Dissertation (PhD) -- University of Stellenbosch, 2002. / ENGLISH ABSTRACT: More than sixteen isolates of iron-oxidizing bacteria belonging to the genus Leptospirillum were included in this study, with the finding that they were clearly divisible into two major groups. Group I leptospirilla had mol% G+C ratios within the range 49-52%, three copies of rrn genes and based on 16S rRNA sequence data, clustered together with the Leptospirillum ferrooxidans type strain (DSM2705or LI5). Group II leptospirilla had mol% G+C ratios of 55-58%, two copies of rrn genes and based on 16S rRNA sequence form a separate cluster. Genome DNA-DNA hybridization experiments indicated that three similarity subgroups were present amongst the leptospirilla tested with two DNA-DNA hybridization similarity subgroups being found within group I. The two groups could also be distinguished based on the sizes of their 16S-23SrRNA gene spacer regions. We propose that the group II leptospirilla should be recognized as a new species with the name Leptospirillum ferriphilum sp. nov. Members of the two species can be rapidly distinguished from each other by amplification of their 16S rRNA genes and carrying out restriction enzyme digests of the products. Several but not all isolates of the group II leptospirilla, but none from group I (L. ferrooxidans) were capable of growth at 45°C. Plasmid DNA was isolated from strain ATCC49879 (L. ferrooxidans). Restriction endonuclease mapping of what appeared to be about 60 kb of plasmid DNA, established that two plasmids of approximately 30.0 kb and 27.0 kb were present. These were named p49879.1 and p49879.2 respectively. Attempts to isolate the plasmids separately were not successful. Partial sequencing of the two plasmids was carried out and sequence analysis of p49879.1 and p49879.2 indicated that the plasmids shared regions of homology. Total plasmid DNA was DIG-labelled and used as a probe in Southern hybridization experiments with genomic DNA from all sixteen original leptospirilla isolates as the target DNA. All leptospirilla belonging to Group I gave a positive signal, little or no homology to Group II leptospirilla was obtained. The region of homology present in all L. ferrooxidans strains was localized to an area on plasmid p49879.2 showing high amino acid identity to a transposase/putative transposase of Methanosarcina acetivorans and plasmid CPl from Deinococcus radiodurans Rl respectively. Whether these regions of homology indicate that complete, functional transposons are present in all L. ferrooxidans isolates still remains to be determined. Preliminary sequence analysis of both plasmids resulted in the identification of regions with amino acid sequence identity to the TnpA and TnpR of the Tn2l-like transposon family, and the mobilization regions of IncQ-like plasmids (particularly that of pTFl from At. ferrooxidans). Another potentially interesting ORF was identified in p49879.2 with high amino acid sequence identity to an ArsR-like protein that belongs to a second atypical family of ArsR transcriptional regulators. Whether this protein is functional in the regulation of arsenic resistance genes has not yet been determined, nor have other arsenic resistance genes been identified. Future work includes further sequence analysis of these plasmids to better understand their contribution to the isolates in which they are found. / AFRIKAANSE OPSOMMING: Meer as sestien isolate van die yster-oksiderende bakterieë, wat aan die genus Leptospirillum behoort, is in die studie ingesluit en die resultate het getoon dat dié groep verder in twee hoof groepe verdeel kan word. Groep I het "n mol% G+C van tussen 49% en 52% gehad, sowel as drie kopieë van die ribosomale gene (rrn). Hiermeesaam het die 16SrRNA volgorde data getoon dat hierdie isolate groepeer saam met Leptospirillum ferrooxidans (DSM2705T en LI5). Groep II leptospirilla het "n mol% G+C van tussen 55% en 58% gehad sowel as twee kopieë van die rrn gene en saam met die 16SrRNA volgorde data het hierdie isolate "n aparte groep gevorm. Genoom DNA-DNA hibridisasie eksperimente het gewys dat daar drie subgroepe onder die Leptospirillum wat getoets was is, met twee naverwante groepe wat onder Groep I val. Daar kan ook tussen die twee hoof groepe onderskei word op grond van die grootte van hul 16S- 23SrRNA intergeniese gebiede. Ons stel dus hier voor dat die Groep II leptospirilla as "n nuwe spesie beskou word naamlik, Leptospirillum ferriphilum sp, nov. Die twee spesies kan maklik onderskei word deur die PKR amplifikasie produk van die 16SrRNA te verteer met restriksie ensieme. Vele, maar nie al van die Groep II isolate kan by 45°C groei nie, terwyl geen van die Groep I leptospirilla (L.ferrooxidans) kan nie. Plasmied DNA was geisoleer uit Leptospirillum ferrooxidans ATCC49879. Aanvanklike analise het gedui op die teenwoordigheid van een 60.0 kb plasmied. Verdere restriksie ensiem kartering het wel getoon dat hierdie, in teen deel, twee plasmiede van ongeveer 30.0 kb en 27.0 kb in grootte is: p49879.1 en p49879.2. Pogings om die twee plasmiede apart te isoleer was onsuksesvol. Totale plasmied DNA is gemerk met die Random primed DNA labelling kit (Roche diagnostics) en gebruik as peiler in Southern klad eksperimente met genoom DNA, van al sestien isolate, as teiken. Alle leptospirilla wat aan Groep I behoort het "n positiewe sein gegee terwyl geen sein teen Groep II DNA opgemerk was nie. Die area wat, tussen die plasmiede en Groep I homologie getoon het, is gelokaliseer tot "n area op plasmied p49879.2 wat hoë amino suur identiteit toon aan "n transposase geen van Methanosarcina acetivorans, en "n voorgestelde transposase geen op plasmied CPI van Deinococcus radiodurans Rl. Dit moet nog vasgestel word of hierdie area van homologie dui op die teenwoordigheid van "n volledige, funksionele transposon in alle L. ferrooxidans isolate. Gedeeltelike DNA volgorde bepalings van beide plasmiede het gelei tot die identifikasie van areas met hoë amino suur volgorde identiteit aan die TnpA en TnpR gene van die Tn21-tipe transposon familie, sowel as aan die mobilisasie gene van IncQsoortige plasmiede (veral die van pTFI uit Acidithiobacillus ferrooxidans). "n Oop lees raam van belang, wat op plasmied p49879.2 geidentifiseer was, het hoë amino suur volgorde identiteit aan "n ArsR-tipe geen getoon wat aan "n tweede atiepiese familie van ArsR transkripsionele reguleerders behoort. Op die stadium is dit nog onbekend of hierdie protein funksioneel is in die regulering van arseen weerstandbiedenheidsgene.

Thesis (MScIng)--University of Stellenbosch, 2003. / ENGLISH ABSTRACT: This thesis investigates the control of calcium and magnesium in a base metal sulphate leach solution containing nickel and cobalt. The presence of calcium and magnesium in the hydrometallurgical processing of base metals, result in a number of difficulties. These problems range from the contamination of the final product, to high energy consumption and large bleed streams during electrowinning. Calcium poses a greater problem in sulphate solutions due to the low solubility of its sulphate salts. No conventional method exists for the control of calcium and magnesium. As part of this study a review of possible control methods was conducted, which is listed within. From this list the precipitation of fluorides was selected for further investigation. The results showed that it is possible to control calcium and magnesium through the precipitation of their respective fluorides, without the co-precipitation of nickel and cobalt. For 10% stoichiometric excess of fluoride 96.5% calcium and 98.5% magnesium were removed during batch experiments. It is known that mixing and hydrodynamics plays an important role on the characteristics of the formed precipitate, making these processes inherently difficult to scale-up. To evaluate these effects on a continuous process, the three-zone model proposed by Gösele and Kind (1991) was used. A precipitate with consistent characteristics was produced while varying the mixing on the macro, meso and micro scale. Additionally, methods were investigated for the removal or possible recycling of the unreacted fluoride, for which activated alumina was identified. It was observed that activated alumina could adsorb fluoride to low levels in the presence of the base metal solution, after which it could be regenerated again. The activated alumina (AA) had a capacity of 8.65 gF/lAA at a 10 mg/l fluoride breakthrough level during column tests. Based on the experimental results a conceptual process was devised whereby only a portion of the leach stream is subjected to the fluoride precipitation process, after which it is returned to lower the overall calcium and magnesium concentrations. This method would reduce the effect of the observed dominance of magnesium precipitation, in processes where the maximum removal of both elements is not required. The fluoride precipitation process consisted of three steps being precipitation, solid-liquid separation and adsorption of the unreacted fluoride. Sufficient information is provided on the process for a cost estimation to be carried out. Should this found to be feasible, a continuation of the project is recommended. Different reactor configurations could be evaluated for precipitation. The scaling observed during the continuous experiments should also be investigated to minimise its effect. The investigation of activated alumina was only a secondary project and more work is required on optimisation, particularly for the desorption cycle to enable the recycling of the unreacted fluoride. / AFRIKAANSE OPSOMMING: Saamgestel in hierdie tesis is 'n studie van die beheer van kalsium en magnesium in 'n basismetaal-sulfaatoplossing, bevattende nikkel en kobalt. Die teenwoordigheid van kalsium en magnesium in dié oplossings veroorsaak 'n verskeidenheid van probleme, wat wissel van produkkwaliteit verlaging tot hoë energieverbruik en groot bloei strome tydens platering. 'n Groter probleem word ondervind met kalsium as gevolg van die lae oplosbaarheid van sy sulfaatsoute. Geen konvensionele metode kon gevind word vir die beheer van kalsium en magnesium gedurende die oorsig van moontlike metodes nie. Hierdie moontlike metodes is geïdentifiseer en kortliks bespreek in die tesis. Van die moontlike metodes is die presipitasie van fluoried-soute gekies vir verdere eksperimentele ondersoek. Die ondersoek het getoon dat dit moontlik is om kalsium en magnesium te beheer deur die presipitasie van fluoriede sonder om die basismetale saam te presipiteer. Vir 'n 10% oormaat fluoried toevoeging is 96.5% van die kalsium en 98.5% van die magnesium gepresipiteer gedurende die enkelladingstoetse. Dit is bekend dat vermenging en hidrodinamika 'n groot rol speel in die kwaliteit van die presipitaat wat gevorm word. Dit bemoeilik die opskalering van presipitasie prosesse. Vir die ondersoek oor die invloed van vermenging op 'n kontinu proses is die drie-sel model van Gösele en Kind (1991) gebruik. Dit is gevind dat die karakter van presipitaat relatief konstant gebly het vir variasies van vermenging op die makro, meso en mikro skaal, wat opskaling behoort te vergemaklik. Addisioneel is die verwydering of moontlike hersirkulasie van die ongereageerde fluoried ondersoek, en geaktiveerde alumina is geïdentifiseer as 'n moontlike adsorbeermiddel. 'n Eksperimentele ondersoek het getoon dat geaktiveerde alumina fluoried tot lae vlakke kan adsorbeer in die teenwoordigheid van die basismetale, waarna dit weer geregenereer kan word. Die kapasiteit van die geaktiveerde alumina (GA) was bereken as 8.65 gF/lGA by 'n 10 mg/l fluoried vlak gedurende die kolom toetse. 'n Konsep-proses is opgestel na aanleiding van die eksperimentele resultate, waarvolgens slegs 'n gedeelte van die logingstroom na die fluoried presipitasie proses gestuur word, waarna dit weer teruggevoeg word om die algehele kalsium en magnesium konsentrasie te verlaag. Dié metode sal voorkom dat magnesium presipitasie domineer vir 'n toepassing waar slegs 'n gedeelte van kalsium en magnesium verwyder word. Die fluoried presipitasie proses behels drie stappe waarvolgens die fluoriede eers gepresipiteer word, waarna dit geskei word, en dan die ongereageerde fluoried geadsorbeer word. Genoeg inligting is versamel sodat 'n kosteberaming van die proses gedoen kan word. As die koste van die proses aanvaarbaar is, word dit voorgestel dat die ondersoek voortgesit word. Verskillende reaktor konfigurasies kan vir die presipitasie stap getoets word en daar moet ook ondersoek ingestel word hoe om die korslaag wat gedurende die kontinu eksperimente geobserveer is, te verminder. Die ondersoek van geaktiveerde alumina was ondergeskik in die projek en nog werk sal gedoen moet word om dit te optimiseer, spesifiek gedurende die desorpsie siklus vir die hersirkulasie van die ongereageerde fluoried.

published_or_final_version / Civil Engineering / Doctoral / Doctor of Philosophy

published_or_final_version / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

The main goal of this study consists of the development of new asphalt mixes, based on industrial waste materials as replacement of natural aggregates. To achieve this purpose, a new characterisation of these pavements was proposed so to verify that the new mix has good mechanical performance without any detrimental impact to the environment. This characterisation was divided in three distinct steps: • a physical and chemical characterisation of the different constituents of asphalt concrete, as well the natural materials as the industrial waste considered as potentially secondary aggregates, • a study of the bitumen-aggregate interface by means of two techniques: a qualitative method (scanning electron microscope) and a quantitative one (nanoindentation) • an evaluation of the mechanical performance of mixes containing industrial waste, before and after recycling, by means of four standard road-engineering tests. The numerous results allowed to put in evidence the possibility to reuse some industrial waste materials in asphalt concrete. In addition, this characterisation containing both chemical and mechanical aspects, at the microscopic and macroscopic scales, would permit the transposition of this study to the whole of asphalt concrete./ Le principal objectif de ce travail consiste en le développement de nouveaux mélanges bitumineux utilisant des déchets industriels en tant que remplacement des matériaux naturels. Pour ce faire, une nouvelle caractérisation de ces revêtements a été proposée afin de vérifier que le nouveau revêtement obtenu présente de bonnes performances mécaniques tout en évitant un impact environnemental néfaste. Cette caractérisation a été scindée en trois étapes distinctes : • une caractérisation physique et chimique des différents constituants de l’enrobé bitumineux, à savoir les granulats naturels mais également les déchets industriels, candidats en tant que matériaux secondaires, • une étude de l’interface bitume-granulat et ce, au moyen de deux techniques : une méthode qualitative (microscope électronique à balayage)et une méthode quantitative (nanoindentation), • une évaluation des performances mécaniques des mélanges comportant des déchets industriels avant et après recyclage et ce, au moyen de quatre tests usuels de l’ingénierie routière. Les nombreux résultats obtenus ont permis de mettre en évidence la possibilité de valoriser certains déchets industriels dans les enrobés bitumineux. De plus, la mise en place d’une caractérisation comportant des aspects chimiques et mécaniques, à la fois à l’échelle microscopique et macroscopique, permettra la transposition de cette étude à l’ensemble des enrobés bitumineux.

<p>Nitrogen deposition leads to environmental damage in areas where the nitrogen deposition is high. Southwest Sweden receives an annual nitrogen deposition of up to 20 kg N/ha. Nitrogen that is not assimilated by the vegetation is accumulated in the soil, which may lead to nitrogen saturation and an elevated risk of nitrogen leaching. Nitrogen leaching from forest areas in southern Sweden has proven to be higher than from agricultural areas, which have been thought to be the main contributors to elevated nitrogen levels in rivers and lakes. The amount of nitrogen that leaches depends on the fraction of the total nitrogen in the soil that consists of nitrate, since nitrate is easily transported through the soil. Nitrogen leaching increases after clear-cutting since the uptake by vegetation is greatly reduced.</p><p>In this study the soil chemistry of two clear-cut spruce stands in Halland, in southwest Sweden, has been analyzed. A previous study in these areas has indicated higher nitrate concentrations in the groundwater in one of the areas and thus a greater nitrogen leaching. Nitrogen deposition in the two areas is estimated to be the same and therefore the soil chemistry has been analyzed to evaluate if differences in the soil can have resulted in differences in the nitrate concentration in the groundwater. The hypothesis is that the area with higher nitrate concentrations in the groundwater has properties more favorable for nitrification, which would be especially apparent in a lower carbon to nitrogen ratio. The pH and storage of nitrate, ammonium, total carbon, total nitrogen and exchangeable cations was analyzed in soil samples from both areas. In addition, a study of stand properties and previous use of the areas was made.</p><p>The analyses performed in this study indicate that the soil properties could not explain the differences in nitrate concentration in the groundwater. The differences found between the areas were that the area with lower nitrate concentrations in the groundwater had higher nitrate and ammonium concentrations and higher pH in the soil. The reason for this might be that the soil in this area has larger capacity to bind elements. The fact that the soil samples were sampled during different seasons probably had a major effect on these results. The history and stand properties of the two areas were similar. According to site index one area was more fertile, which benefits nitrification. This fact was not confirmed by the analyses, but it probably caused the nitrification rate to be higher in this area.</p> / <p>Det stora nedfallet av föroreningar i form av kväve i framförallt sydvästra Sverige leder till försurning och övergödning av både skogsmarker och vattendrag. Kvävedepositionen i södra Sverige kan uppgå till 20 kg N/ha och år. Det kväve som inte tas upp av vegetationen ackumuleras i marken som efterhand riskerar att bli kvävemättad vilket ökar risken för kväveutlakning. Kväveutlakningen från svenska skogsmarker har visat sig kunna vara i samma storleksordning som från jordbruksmarker som anses vara en av de största orsakerna till ökande kvävehalter i sjöar och vattendrag. Kväveutlakningens storlek beror till stor del på hur stor del av markens kväveförråd som finns i den oorganiska formen nitrat eftersom den är en lättrörlig jon. Efter skogsavverkning ökar nitratutlakningen betydligt på grund av att det finns väldigt lite vegetation kvar som tar upp kväveföreningarna.</p><p>I den här studien har markkemin i två avverkade granskogsområden i Halland undersökts. Tidigare studier i dessa två områden har visat att halterna av nitrat var högre i grundvattnet i det ena området än i det andra, och således var även nitratutlakningen större i detta område. Eftersom kvävedepositionen anses vara densamma i de två områdena har markemin undersökts för att finna skillnader där som kan förklara de olika nitratnivåerna i grundvattnet. Hypotesen var att det ena området skulle ha mer gynnsamma förhållanden för nitrifikation, framförallt en lägre C/N-kvot. Markens förråd av nitrat- och ammoniumkväve, totalkol, totalkväve, utbytbara katjoner samt pH undersöktes i båda områdena. En studie av områdenas historia gjordes även för att kunna utesluta skillnader där som kunde ge upphov till skillnaden i nitrat i grundvattnet.</p><p>Slutsatsen som kan dras från studien är att de analyserade egenskaperna inte visade på mer gynnsamma förhållanden för nitrifikation i det ena området än i det andra. Ingen skillnad i C/N-kvot uppmättes. Skillnaderna som hittades var att området med lägst halter av nitrat i grundvattnet hade högst halter av oorganiskt kväve i marken och högre pH. Att nitrathalterna var högre i grundvattnet men inte i marken kan ha sin förklaring i att marken i det ena området har större förmåga att binda till sig kväve vilket gör att det inte lika lätt kommer ut i grundvattnet. Antagligen spelade det stor roll för dessa resultat att jordproven tagits vid olika årstider. Undersökningen av tidigare användningsområde i skogarna visade att de hade en tämligen liknade historia. Det ena området har enligt ståndortsindex högre bördighet vilket gynnar nitrifikation. Detta framgick dock inte av analyserna men är antagligen orsaken till de högre nitrathalterna i grundvattnet i detta område.</p>

The objective of this study is to identify and examine potential mechanisms of radionuclide transport as vapor at a high-level radioactive waste repository located in unsaturated fractured rock. Transport mechanisms and processes have been investigated near the repository and at larger distances. Transport mechanisms potentially important at larger distances include ordinary diffusion, viscous flow and free convection. Ordinary diffusion includes self and binary diffusion, Knudsen flow and surface diffusion. Pressure flow and slip flow comprise viscous flow. Free convective flow results from a gas density contrast. Transport mechanisms or processes dominant near the repository include ordinary diffusion, viscous flow plus several mechanisms whose driving forces arise from the non-isothermal, radioactive nature of high-level waste. The additional mechanisms include forced diffusion, aerosol transport, thermal diffusion and thermophoresis. Near a repository vapor transport mechanisms and processes can provide a significant means of transport from a failed canister to the geologic medium from which other processes can transport radionuclides to the accessible environment. These issues are believed to be important factors that must be addressed in the assessment of specfic engineering designs and site selection of any proposed HLW repository.

Methodologies for estimating hydraulic and solute transport properties of unsaturated, fractured rock are developed. The methodologies are applied to networks of discrete fractures for the purpose of estimating steady fluid flow rates and breakthrough curves of entrained solutes. The formulations employ the boundary integral method to discretize the outer rim of each fracture and to solve a two dimensional flow equation within fracture planes. A three dimensional variant of the two dimensional boundary integral method is used to calculate flow through a permeable matrix with embedded permeable fractures. Exterior and interior surfaces are discretized using boundary elements to account for flow between fractures and the matrix, and between the matrix and fractures and the exterior boundaries. Synthetic fracture networks are created using planar fractures of finite areal extent embedded within a three dimensional rock matrix for the purpose of performing sensitivity studies of network hydraulic conductivity with respect to geometric parameters, such as fracture orientation and density. Results of the sensitivity studies show that: (1) The global hydraulic conductivity is linearly dependent on the product of fracture transmissivity and density for fractures of which fully penetrate the rock volume; (2) The effect of correlation between fracture length and transmissivity is to increase the global hydraulic conductivity; and (3) Results using a three dimensional coupled fracture— matrix flow regime compare favorably with analytic results. Flow through variably saturated fracture networks is modeled by assuming a constant capillary head within individual fractures. A free surface is found using an iterative procedure which locates nodal points at the intersection of constant total head and pressure head contours. The simulated free surface compares favorably with an approximate analytic solution and with laboratory results. Simulations indicate the presence of zones of water under both positive and negative pressure, as well as regions of air—filled voids. Travel times and breakthrough curves are determined by integrating the inverse velocity over a streamline, and then summing over all streamlines. For the fracture network examined, travel times decrease with decreasing fracture saturation. The effects of retardation and matrix diffusion are also examined.

This research involves the evaluation of municipal landfill leachates for specific hazardous compounds in an effort to qualitatively determine the potential for groundwater contamination. Leachate samples from five landfills were evaluated for thirteen EPA priority pollutants using gas chromatography. In addition, samples were analyzed for total organic carbon (TOC) and total organic halide (TOX). A solids analysis was performed on refuse excavated from one landfill. This analysis included organic halide determination of interstitial liquids, and a total halide determination for each solid sample. A solids/liquid partition coefficient was calculated from the results. The literature review includes a detailed section outlining the biological degradation of hazardous organic compounds in anaerobic environments similar to conditions found in landfills.

Samples of ordinary copper, hot-isotactically-pressed (HIP) copper, and simulated borosilicate high-level waste glass were leached at 25°C, 51°C, and 80°C in solutions simulating brine and silicate groundwaters. It was found that the amount of glass leached increased at higher temperatures, and more leaching occurred in brine than in silicate groundwater. This behavior is predicted by Le Chatelier's Principle. Similarly, more copper was dissolved at higher temperatures, and more was dissolved in brine than in silicate groundwaters.