d’amibes. Certaines amibes ont un potentiel pathogène et peuvent causer des infections graves. Deux cas d’infections amibiennes et possiblement reliées aux unités dentaires ont retenu notre attention et sont à l’origine du présent projet. L’identification morphologique des amibes afin de déterminer si elles présentent un potentiel pathogène ou non est une tâche ardue, même pour les protozoologistes chevronnés. Nous avons donc utilisé la réaction de polymérase en chaîne (PCR) pour identifier les amibes. Des nouvelles amorces ont été élaborées pour détecter les amibes des genres Acanthamoeba ainsi que Naegleria. Des échantillons d’eau et de terre ont été prélevés dans l’environnement, et des échantillons d’eau et de biofilm ont été prélevés dans les unités dentaires. Une partie de chaque échantillon a été mise en culture selon une méthode améliorée pour une identification morphologique, et l’autre partie a été soumise à un PCR direct. Des Acanthamoebae et/ou des Naegleriae ont été détectées dans 100% des échantillons, mais les espèces varient d’un échantillon à l’autre. Des amibes à potentiel pathogènes sont détectables dans les unités dentaires ainsi que dans l’environnement, et celles-ci pourraient représenter un risque pour la santé de certains individus. / It has been well documented that the various tubing of a dental unit are covered with a thick biofilm. This biofilm mostly consists of bacteria, but amoebae can be found within the biofilm as well. Some amoebae are potential pathogens and may cause serious infections. Two cases of amoebic infections that were possibly linked with dental units drew our attention and stimulated our researches. Morphologic identification of amoebae in order to determine their possible pathogenicity requires much expertise, and is even difficult for proficient protozoologists. Therefore, the use of PCR is essential to detect potentially pathogenic amoebae with subjectivity. We elaborated new primers for the detection of Acanthamoeba spp. and Naegleria spp. Samples of water and dirt were taken in the environment, and samples of water and biofilm were taken in dental units. A part of each samples was cultivated for morphological identification, when a second part was utilized for PCR identification. Acanthamoebae and/or Naegleriae were detected in 100% of our samples, but the species varied from one sample to another. Potentially pathogenic amoebae were detected in dental units and in the environment, which could represent a health risk for some individuals.

Contamination of groundwater that is suitable for drinking is of growing concern as the water supply of South Africa is becomingincreasingly limited. This is especially the case in the North West province, with its semi – arid climate and variable rainfall patterns. The aim of the study was to evaluate the microbiological and physico – chemical qualities of groundwater obtained from selected DWA (Department of Water Affairs) monitoring boreholes in the Mooi River and Harts River catchment areas. Physico -chemical parameters included temperature, pH, electrical conductivity (EC), salinity, total dissolved solids (TDS), sulphate and nitrate concentrations. Physical parameters were measured using a calibrated submerge-able multimeter and chemical parameters using specialised kits and a spectrophotometer. Microbiological parameters included heterotrophic plate counts and total and faecal coliform enumeration. Membrane filtration and culture based methods were followed for enumeration of bacteria. During the identification procedures multiplex PCR for E. coli identification and 16S rRNA gene sequencing for identification of heterotrophic plate count bacteria and amoeba resistant bacteria were used. For antibiotic resistance, the Kirby- Bauer (1996) disk diffusion method was used. During the warm and wet season high electrical conductivity and salinity were observed in the Trimpark (65.3 mS/m; 325 ppm), School (125.1 mS/m; 644 ppm), Warrenton (166.9 mS/m; 867 ppm) and Ganspan (83.3 mS/m; 421 ppm) boreholes. Warrenton borehole had a high sulphate level (450 mg/l) as well. High chemical oxygen demand was observed in the Blaauwbank (62 mg/l) and Warrenton (98.5 mg/l) boreholes. In the dry and cold season similar observations were made for the various boreholes. Electrical conductivity and salinity levels remained high for the Trimpark (70.1 mS/m; 427.5 ppm), School (127 mS/m; 645 ppm), Warrenton (173.3 mS/m; 896.5 ppm) and Ganspan (88.1 mS/m; 444.5 ppm) boreholes. Nitrate levels for the Trimpark (14.1 mg/l) and School (137 mg/l), as well as sulphate levels for the Warrenton (325 mg/l) borehole were also high. Total coliforms, faecal streptococci and HPC bacteria were enumerated from water samples from all boreholes, except Blaauwbank where no faecal streptococci were enumerated. Faecal coliforms were enumerated from 5 of the possible 7 boreholes during a warm and wet season (Trimpark – 42 cfu/100ml; School – 2 cfu/100ml; Cemetery – 175 cfu/100ml; Warrenton – 3.84 x 10³ cfu/100ml; Ganspan – 1.9 x 10³ cfu/100ml). Indicator bacteria (FC, TC, HPC) exceeded target water quality ranges (TWQR) for drinking water in each case. During the cold and dry sampling season, faecal coliforms were enumerated mainly from the Trimpark (11 cfu/100ml) borehole. Total coliforms, faecal streptococci and HPC bacteria were enumerated from all the boreholes, except for Blaauwbank that contained no faecal streptococci or total coliforms. Enumerated indicator bacteria levels again exceeded TWQR for domestic use. Total coliform counts for the Pad dam borehole, however, complied with TWQR for domestic use. Identified E. coli were resistant to Erythromycin, Cephalothin and Amoxicillin and susceptible to Ciprofloxacin. Escherichia coli isolated from the Mooi River catchment shared the same antibiotic resistance phenotype. The most abundant HPC bacterial genus identified was Pseudomonas spp. (7 isolates). Opportunistic pathogens isolated included Pseudomonas aeruginosa, Acinetobacter, Aeromonas, Alcaligenes, Flavobacterium, Bacillus cereus and Mycobacterium spp. Varying degrees of antibiotic resistance were observed. Generally, the same pattern between the same genera were observed. All HPC isolates were resistant to Cephalothin and Amoxicillin and a lower degree Erythromycin and Streptomycin. The most abundant amoeba resistant bacteria was identified as Pseudomonas spp. Other isolates included Alcaligenes faecalis and Ochrobactrum sp. and Achromobacter sp. All of these are opportunistic pathogens, except for Achromobacter. Resistance to more antibiotics (Streptomycin, Chloramphenicol, Cephalothin, and Amoxicillin) was observed in ARBs compared to HPC (Cephalothin, Amoxicillin) from bulk water from the same borehole. The water of all the aquifers sampled is of very poor physico - chemical or microbiological quality or both. Water may be used for irrigation or livestock watering only in the case where these boreholes comply with TWQR for said purposes. Results obtained indicate that the groundwater is faecally contaminated. Amongst the bacteria, opportunistic pathogens displaying various degrees of antibiotic resistance were frequently isolated. These results indicate health risks if untreated groundwater is consumed. Therefore groundwater needs to be treated before distribution especially if the water is for human consumption. / Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013.

Contamination of groundwater that is suitable for drinking is of growing concern as the water supply of South Africa is becomingincreasingly limited. This is especially the case in the North West province, with its semi – arid climate and variable rainfall patterns. The aim of the study was to evaluate the microbiological and physico – chemical qualities of groundwater obtained from selected DWA (Department of Water Affairs) monitoring boreholes in the Mooi River and Harts River catchment areas. Physico -chemical parameters included temperature, pH, electrical conductivity (EC), salinity, total dissolved solids (TDS), sulphate and nitrate concentrations. Physical parameters were measured using a calibrated submerge-able multimeter and chemical parameters using specialised kits and a spectrophotometer. Microbiological parameters included heterotrophic plate counts and total and faecal coliform enumeration. Membrane filtration and culture based methods were followed for enumeration of bacteria. During the identification procedures multiplex PCR for E. coli identification and 16S rRNA gene sequencing for identification of heterotrophic plate count bacteria and amoeba resistant bacteria were used. For antibiotic resistance, the Kirby- Bauer (1996) disk diffusion method was used. During the warm and wet season high electrical conductivity and salinity were observed in the Trimpark (65.3 mS/m; 325 ppm), School (125.1 mS/m; 644 ppm), Warrenton (166.9 mS/m; 867 ppm) and Ganspan (83.3 mS/m; 421 ppm) boreholes. Warrenton borehole had a high sulphate level (450 mg/l) as well. High chemical oxygen demand was observed in the Blaauwbank (62 mg/l) and Warrenton (98.5 mg/l) boreholes. In the dry and cold season similar observations were made for the various boreholes. Electrical conductivity and salinity levels remained high for the Trimpark (70.1 mS/m; 427.5 ppm), School (127 mS/m; 645 ppm), Warrenton (173.3 mS/m; 896.5 ppm) and Ganspan (88.1 mS/m; 444.5 ppm) boreholes. Nitrate levels for the Trimpark (14.1 mg/l) and School (137 mg/l), as well as sulphate levels for the Warrenton (325 mg/l) borehole were also high. Total coliforms, faecal streptococci and HPC bacteria were enumerated from water samples from all boreholes, except Blaauwbank where no faecal streptococci were enumerated. Faecal coliforms were enumerated from 5 of the possible 7 boreholes during a warm and wet season (Trimpark – 42 cfu/100ml; School – 2 cfu/100ml; Cemetery – 175 cfu/100ml; Warrenton – 3.84 x 10³ cfu/100ml; Ganspan – 1.9 x 10³ cfu/100ml). Indicator bacteria (FC, TC, HPC) exceeded target water quality ranges (TWQR) for drinking water in each case. During the cold and dry sampling season, faecal coliforms were enumerated mainly from the Trimpark (11 cfu/100ml) borehole. Total coliforms, faecal streptococci and HPC bacteria were enumerated from all the boreholes, except for Blaauwbank that contained no faecal streptococci or total coliforms. Enumerated indicator bacteria levels again exceeded TWQR for domestic use. Total coliform counts for the Pad dam borehole, however, complied with TWQR for domestic use. Identified E. coli were resistant to Erythromycin, Cephalothin and Amoxicillin and susceptible to Ciprofloxacin. Escherichia coli isolated from the Mooi River catchment shared the same antibiotic resistance phenotype. The most abundant HPC bacterial genus identified was Pseudomonas spp. (7 isolates). Opportunistic pathogens isolated included Pseudomonas aeruginosa, Acinetobacter, Aeromonas, Alcaligenes, Flavobacterium, Bacillus cereus and Mycobacterium spp. Varying degrees of antibiotic resistance were observed. Generally, the same pattern between the same genera were observed. All HPC isolates were resistant to Cephalothin and Amoxicillin and a lower degree Erythromycin and Streptomycin. The most abundant amoeba resistant bacteria was identified as Pseudomonas spp. Other isolates included Alcaligenes faecalis and Ochrobactrum sp. and Achromobacter sp. All of these are opportunistic pathogens, except for Achromobacter. Resistance to more antibiotics (Streptomycin, Chloramphenicol, Cephalothin, and Amoxicillin) was observed in ARBs compared to HPC (Cephalothin, Amoxicillin) from bulk water from the same borehole. The water of all the aquifers sampled is of very poor physico - chemical or microbiological quality or both. Water may be used for irrigation or livestock watering only in the case where these boreholes comply with TWQR for said purposes. Results obtained indicate that the groundwater is faecally contaminated. Amongst the bacteria, opportunistic pathogens displaying various degrees of antibiotic resistance were frequently isolated. These results indicate health risks if untreated groundwater is consumed. Therefore groundwater needs to be treated before distribution especially if the water is for human consumption. / Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013.