Theses and Dissertations (Biosciences)

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Browsing Theses and Dissertations (Biosciences) by Subject "571.950968"

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    Biochemical and molecular characterization of heavy metal resistant bacteria isolated from the Klip River, South Africa
    (Vaal University of Technology, 2014) Chihomvu, Patience; Stegmann, P., Dr.; Pillay, M., Prof.
    The Klip River has suffered severe anthropogenic effects from industrial, agricultural, mining and domestic activities. As a result harmful contaminants such as heavy metals have accumulated in the river, causing microorganisms inhabiting the environment to develop mechanisms to protect them from the harmful effects of the contaminants. The current study deals with the isolation and characterization of heavy metal resistant bacteria isolated from the Klip River Catchment. Water and sediment samples were collected from 6 sites of the Klip River, and the Vaal Barrage (control). In-situ parameters, such as pH, turbidity, salinity, conductivity, temperature and dissolved oxygen were determined. Lead, iron, cadmium, nickel, zinc and copper concentrations of water were determined by atomic absorption spectroscopy. For bacterial analysis sediment and water samples were collected in sterile glass jars and bottles respectively. Heavy metal resistant bacterial isolates were screened on heavy metal constituted Luria Bertani (LB) agar. Biochemical profiles of the isolates were constructed using the API 20E® strips, antibiotic susceptibility tests were done and growth studies were carried out using spectrophotometric methods. The isolates were identified using 16SrDNA sequencing and alignment. A partial sequence of the copper resistance gene pcoA was amplified from strains Lysinibacillus sp. KR25 [KJ935917], and Escherichia coli KR29 [KJ935918]. The pcoR gene was amplified from E. coli (KR29) and the partial sequence for the chromate resistance gene chrB, was amplified from Pseudomonas sp. KR23 [KJ935916]. The gene fragments were then sequenced and translated into protein sequences. The partial protein sequences were aligned with existing copper and chromate resistance proteins in the Genbank and phylogenetic analysis was carried out. The physico-chemical properties of the translated proteins were predicted using the bioinformatics tool Expasy ProtParam Program. A homology modelling method was used for the prediction of secondary structures using SOPMA software, 3D-protein modelling was carried out using I-TASSER. Validation of the 3D structures produced was performed using Ramachandran plot analysis using MolProbity, C-score and TM-scores. Plasmid isolation was also carried out for both the wild type strains and cured derivatives and their plasmid profiles were analysed using gel electrophoresis to ascertain the presence of plasmids in the isolates. The cured derivatives were also plated on heavy metal constituted media. Antibiotic disc diffusion tests were also carried out to ascertain whether the antibiotic resistance determinants were present on the plasmid or the chromosome. The uppermost part of the Klip River had the lowest pH and thus the highest levels of heavy metal concentrations were recorded in the water samples. Turbidity, salinity and specific conductivity increased measurably at Site 4 (Henley on Klip Weir). Sixteen isolates exhibiting high iron and lead resistance (4 mM) were selected for further studies. Antibiotic susceptibility tests revealed that the isolates exhibited multi-tolerances to drugs such as Ampicillin (10 μg/ml), Amoxcyllin (10 μg/ml), Cephalothin acid (30 μg/ml), Cotrimoxazole (25 μg/ml), Neomycin (30 μg/ml), Streptomycin (10 μg/ml), Tetracycline (30 μg/ml), Tobramycin (10 μg/ml) and Vancomycin (30 μg/ml). Growth studies illustrated the effect of heavy metals on the isolates growth patterns. Cadmium and chromium inhibited the growth of most of the microorganisms. The following strains had high mean specific growth rates; KR01, KR17, and KR25, therefore these isolates have great potential for bioremediative applications. Using 16SrDNA sequencing the isolates were identified as KR01 (Aeromonas hydrophila), KR02 (Bacillus sp.), KR04 (Bacillus megaterium), KR06 (Bacillus subtilis), KR07 (Pseudomonas sp), KR17 (Proteus penneri), KR18 (Shewanella), KR19 (Aeromonas sp.), KR22 (Proteus sp.), KR23 (Pseudomonas sp.), KR25 (Lysinibacillus sp.), KR29 (Escherichia coli), KR44 (Bacillus licheniformis) and KR48 (Arthrobacter sp.). Three heavy metal resistance genes were detected from three isolates. The pcoA gene was amplified from strains Lysinibacillus sp KR25, and Escherichia coli KR29; pcoR gene from E. coli KR29 and the chrB gene, from Pseudomonas sp. KR23. The genes encoding for heavy metal resistance and antibiotic resistance were found to be located on the chromosome for both Pseudomonas sp. (KR23) and E.coli (KR29). For Lysinibacillus (KR25) the heavy metal resistance determinants are suspected to be located on a mobile genetic element which was not detected using gel electrophoresis. The translated protein sequence for pcoA_25 showed 82% homology with the copper resistant protein form Cronobacter turicensis [YP003212800.1]. Sequence comparisons between the pcoR partial protein sequence found in E. coli KR29 showed 100% homology with 36 amino acids (which was 20% of the query cover) from a transcriptional regulatory protein pcoR found in E. coli [WP014641166.1]. For the chrB partial protein sequence detected in Pseudomonas sp. (KR23), 97% of the query sequence showed 99% homology to a vitamin B12 transporter btuB in Stenotrophus sp. RIT309.
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    Influence of matrix effect of selected organochlorine pesticide residues in water from the Jukskei River catchment
    (Vaal University of Technology, 2011-11) Rimayi, Chengetayi Cornelius; Mtunzi, F., Dr.; Odusanya, A. O. D., Dr.; Van Wyk, C. S.
    One of the major problems encountered in qualitative and quantitative determination of residual pesticides by gas chromatography is the matrix effects. Matrix components have a considerable effect on the way analysis is conducted and the quality of results obtained, introducing problems such as inaccurate quantification, low analyte delectability and reporting of false positive or even false negative results. It was aimed to develop and validate a suitable method for counteracting the matrix effects so as to improve the detection and quantification of selected organochlorine pesticide residues from real water samples. The real water samples used were sampled from three points along the Jukskei River catchment area in Gauteng, South Africa for a period of 7 months from January to July 201 0 so as to create a representative sample. An automated solid phase extraction (SPE) method coupled to Gas ChromatographyMass Spectrometry (GC-MS) method for the analysis of 20 selected organochlorine pesticides was developed and validated for the purposes of studying the matrix effects. The analytical method showed a significant degree of validity when tested against parameters such as linearity, repeatability and sensitivity. Endosulphan beta, 4,4' Dichlorodiphenyldichloroethane, and Heptachlor-epoxide had the broadest linear calibration ranges of 1 ppm- 0.0156 ppm. Benzene hexachloride (BHC) delta and Lindane had the lowest statistical limits of detection of 0.018 ppm. Statistical hypothesis testing indicated that there was significant linearity in all selected organochlorine calibration curves. Four different reversed sorbent phases, including LC18, SC18- E and Strata-X (styrene divinyl benzene) were tested for organochlorine retention efficiency. The LC-18 200 mg cartridge proved to be the most robust and effective sorbent phase as it produced better recoveries varying from 90-130% for most analytes. A breakthrough volume of 100 ml for the LC-18 200 mg cartridge was determined using an optimum matrix load curve. It was then concluded that the method developed was suitable for further research towards the influence of the matrix on selective determination of the selected organochlorine pesticides. Four different calibration methods, namely matrix-free external standard, matrixmatched external standard, matrix-free internal standard and matrix-matched internal standard were applied to test the efficiency of computing recoveries. All calibration curves for the 20 organochlorine pesticides showed significant linearity > 0.99 when plotted on both Chemstation and Excel. The calibration methods were tested on three different matrices composed of a high sample matrix (synthetic matrix), a low sample matrix (real sample matrix) and a no sample matrix (ultrapure water). Statistical hypothesis testing led to the decision that there are significant differences between the mean recoveries of the three water sample matrices and also that the differences in the mean recoveries of the three sample matrices are independent of the both the two calibration techniques (internal standard and external standard) and calibration types (matrix-matched and matrix-free) applied. This led to the overall conclusion that the matrix effects have an overwhelming influence on the selective determination of the selected organochlorine pesticides.