Tertiary butyl alcohol (TBA), methyl tertiary butyl ether (MTBE) and ethyl tertiary butyl ether (ETBE) are compounds with the potential for use as oxygenates in reformulated gasolines. Being relatively soluble in water, these organics, if accidentally discharged into the subsurface, may rapidly spread and pose threats to groundwater. The purpose of this work was to evaluate the biodegradation potential of these oxygenates in soils and to determine the influence of subsurface environments on their degradation. Biodegradation was evaluated in static soil/water microcosms. Aquifer material was collected from various depths at three sites with different soil characteristics. Potential electron acceptors including O₂ in the form of H₂O₂, nitrate or sulfate were added to induce the desired metabolism (aerobic respiration, denitrification, sulfate reduction, or methanogenesis). In each metabolic process, the influence of several subsurface environmental factors on biodegradation was investigated. The data show that biodegradation potential of MTBE, ETBE and TBA varied substantially with site and depth. TBA was the easiest compound to biodegrade, whereas MTBE was the most recalcitrant. Cleavage of the ether bond is the first and rate-limiting step in the degradation of ETBE and possibly MTBE. Addition of H₂O₂, caused chemical oxidation of MTBE and ETBE. The chemical oxidation was faster in the organically rich soils, but slower in the organic-poor soils. Soil microorganisms were able to catalyze the cleavage of the ether bond in ETBE but not MTBE. This biological reaction was not significant when chemical oxidation occurred. TBA, on the other hand, was aerobically biodegraded in all soils. Under denitrifying and anaerobic conditions TBA degradation occurred in all soils but the degradation of ETBE and MTBE was only observed at one of three sites. TBA degradation was enhanced by nutrient addition in the nutrient-poor soil but hindered by the presence of other easily-degraded organic compounds. Degradation of MTBE and ETBE occurred only in soils containing low organic matter with a pH around 5.5. No degradation of MTBE and ETBE was observed in the organic-rich soils and in the organically poor soils, the addition of ethanol inhibited MTBE and ETBE degradation. / Ph. D.

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnology, Durban University of Technology, 2007 xxi, 117 leaves / The aromatic compounds Polychlorinated Biphenyls (PCBs) are one of the largest groups of environmental pollutants. The greatest concern is the release of PCBs in the water systems by industrial effluent, accidental spillages or leaks. PCBs are able to bioaccumulate in the fatty tissues of animals, fish and humans. The impact on human health due to PCBs has prompted interest in their degradation. The application of microbial degradation of PCBs can transform many PCB metabolites. There are a wide variety of microorganisms that can degrade PCBs or utilise them as sole carbon sources. This study focused on isolating microrganisms from industrial wastewater capable of aerobic degradation of PCBs. The degradation potential of the selected isolates were investigated by using different analytical techniques viz. ultra violet or visible spectrophotometer (UV/Vis), thin layer chromatography (TLC) and gas chromatography electron capture detector (GC-ECD).

Phytosterols are steroid chemicals produced by plants for the purposes of membrane function and hormone production. Phytosterols can cause endocrine disruption in aquatic species at very low concentrations and are suspected of contributing to endocrine disruption linked to pulp and paper effluent. Wastewater from the pulp and paper industry is often treated biologically in aerated stabilization basins (ASBs) that expose phytosterols to a range of redox zones. Phytosterol removal in ASBs varies and stigmasterol has even been shown to increase across the treatment system. Little is known about the microbial processes that occur within ASBs and their effect on phytosterol removal. The objective of this research was to assess the biotransformation potential of phytosterols in a simulated ASB treatment system and to improve understanding of the processes that occur within the various redox zones and their impact on the removal of phytosterols. To assess the biotransformation of phytosterols under aerobic conditions, three assays were conducted using a stock aerobic culture fed with pulp and paper wastewater. The assays tested three conditions: phytosterols present as a sole added carbon source, phytosterols with dextrin as an added carbon source, and phytosterols with ethanol as a solubilizing agent and added carbon source. Phytosterol biotransformation was found to be limited by low phytosterol solubility. When solubilized, phytosterol removal occurred in two phases: an initial near-linear removal, followed by accelerated removal during the culture's stationary stage, possibly due to the release of extracellular cholesterol oxidase. The anoxic and anaerobic biotransformation of phytosterols was examined through a series of three semi-batch cultures maintained under nitrate-reducing, sulfate-reducing and fermentative/methanogenic conditions, all developed from stock cultures fed with pulp and paper wastewater. Phytosterol removal was significant in the nitrate-reducing culture, although microbial activity and phytosterol removal declined in later stages. Phytosterol removal was also observed in the sulfate-reducing culture, although there was a significant lag period before removal occurred. No phytosterol removal was observed in the fermentative/methanogenic culture. Phytosterol biotransformation was also examined in the context of a lab-scale ASB fed continuously with pulp and paper wastewater. The steady-state ASB effluent and sediment characteristics were examined over three hydraulic retention times (HRTs). Effluent quality was not significantly affected by a change in HRT but sediment characteristics were significantly affected and, at shorter HRTs, phytosterols accumulated in the sediment. Wastewater bioassays demonstrated the release of phytosterols during the breakdown of solids. This research improves the understanding of biological processes within ASBs and their effect on phytosterol removal.

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnology, Durban University of Technology, 2007 xxi, 117 leaves / The aromatic compounds Polychlorinated Biphenyls (PCBs) are one of the largest groups of environmental pollutants. The greatest concern is the release of PCBs in the water systems by industrial effluent, accidental spillages or leaks. PCBs are able to bioaccumulate in the fatty tissues of animals, fish and humans. The impact on human health due to PCBs has prompted interest in their degradation. The application of microbial degradation of PCBs can transform many PCB metabolites. There are a wide variety of microorganisms that can degrade PCBs or utilise them as sole carbon sources. This study focused on isolating microrganisms from industrial wastewater capable of aerobic degradation of PCBs. The degradation potential of the selected isolates were investigated by using different analytical techniques viz. ultra violet or visible spectrophotometer (UV/Vis), thin layer chromatography (TLC) and gas chromatography electron capture detector (GC-ECD).

Soil microcosm experiments were conducted to identify soil amendments which enhance the biodegradation of a No. 2 (diesel) fuel in soil. Microcosm amendments in Phase 1 included yeast extract, acetate, methane, and activated sludge. Combinations of these amendments resulted in 16 different treatments. Phase 2 soil microcosms contained combinations of methane and methanotroph additions resulting in four different treatments. Gas chromatography was used to determine the time and treatment-dependent concentration of C12-C18 n-alkanes during Phase 1 and, C14-C19 n-alkanes during Phase 2. Results from Phase 1 indicated that the most extensive biodegradation occurred in methane and activated sludge-supplemented microcosms. Acetate and/or yeast extract inhibited biodegradation by soil and/or activated sludge microorganisms. Addition of methane relieved inhibition by these amendments. Methane and/or methanotroph additions to Phase 2 microcosms did not enhance biodegradation relative to unamended microcosms. In general, n-alkanes longer than n-C12 were equally degraded in soil microcosms.

Dissertation (PhD)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: Aflatoxins are mycotoxins predominantly produced by the filamentous fungi Aspergillus flavus and Aspergillus parasiticus. Aflatoxin B1 (AFB1), the most abundant aflatoxin, is highly mutagenic, toxic, carcinogenic and teratogenic to humans and animals and is particularly correlated with the incidence of hepatocellular carcinoma in parts of Africa, China and South East Asia. In this regard aflatoxin is classified as a type I human carcinogen by the International Agency for Research on Cancer. Furthermore, aflatoxin contamination of food and feed is responsible for extensive economic losses due to loss of crops and farm animals. In spite of regulations regarding acceptable levels of aflatoxin in food, aflatoxin contamination remains a serious worldwide problem, especially in developing countries where it occurs predominantly in dietary staples. Inactivation of aflatoxin by physical and chemical methods has not yet proved to be effective and economic. However, biological detoxification offers an attractive alternative for eliminating toxins as well as safe-guarding the desired quality of food and feed. In this study, the biological degradation of AFB1 by bacteria and fungi was investigated. Several bacteria, including Rhodococcus spp., as well as white rot fungi have the potential to degrade a wide range of polycyclic hydrocarbon compounds due to the large repertoire of enzymes they produce and therefore the ability of some of these microorganisms to degrade AFB1 was investigated. Effective degradation of AFB1 by intracellular extracts of Mycobacterium fluoranthenivorans sp. nov. DSM 44556T, Nocardia corynebacterioides DSM 20151 and N. corynebacterioides DSM 12676 was demonstrated. Furthermore, AFB1 was effectively degraded by liquid cultures as well as intra- and extracellular extracts of Rhodococcus erythropolis DSM 14303. Significant (P<0.001) reduction in AFB1 was observed following treatment with R. erythropolis extracellular extracts with only 33.20% residual AFB1 after 72 h. Results indicated that the degradation by R. erythropolis DSM 14303 is enzymatic and that the enzymes are constitutively produced. The degradation of AFB1 when treated with R. erythropolis DSM 14303 extracellular extract coincided with a total loss of mutagenicity. In addition, treatment of AFB1 with culture fractions containing recombinant 2,3-dihydroxybiphenyl dioxygenase, which was produced through extracellular expression of the bphC1 gene of R. erythropolis DSM 14303 in Escherichia coli BL21, resulted in significant (P<0.0001) degradation (49.32%) and reduced mutagenic potency (42.47%) of the molecule. Significant (P<0.0001-0.05) degradation of AFB1 was obtained following treatment with culture extracts containing laccase enzyme produced by white rot fungi (17.10- 76.00%), purified fungal laccase from Trametes versicolor (1 U/ml, 87.34%) as well as with recombinant laccase produced by Aspergillus niger (118 U/L, 55.00%). Furthermore, treatment of AFB1 with purified fungal laccase enzyme (1 U/ml) resulted in loss of the mutagenic potency of the molecule. The decrease in the fluorescence and mutagenic properties of AFB1 following treatment with the microbial preparations imply changes to the furofuran- and/or lactone rings of the molecule. The current study contributes towards developing genetic engineered microbial strains which could be applied as an important bio-control measure. Such strains could exhibit multifunctional technological properties including degradation of AFB1, to significantly improve the quality, safety and acceptability of food. / AFRIKAANSE OPSOMMING: Aflatoksiene is mikotoksiene wat hoofsaaklik deur die filamentagtige fungi, Aspergillus flavus en Aspergillus parasiticus geproduseer word. Die algemeenste aflatoksien, aflatoksien B1 (AFB1), is hoogs mutagenies, toksies, karsinogenies en teratogenies vir mense en diere. Veral in sekere dele van Afrika, China en Suid-Oos Asië bestaan daar `n korrelasie tussen aflatoksien en die voorkoms van hepatosellulêre karsinoom en gevolglik word aflatoksiene as `n tipe I menslike karsinogeen deur die Internasionale Agentskap vir Kankernavorsing geklassifiseer. Aflatoksien kontaminasie in voedsel het ook `n ekonomiese impak as gevolg van verlies aan landbougewasse en diere. Ten spyte van maatreëls betreffende die toelaatbare vlakke van aflatoksiene in voedel, is aflatoksien kontaminasie steeds `n groot probleem wêreldwyd, veral in ontwikkelende lande waar dit hoofsaaklik in stapelvoedsel voorkom. Huidiglik is die inaktivering van aflatoksiene deur fisiese en chemiese metodes nie effektief en ekonomies nie. Daarteenoor bied biologiese tegnieke `n gunstige opsie vir die eliminering van die toksiene, terwyl die organoleptiese eienskappe van die voedsel steeds behoue bly. Hierdie studie fokus op die biologiese afbraak van AFB1 deur bakterieë en fungi. Verskeie bakterieë, insluitend Rhodococcus spp., sowel as witvrot fungi produseer `n verskeidenheid ensieme wat hulle in staat stel om `n wye reeks polisikliese hidrokoolstofverbindings af te breek en gevolglik is afbraak van AFB1 deur sommige van hierdie mikroörganismes bestudeer. Effektiewe afbraak van AFB1 deur intrasellulêre ekstrakte van Mycobacterium fluoranthenivorans sp. nov. DSM 44556T, Nocardia corynebacterioides DSM 20151 en N. corynebacterioides DSM 12676 is aangetoon. AFB1 is ook effektief in vloeibare kulture sowel as intra- en ekstrasellulêre ekstrakte van Rhodococcus erythropolis DSM 14303 afgebreek. `n Beduidende (P<0.001) afbraak van AFB1 is waargeneem na behandeling met R. erythropolis DSM 14303 ekstrasellulêre ekstrakte, met slegs 33.20% oorblywende AFB1 na 72 h. Resultate het getoon dat die afbraak deur R. erythropolis DSM 14303 ensimaties is en dat die ensieme konstitutief geproduseer word. Afbraak van AFB1 deur R. erythropolis DSM 14303 het ook tot `n totale verlies aan mutagenisiteit gelei. Verder het behandeling van AFB1 met rekombinante 2,3-dihidroksiebifenieldioksiginase fraksies wat geproduseer is deur ekstrasellulêre uitdrukking van die bphC1 geen van R. erythropolis DSM 14303 in Escherichia coli BL21, beduidende (P<0.0001) afbraak (49.32%) en vermindering in mutagenisiteit (42.47%) van die molekuul teweeggebring. Beduidende (P<0.0001-0.05) afbraak van AFB1 is verkry na behandeling met witvrot fungus kultuurekstrakte wat lakkase-ensiem bevat (17.10-76.00%), gesuiwerde lakkase geproduseer deur Trametes versicolor (1 U/ml, 87.34%), sowel as rekombinante lakkase geproduseer deur Aspergillus niger (118 U/L, 55.00%). Verder het die behandeling van AFB1 met gesuiwerde lakkase-ensiem (1 U/ml) gelei tot verlies aan mutagenisiteit van AFB1. Die afname in fluoressensie en mutageniese eienskappe van die AFB1-molekuul na behandeling met die onderskeie mikrobiese preparate dui op struktuurveranderings aan die furofuraan- en/of laktoonringe van die molekuul. Hierdie studie lewer `n bydrae tot die ontwikkeling van geneties gemanipuleerde mikrobiese rasse wat as `n belangrike biokontrole kan dien. Sulke rasse met multifunksionele tegnologiese eienskappe, insluitend die afbraak van AFB1, kan die kwaliteit, veiligheid en aanvaarbaarheid van voedsel verbeter.

Thesis (PhD)--Stellenbosch University, 2003. / ENGLISH ABSTRACT: Plant biomass, the most abundant renewable resource in nature, consists of matrices of mainly lignin, cellulose, hemicellulose as well as inorganic components. Xylan, the major hemicellulose component in plant cell walls, is the most abundant polysaccharide after cellulose. This makes the main constituent sugar of xylan, D-xylose, the second most abundant renewable monosaccharide in nature. Very few hemicelluloses are either homopolymeric or entirely linear. Therefore, the variety of enzymes involved in their hydrolysis is more complex than the enzyme group responsible for the hydrolysis of cellulose. Although the ability to degrade xylan is common among bacteria and filamentous fungi, this trait is relatively rare among yeasts. However, some strains of the yeast Pichia stipitis are, amongst others, able to degrade xylan. As P. stipitis is also one of the best D-xylose fermenting yeasts thus far described, this yeast has the potential of fermenting polymeric xylan directly to ethanol. However, it was shown that the natural xylanolytic ability of this yeast is very weak. In this study, xylanolytic genes were expressed in P. stipitis to test the ability of the yeast to produce heterologous proteins, and to determine the enhancement of xylan utilisation by the recombinant strain. The native xylose reductase gene (XYLl) and transketolase gene (TKL) and the heterologous Saccharomyces cerevisiae phosphoglycerate kinase (PGKl) gene promoter were cloned into P. stipitis transformation vectors and used to express the Trichoderma reesei ~-xylanase encoding gene (xyn2) as reporter gene. It was shown that the XYLl promoter was induced in the presence of D-xylose and that the TKL promoter was constitutively expressed. The PGKl promoter of S. cerevisiae did not function in P. stipitis . When the T reesei xyn2 gene and the Aspergillus kawachii ~-xylanase encoding gene (xynC) were expressed under control of the XYLl promoter, extracellular ~-xylanase activity of up to 136 nkat/ml and 171 nkatlml was observed, respectively. This activity declined over time due to the presence of extracellular proteases, secreted by P. stipitis. Growing the cultures in a fermentor and controlling the pH level to pH 6 did not alleviate the reduction of heterologous l3-xylanase activity. When the Aspergillus niger l3-xylosidase encoding gene (xlnD) was expressed as a fusion gene (designated XL02) with the S. cerevisiae mating factor secretion signal (MFal) under control of the P. stipitis TKL promoter, extracellular l3-xylosidase activity of 0.132 nkatlml was observed. Co-expression of the xyn2 and XL02 genes led to B-xylanase and l3-xylosidase activities of 128 nkatlml and 0.113 nkat/ml, respectively. Co-expression of the xynC and XL02 genes led to l3-xylanase and l3-xylosidase activities of 165 nkat/ml and 0.124 nkatlml, respectively. The expression of the fungal xylanolytic genes in P. stipitis also led to an increased biomass yield when the recombinant strains were cultured on birchwood xylan as sole carbon source. The strain co-expressing the A. kawachii l3-xylanase and A. niger l3-xylosidase encoding genes was the most successful, yielding a 3.2-fold higher biomass level than the control strain. Biomass levels of the recombinant strains were further improved on average by 85% by growing them in a fermentor under conditions of high oxygenation. The strains were also tested for direct conversion of xylan to ethanol and the strain co-expressing the A. kawachii l3-xylanase and A. niger l3-xylosidase encoding genes produced 1.35 giL ethanol, which represents a 3.6-fold increase in ethanol yield over the reference strain. These strains represent a step towards the efficient degradation and utilisation of hemicellulosic materials by ethanol-producing yeasts. / AFRIKAANSE OPSOMMING: Plant biomassa, die volopste hernubare koolstotbron in die natuur, bestaan uit matrikse van lignien, sellulose en hemisellulose. Xilaan, die hoof hemisellulose komponent in plantselwande, is na sellulose die volopste polisakkaried. Gevolglik is die hoof suikerkomponent van xilaan, naamlik D-xilose, die tweede volopste hernubare monosakkaried in die natuur. Baie min hemisellulose molekules is homopolimere of heeltemal linieêr. Daarom is die ensieme betrokke by die atbraak van hemiselluloses meer kompleks as die ensieme betrokke by die atbraak van sellulose. Bakterieë en filamentagtige fungi wat oor die vermoë om xilaan af te breek beskik, kom wydversprei voor maar relatief min giste kan xilaan benut. Sommige rasse van die gisspesie Pichia stipitis het egter beperkte vermoë om xilaan af te breek. P. stipitis is ook een van die beste D-xilose fermenterende giste wat tot dusver beskryf is en het dus die potensiaalom etanol vanafpolimeriese xilaan te produseer. In hierdie studie is gene wat kodeer vir xilaanatbrekende ensieme in P. stipitis uitgedruk om die vermoë van die gis as heteroloë uitdrukking sisteem te evalueer. Verder is die effek van die heteroloë xilaanatbrekende ensieme tydens groei op xilaan as enigste koolstotbron getoets. Die promoters van die xilosereduktasegeen (XYLl), die transketolasegeen (TKL) van P. stipitis en die fosfogliseraatkinasegeen (PGKl) van Saccharomyces cerevisiae is in P. stipitis transformasie vektore gekloneer en gebruik om die Trichoderma reesei ~-xilanasegeen (xyn2) as verklikkergeen uit te druk. Dit het bewys dat die XYLI promotor induseerbaar is in die teenwoordigheid van D-xilose terwyl die TKL geen konstant uitgedruk was. Die PGKI promotor van S. cerevisiae was nie funksioneel in P. stipitis nie. Ekstrasellulêre ~-xilanase aktiwiteit van onderskeidelik 136 nkatlml en 171 nkatlml kon waargeneem word wanneer die T reesei xyn2 geen of die Aspergillus kawachii ~-xilanasegeen (xynC) onder beheer van die XYLI promotor uitgedruk is. Hierdie aktiwiteit het afgeneem na gelang van tyd a.g.v. die teenwoordigheid van ekstrasellulêre proteases wat deur P. stipitis uitgeskei word. Die afname van ekstrasellulêre ~-xilanase aktiwiteit kon nie voorkom word deur die kulture in 'n fermentor te groei en die pH vlak tot pH 6 te beheer nie. Tydens uitdrukking van die Aspergillus niger ~-xilosidase geen (xlnD) as 'n fusiegeen (genoem XL02) met die paringsfaktor sekresiesein (MFal) van S. cerevisiae onder transkripsionele beheer van die P. stipitis TKL promotor, kon ekstrasellulêre ~-xilosidase aktiwiteit van 0.132 nkatlml waargeneem word. Gesamentlike uitdrukking van die xyn2 en XL02 gene het gelei tot ~-xilanase en ~-xilosidase aktiwiteite van 128 nkatlml and 0.113 nkat/ml, onderskeidelik. Gesamentlike uitdrukking van die xynC en XL02 gene het gelei tot ~-xilanase en ~-xilosidase aktiwiteite van 165 nkatlml and 0.124 nkatlml, onderskeidelik. Die uitdrukking van xilaanatbrekende ensieme III P. stipitis het verhoogbe biomassaproduksie teweeg gebring wanneer die rekombinante gisrasse op birchwood xilaan as enigste koolstotbron gegroei het. Die rekombinante ras wat die A. kawachii ~-xilanasegeen en die A. niger ~-xilosidase geen gesamentlik uitdruk, was die mees suksesvolle ras en het 3.2-voudig hoër biomassa as die kontrole ras opgelewer. Die biomassa van die rekombinante rasse tydens groei op xilaan as enigste koolstotbron kon gemiddeld met 85% verhoog word deur die giste onder hoë suurstotkonsentrase in 'n fermentor te kweek. Die rekombinante rasse is verder ook getoets vir hul vermoë om xilaan direk tot etanol om te skakel. Die rekombinante ras wat die A. kawachii ~-xilanasegeen en die A. niger ~-xilosidase geen gesamentlik uitgedruk het, het 'n 3.6- voudige verhoging in etanolproduksie getoon en 1.35 gIL ethanol gelewer. Hierdie rekombinante gisrasse verteenwoordig 'n stap nader aan die doeltreffende atbraak en benutting van hemisellulose deur etanolproduserende giste.

published_or_final_version / Environmental Management / Master / Master of Science in Environmental Management

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Semiconductor manufacturing is one of the most advancing, growing and evolving industries. The production of semiconductors presents several challenges, both technologically and environmentally. The amount and complexity of the chemical substances utilized in the manufacturing process has been growing exponentially, and new chemicals are often introduced to the process and the environment. Two steps of this process play a special important role in the introduction of new chemical and demand of natural resources: Chemical Mechanical Planarization (CMP) and Photolithography.Wastewaters from the semiconductor manufacturing are complex and have several chemicals in different concentrations. Heavy metals, acids, chelators, surfactants and other chemicals are found in semiconductor effluents. Part of the scope of this study is to evaluate and remediate wastewaters produced in semiconductor manufacturing.During the development of this project it was found that copper can be successfully removed and recovered from CMP wastewaters by the use of a sulfate reducing bioreactor and a crystallization reactor, promoting precipitation of copper sulfides on the surface of silica sand. High removal and recovery efficiencies were found as result of the study. Another finding include that citrate is a readily biodegradable compound which can be successfully utilized as electron donor for anaerobic processes such as methanogenesis and sulfate reductions. However other important chelator, like EDTA, can cause toxicity to these microorganisms and affect important biological processes. PFOS is an important chemical for the semiconductor industry; however, the physical and chemical properties make this compound persistent in the environment and bioaccumulative. New substitutes for PFOS were tested and evaluated for their environmental impact. It was found that perfluorination plays an important role in the chemical properties of PFOS and removal of this characteristic improves the environmental performance of the new substitutes. Evaluation of these new chemicals was also performed by simulation and modeling. The software utilized in this study identified properties like toxicity and octanol-water partition coefficient accurately. On the other hand biodegradability was poorly estimated and new models are suggested for evaluation of this property for compounds with characteristics similar to the ones studied here (specifically high fluorination).