L'Ingénierie Dirigée par les Modèles (IDM) est un domaine de recherche en pleine émergence qui considère les modèles comme des éléments de base. Chaque modèle est conforme à un autre modèle, appelé son méta-modèle, qui définit sa syntaxe abstraite et ses concepts. Dans un processus IDM, différents types de modèles sont manipulés par des transformations de modèles. Une transformation génère un modèle dans un langage cible à partir d'un modèle dans un langage source. Pour concevoir une transformation, les développeurs doivent avoir une bonne connaissance des méta-modèles concernés ainsi que des langages de transformation, ce qui rend cette tâche difficile. Dans cette thèse, nous proposons d'assister l'écriture des transformations et plus généralement de comprendre comment une transformation opère. Nous adhérons à l'approche de transformation de modèles par l'exemple qui propose de créer une transformation de modèles à partir d'exemples de transformation. Cela permet d'utiliser la syntaxe concrète définie pour les méta-modèles, et cela évite donc de requérir que les développeurs aient une bonne maîtrise des méta-modèles utilisés. Dans ce contexte, nous proposons deux contributions. La première consiste à définir une méthode pour générer des règles de transformation opérationnelles à partir d'exemples. Nous nous basons sur une approche qui utilise l'Analyse Relationnelle de Concepts (ARC) comme technique d'apprentissage pour obtenir des patrons de transformation à partir d'un appariement de type 1-1 entre les modèles. Nous développons une technique pour extraire des règles de transformation opérationnelles à partir de ces patrons. Ensuite, nous utilisons le langage et le moteur de règles JESS pour exécuter ces règles. Nous étudions aussi comment mieux apprendre des règles de transformations à partir d'exemples, en utilisant séparément chaque exemple ou en réunissant tous les exemples. La deuxième contribution consiste à récupérer les traces de transformation à partir d'exemples de transformation. Ces traces peuvent être utilisées par exemple pour localiser des erreurs durant l'exécution des programmes de transformation ou vérifier la couverture de tous les modèles d'entrée par une transformation. Dans notre contexte, nous supposons que ces traces vont servir pour un futur apprentissage des règles de transformation. Nous traitons tout d'abord le problème de récupération des traces avec des exemples provenant d'un programme de transformation. Nous proposons une approche basée sur une méta-heuristique multi-objectifs pour générer des traces sous forme d'appariement de type n-m entre des éléments de modèles. La fonction objectif s'appuie sur une similarité lexicale et structurelle entre ces éléments. Une extension de cette méthode est proposée pour traiter le problème plus général de l'appariement entre modèles. / Model Driven Engineering (MDE) considers models as first class artifacts. Each model conforms to another model, called its metamodel which defines its abstract syntax and its semantics.Various kinds of models are handled successively in an MDE development cycle. They are manipulated using, among others, programs called model transformations. A transformation takes as input a model in a source language and produces a model in a target language. The developers of a transformation must have a strong knowledge about the source and target metamodels which are involved and about the model transformation language. This makes the writing of the model transformation difficult.In this thesis, we address the problem of assisting the writing of a model transformation and more generally of understanding how a transformation operates.We adhere to the Model Transformation By example (MTBE) approach, which proposes to create a model transformation using examples of transformation. MTBE allows us to use the concrete syntaxes defined for the metamodels. Hence, the developers do not need in-depth knowledge about the metamodels. In this context, our thesis proposes two contributions.As a first contribution, we define a method to generate operational transformation rules from transformation examples. We extend a previous approach which uses Relational Concept Analysis as a learning technique for obtaining transformation patterns from 1-1 mapping between models. We develop a technique for extracting relevant transformation rules from these transformation patterns and we use JESS language and engine to make the rules executable. We also study how we better learn transformation rules from examples, using transformation examples separately or by gathering all the examples.The second contribution consists in recovering transformation traces from transformation examples. This trace recovery is useful for several purposes as locating bugs during the execution of transformation programs, or checking the coverage of all input models by a transformation. In our context, we expect also that this trace will provide data for a future model transformation learning technique. We first address the trace recovery problem with examples coming from a transformation program. We propose an approach, based on a multi-objective meta-heuristic, to generate the textit{many-to-many} mapping between model constructs which correspond to a trace. The fitness functions rely on the lexical and structure similarity between the constructs. We also refine the approach to apply it to the more general problem of model matching.

Molecular simulations have become an important tool within the last few decades to understand physical processes in the microscale and customize processes in the macroscale according to the understanding developed at the molecular level. We present results from molecular simulations we performed to study the adsorption of hazardous organics in nanoporous materials. Adsorption of water in silicalite, a hydrophobic material, and the effect of defects were investigated by Monte Carlo simulations. Silanol nests were found to have a big impact on the hydrophobicity of silicalite. Even the presence of one silanol nest per unit cell caused a significant amount of water adsorption. We also investigated the effect of four different cations, H+, Li+, Na+, and Cs+. Their presence in silicalite increased the amount of water adsorbed. Monte Carlo and molecular dynamics simulations of MTBE adsorption in silicalite, mordenite, and zeolite beta with different Na+ cation loadings were carried out. The results revealed the importance of the pore structure on the adsorption of MTBE. Although these three zeolites have similar pore volumes, zeolite beta, with its pore structure which is mostly accessible to MTBE molecules, is predicted to adsorb significantly more MTBE than silicalite and mordenite. The Na+ cation loading, up to four cations does not have a significant effect on the adsorption capacity of the zeolites studied here, however, for silicalite and zeolite beta increasing the Na+ content increases the amount adsorbed at very low pressures. A new force field was developed by Monte Carlo simulations for 1,4-Dioxane, an important industrial solvent which has emerged as a potentially significant threat to human health. The objective was to develop reliable atom-atom interaction parameters to use in the simulations of the adsorption of 1,4-Dioxane in different adsorbent materials. Predictions of critical point data, liquid and vapour densities, heats of vaporization with our new force field were in good agreement with experimental data and outperformed predictions from simulations with other force field parameters available in literature. To obtain the isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite Monte Carlo simulations were performed. First we optimized the interaction parameters between the atoms of silicalite and the atoms of MTBE and 1,4-Dioxane. Using these optimized parameters we simulated the adsorption of MTBE and 1,4-Dioxane from water in silicalite. Despite the agreement of simulated and experimental isotherms of pure components, simulated isotherms of MTBE and 1,4-Dioxane adsorption from water in silicalite did not yield satisfactory results. Monte Carlo simulations were performed to investigate the affinity between two hazardous materials, PFOA and 1,1-DCE; and four different zeolites. Binding energies and Henry's constants were computed. For both PFOA and 1,1-DCE zeolite-beta had the highest affinity. The affinity between activated carbon with polar surface groups and water, and 1,4-Dioxane were investigated to shed light on why activated carbon is ineffective to remove 1,4-Dioxane from water. Results showed that presence of polar surface groups increased the affinity between water and activated carbon, while the affinity between 1,4-Dioxane and activated carbon was not effected by the presence of polar surface groups.

O petróleo é a principal fonte de energia no mundo, mas alguns de seus derivados podem ser prejudiciais à natureza e à saúde. O BTEX, um derivado do petróleo, é usado em combustíveis, sendo estes a maior causa de contaminação ambiental, pois no transporte ou armazenamento destes ocorrem vazamentos que poluem solo e fontes de água. Como alternativas para diminuir a concentração do BTEX no combustível surgiram os aditivos oxigenados, os quais melhoram a qualidade do combustível e reduzem as emissões de monóxido de carbono. Os aditivos mais comuns são o MTBE e o etanol. No entanto, o MTBE é oncogênico e por isso, alguns países o substituem pelo etanol. Porém, o etanol aumenta a solubilidade do BTEX na água, a migração deste no solo, e diminui sua degradação natural. A degradação destes compostos é possível pela ação de microrganismos nativos. Em vista disto, no presente trabalho, bactérias foram isoladas de uma planta de tratamento de águas residuais da indústria petroquímica, com o objetivo de encontrar bactérias tolerantes com capacidade de degradação do BTEX. Os 30 isolados obtidos foram identificados como pertencentes aos gêneros Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomona, Lysinobacterium, Neisseria, Corynobacterium e Leucobacter. Quinze isolados foram tolerantes ao B, T, E, X, e destes, os isolados 16 e 25 pertencentes ao gênero Bacillus, foram testados para a degradação de BTEX, BTEX/MTBE, BTEX/Etanol. A maior porcentagem de degradação foi detectada no tratamento com BTEX seguido por BTEX/MTBE e BTEX/Etanol. O isolado 25 mostrou maior capacidade de degradação dos compostos. / Oil is the main source of energy in the world; nevertheless, some of its derivatives could be harmful to the environment and health. BTEX is a petroleum derivative. It is used in fuels; this one is the main cause of environmental pollution, because during the transport or storage of them there are leaks that pollute the soil and water sources. In order to reduce BTEX concentration in fuel, oxygenated additives emerged; these improve the quality of the fuel and reduce carbon monoxide emissions. The most common additives are MTBE and ethanol. Due to fact that MTBE is oncogenic, some countries replace it with ethanol. Ethanol increases the solubility of BTEX in water, its migration in the ground and decreases its natural degradation. The degradation of harmful compounds by action of native microorganisms has proven to be effective. With this purpose, in the current research, bacteria were isolated from a wastewater treatment plant of petrochemical industry, in order to find tolerant bacteria and with ability to degrade BTEX. The 30 isolates obtained were identified as belonging to the genus Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomonas, Lysinobacterium, Neisseria, Corynobacterium, and Leucobacter. Fifteen isolates were tolerant to B, T, E, X, and out them, isolates 16 and 25 belong to genus Bacillus were tested for degradation of BTEX BTEX / MTBE, BTEX / Ethanol. The highest percentage of degradation was found in the assay with BTEX followed by BTEX / MTBE and BTEX / Ethanol. Isolate 25 showed the highest capacity of degradation.

Afin d'obtenir le niveau requis d'indice d'octane et de limiter les rejets en monoxyde de carbone, les éthers carburants, principalement le méthyl tert-butyl éther (MTBE), sont incorporés dans les essences. A la suite de fuites, le MTBE est apparu comme un polluant majeur des nappes aquifères en raison de sa très faible biodégradabilité. L'objectif de ce travail a été d'étudier la dégradation du MTBE par Mycobacterium austroafricanum IFP 2012. La voie métabolique a été partiellement élucidée par l'identification de plusieurs intermédiaires (tert-butyl formiate (TBF), tert-butyl alcool (TBA), acide -hydroxyisobutyrique et acétone) et activités enzymatiques (MTBE/TBA mono-oxygénase non-hémique et inductible, TBF estérase, 2-propanol : NDMA oxydoréductase et une mono-oxygénase impliquée dans la dégradation de l'acétone). Le rôle du TBF et la nécessité de cobalt ont été proposés pour expliquer la faible biodégradation du MTBE ; le rôle de la liaison méthoxy semblant limité.

O petróleo é a principal fonte de energia no mundo, mas alguns de seus derivados podem ser prejudiciais à natureza e à saúde. O BTEX, um derivado do petróleo, é usado em combustíveis, sendo estes a maior causa de contaminação ambiental, pois no transporte ou armazenamento destes ocorrem vazamentos que poluem solo e fontes de água. Como alternativas para diminuir a concentração do BTEX no combustível surgiram os aditivos oxigenados, os quais melhoram a qualidade do combustível e reduzem as emissões de monóxido de carbono. Os aditivos mais comuns são o MTBE e o etanol. No entanto, o MTBE é oncogênico e por isso, alguns países o substituem pelo etanol. Porém, o etanol aumenta a solubilidade do BTEX na água, a migração deste no solo, e diminui sua degradação natural. A degradação destes compostos é possível pela ação de microrganismos nativos. Em vista disto, no presente trabalho, bactérias foram isoladas de uma planta de tratamento de águas residuais da indústria petroquímica, com o objetivo de encontrar bactérias tolerantes com capacidade de degradação do BTEX. Os 30 isolados obtidos foram identificados como pertencentes aos gêneros Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomona, Lysinobacterium, Neisseria, Corynobacterium e Leucobacter. Quinze isolados foram tolerantes ao B, T, E, X, e destes, os isolados 16 e 25 pertencentes ao gênero Bacillus, foram testados para a degradação de BTEX, BTEX/MTBE, BTEX/Etanol. A maior porcentagem de degradação foi detectada no tratamento com BTEX seguido por BTEX/MTBE e BTEX/Etanol. O isolado 25 mostrou maior capacidade de degradação dos compostos. / Oil is the main source of energy in the world; nevertheless, some of its derivatives could be harmful to the environment and health. BTEX is a petroleum derivative. It is used in fuels; this one is the main cause of environmental pollution, because during the transport or storage of them there are leaks that pollute the soil and water sources. In order to reduce BTEX concentration in fuel, oxygenated additives emerged; these improve the quality of the fuel and reduce carbon monoxide emissions. The most common additives are MTBE and ethanol. Due to fact that MTBE is oncogenic, some countries replace it with ethanol. Ethanol increases the solubility of BTEX in water, its migration in the ground and decreases its natural degradation. The degradation of harmful compounds by action of native microorganisms has proven to be effective. With this purpose, in the current research, bacteria were isolated from a wastewater treatment plant of petrochemical industry, in order to find tolerant bacteria and with ability to degrade BTEX. The 30 isolates obtained were identified as belonging to the genus Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomonas, Lysinobacterium, Neisseria, Corynobacterium, and Leucobacter. Fifteen isolates were tolerant to B, T, E, X, and out them, isolates 16 and 25 belong to genus Bacillus were tested for degradation of BTEX BTEX / MTBE, BTEX / Ethanol. The highest percentage of degradation was found in the assay with BTEX followed by BTEX / MTBE and BTEX / Ethanol. Isolate 25 showed the highest capacity of degradation.

O petróleo é a principal fonte de energia no mundo, mas alguns de seus derivados podem ser prejudiciais à natureza e à saúde. O BTEX, um derivado do petróleo, é usado em combustíveis, sendo estes a maior causa de contaminação ambiental, pois no transporte ou armazenamento destes ocorrem vazamentos que poluem solo e fontes de água. Como alternativas para diminuir a concentração do BTEX no combustível surgiram os aditivos oxigenados, os quais melhoram a qualidade do combustível e reduzem as emissões de monóxido de carbono. Os aditivos mais comuns são o MTBE e o etanol. No entanto, o MTBE é oncogênico e por isso, alguns países o substituem pelo etanol. Porém, o etanol aumenta a solubilidade do BTEX na água, a migração deste no solo, e diminui sua degradação natural. A degradação destes compostos é possível pela ação de microrganismos nativos. Em vista disto, no presente trabalho, bactérias foram isoladas de uma planta de tratamento de águas residuais da indústria petroquímica, com o objetivo de encontrar bactérias tolerantes com capacidade de degradação do BTEX. Os 30 isolados obtidos foram identificados como pertencentes aos gêneros Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomona, Lysinobacterium, Neisseria, Corynobacterium e Leucobacter. Quinze isolados foram tolerantes ao B, T, E, X, e destes, os isolados 16 e 25 pertencentes ao gênero Bacillus, foram testados para a degradação de BTEX, BTEX/MTBE, BTEX/Etanol. A maior porcentagem de degradação foi detectada no tratamento com BTEX seguido por BTEX/MTBE e BTEX/Etanol. O isolado 25 mostrou maior capacidade de degradação dos compostos. / Oil is the main source of energy in the world; nevertheless, some of its derivatives could be harmful to the environment and health. BTEX is a petroleum derivative. It is used in fuels; this one is the main cause of environmental pollution, because during the transport or storage of them there are leaks that pollute the soil and water sources. In order to reduce BTEX concentration in fuel, oxygenated additives emerged; these improve the quality of the fuel and reduce carbon monoxide emissions. The most common additives are MTBE and ethanol. Due to fact that MTBE is oncogenic, some countries replace it with ethanol. Ethanol increases the solubility of BTEX in water, its migration in the ground and decreases its natural degradation. The degradation of harmful compounds by action of native microorganisms has proven to be effective. With this purpose, in the current research, bacteria were isolated from a wastewater treatment plant of petrochemical industry, in order to find tolerant bacteria and with ability to degrade BTEX. The 30 isolates obtained were identified as belonging to the genus Bacillus, Enterococcus, Staphylococcus, Streptococcus, Pseudomonas, Lysinobacterium, Neisseria, Corynobacterium, and Leucobacter. Fifteen isolates were tolerant to B, T, E, X, and out them, isolates 16 and 25 belong to genus Bacillus were tested for degradation of BTEX BTEX / MTBE, BTEX / Ethanol. The highest percentage of degradation was found in the assay with BTEX followed by BTEX / MTBE and BTEX / Ethanol. Isolate 25 showed the highest capacity of degradation.

The switch to unleaded fuels in the 1970s and the high air pollution in areas of high population density due to traffic particularly since the 1990s required the use of alternative fuel additives to achieve an improvement of the combustion. The utilization of oxygenated hydrocarbons as antiknock additives and so-called oxygenates provided a more complete and efficient combustion with simultaneously less harmful and polluting emissions. These include the synthetic ethers methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), tert-amyl methyl ether (TAME) and tert-amyl ethyl ether (TAEE). MTBE has a particular position as within some years it became the dominant oxygenate worldwide. Since then, over 100.000 leakages, most often in close proximity to gas stations, resulted in just as many oxygenate-contaminated sites of soil and groundwater within few years. The high water solubility of these ethers leads to an especially fast and extensive spread of the contamination plumes. Ether-contaminated groundwater has a turpentine-like taste that is noticed already in really low concentrations. Thus, such water can no longer serve as drinking water and requires a counter-measure. The chemical parameters of oxygenates decrease the efficiency of otherwise successfully applied techniques such as adsorption or aeration. In addition the ethers proved recalcitrant against microbial attack. The search for microorganisms that could degrade these synthetic oxygenates indeed resulted in the enrichment of many isolates. The majority of these isolates oxidize the ethers in a cometabolic manner either partially or completely to CO2. However, only few cultures are capable of independent growth on these oxygenates. These include the beta-proteobacteria Methylibium petroleiphilum PM1 and Aquincola tertiaricarbonis L108, of which the latter is of particular interest for the present work. Strain L108 is characterized by good growth on MTBE and is presently the only known isolate which is able to mineralize ETBE, TAME and TAEE at similar rates. This work examined the seemingly particularly well adapted oxygenate ether metabolism of strain L108, that was formerly isolated from an aquifer highly contaminated with MTBE. Via diverse deletion studies key enzymes of the degradative metabolism and their genetic background were clearly identified. Hence, the results of this work contribute to verify so far just hypothesized metabolic steps by detailed enzymatic and genetic studies. Based on detected metabolites, first studies on MTBE biodegradation already postulated an oxidative pathway via TBA, 2-methyl-1,2-propane-diol (MPD) and 2-HIBA. In case of a monoxygenatic hydroxylation of the methoxy group of MTBE a hemiacetale results as reaction product, from which the tertiary alcohol TBA can be formed easily in subsequent reactions. By comparing wild type strain L108 with the spontaneous mutant strain L10, we were now able to clearly show that the cytochrome P-450 monoxygenase system EthABCD accounts solely for this MTBE-oxidizing activity. It is also the only enzyme catalyzing the corresponding hydroxylation of ETBE, TAME and TAEE. In strain L108 this enzyme complex is expressed constitutively. TBA, which is also generated from hydroxylation of ETBE, is, as postulated and verified by this study, degraded by a different monoxygenase resulting in MPD. Via Tn5-mediated mutations this enzyme was confirmed as Rieske non-heme mononuclear iron monooxygenase MdpJ. MPD is further altered to the corresponding branched acid 2-HIBA, presumably by two dehydrogenation reactions. For the degradation of 2-HIBA, diverse hypotheses exist on the basis of known enzymatic reactions. Another Tn5 mutation now gave evidence, that in the mentioned beta-proteobacteria the novel mutase HcmAB linearizes 2-HIBA to 3-hydroxybutyric acid (3-HB) dependent on cobalamin and coenzyme A (CoA). Sequence comparison revealed, that strain L108 acquired all three key enzyme complexes, EthABCD, MdpJ and HcmAB via horizontal gene transfer (HGT). For TAME and TAEE a completely new degradation pathway was found. In strain L108, the resulting degradation product tert-amyl alcohol (TAA) of these ethers is, like TBA, also specifically oxidized by MdpJ. In Tn5-deletion studies and metabolite analyzes, however, no hydroxylation could be detected. Instead, TAA is rather desaturated. Therefore within the metabolism no diols or acids analogue to MPD or 2-HIBA were formed. Instead, via MdpJ TAA is initially degraded to the unsaturated tertiary alcohol and hemiterpene 2-methyl-3-butene-2-ol. Prenol (3-methyl-2-buten-2-ol), prenal (3-methyl-2-buten-2-al) and 3-methyl crotonic acid were detected as additional metabolites. Hence, an isomerization of the branched acid by HcmAB is apparently irrelevant in TAA biodegradation. Accordingly it could be shown, that deletion mutants for HcmAB indeed could not grow on TBA, but are still able to grow on TAA, just as fast as the wild type, in fact. The tertiary alcohol 2-methyl-3-butene-2-ol is presumably transformed via another isomerase resulting in the primary alcohol prenol. Prenol is further oxidized by postulated dehydrogenases to 3-methyl crotonic acid. This would also be in correlation to the already observed degradation pathway of the monoterpene linalool in other bacteria. However, the responsible enzymes in strain L108 are not yet identified. Besides this principal gain of knowledge in the degradation of xenobiotic ether structures and the evolution of degradative microorganism, the now confirmed key enzymes EthB, MdpJ and HcmAB, respectively their coding genes, can be used as specific markers to monitor natural degradation processes in in situ studies. On this basis, the presence of active microorganisms and additionally - derived from the confirmed single key enzymes - a potentially complete degradation can be concluded. In the long run, it might be possible to stimulate the natural microbiological activity, e.g. via bioaugmentation with degradation specialists. Furthermore, regarding the potential progress of remediation procedures, potentially limiting steps can be distinguished via respective markers and narrowed down as possible cause of deficient degradation activity. However, such function-based monitoring requires specific verification. Therefore, subsequent studies have to analyze, if there is a sequence diversity among these three key enzymes. Previous sequence comparisons hypothesize that up to 60% accordance in the protein sequence in homologues of MdpJ and HcmA they can still be assumed to possess the same enzymatic function. This diversity has to be considered in the development of specific probes. / Die Einführung bleifreien Benzins in den 1970er-Jahren und die hohe Emissionsbelastung von Ballungszentren durch den Straßenverkehr insbesondere seit den 1990er-Jahren erforderte den Einsatz alternativer Benzinadditive, um eine Verbesserung der Verbrennung zu erreichen. Die Nutzung sauerstoffhaltiger Kohlenwasserstoffe als Antiklopfmittel und als sogenannte Oxygenate bot sich an, da diese eine effizientere Verbrennung mit gleichzeitig niedrigeren gesundheits- und umweltschädigenden Emissionen fördern. Zu den Oxygenaten gehören die synthetischen Ether Methyl-tert-butylether (MTBE), Ethyl-tert-butylether (ETBE), tert-Amylmethylether (TAME) und tert-Amylethylether (TAEE). Eine herausragende Stellung nimmt MTBE ein. Innerhalb weniger Jahre wurde es zum hauptsächlich verwendeten Oxygenat weltweit. Seitdem führten jedoch über 100.000 Leckagen, zumeist in Tankstellennähe, innerhalb weniger Jahre zu ebenso zahlreichen Kontaminationen des Grundwassers mit Oxygenaten. Aufgrund der hohen Wasserlöslichkeit kommt es dabei zu einer besonders schnellen und großflächigen Ausbreitung der Ether. Derart belastetes Grundwasser weist schon bei geringsten Etherkonzentrationen einen als terpentinartig wahrgenommenen Geruch und Geschmack auf und kann daher nicht mehr als Trinkwasserzufuhr genutzt werden. Es bedarf einer Lösung dieses Problems. Die chemischen Parameter der Ether senken allerdings die Effizienz anderweitig erfolgreich genutzter technischer Sanierungsverfahren auf Basis von z. B. Adsorption oder Aerisierung. Auch gegenüber mikrobiellen Abbau erweisen sie sich als rekalzitrant. Die Suche nach oxygenatabbauenden Mikroorganismen führte zwar zur Anreicherung vieler Isolate, welche die Oxygenate cometabolisch partiell oder sogar komplett oxidieren, nur sehr wenige Kulturen sind aber zu autarkem Wachstum auf diesen Ethern fähig. Dazu gehören die Beta-Proteobacteria Methylibium petroleiphilum PM1 und der dieser Arbeit zugrunde liegende Aquincola tertiaricarbonis L108. Der Stamm L108 zeichnet sich durch ein vergleichsweise gutes Wachstum auf MTBE aus und ist als bisher einzig bekanntes Isolat in der Lage, auch ETBE, TAME und TAEE ähnlich schnell zu mineralisieren. Die vorliegende Arbeit handelt von dem scheinbar besonders gut an den Oxygenatabbau adaptierten Stoffwechsel des ursprünglich aus MTBE-kontaminiertem Grundwasser angereicherten Stammes L108. Durch verschiedene Deletionsstudien wurden Schlüsselenzyme des Abbaus und deren genetischer Hintergrund eindeutig identifiziert. Die Ergebnisse der genetischen, enzymatischen und physiologischen Studien des Wildtyps im Vergleich zu den erzeugten Deletionsstämmen tragen dazu bei, bisher nur postulierte Reaktionsschritte zu verifizieren. Schon seit den ersten Studien zum MTBE-Abbau wird anhand markanter Metabolite ein oxidativer Abbau via TBA, 2-Methyl-1,2-propandiol (MPD) und 2-Hydroxyisobuttersäure (2-HIBA) vermutet. Im Fall einer Hydroxylierung der Methoxygruppe von MTBE wird ein Hemiacetal als Reaktionsprodukt erzeugt, aus dem nachfolgend leicht der tertiäre Alkohol TBA entstehen kann. Durch den Vergleich des Wildtyps mit der Spontanmutante Stamm L10 konnte jetzt gezeigt werden, dass hierfür allein das Cytochrom-P450-Monooxygenasesystem EthABCD verantwortlich ist. Dieses katalysiert auch exklusiv die entsprechende Hydroxylierung von ETBE, TAME und TAEE. In Stamm L108 wird das Enzym konstitutiv exprimiert. TBA, das auch aus der Hydroxylierung von ETBE resultiert, wird, wie postuliert und in dieser Arbeit verifiziert, durch eine weitere Monooxygenase zu MPD abgebaut. Durch eine Tn5-Transposon-vermittelte Mutation konnte verifiziert werden, dass es sich bei diesem Enzym um die Rieske-nicht-Häm-Monooxygenase MdpJ handelt. MPD wird im weiteren Verlauf voraussichtlich durch zwei Dehydrogenierungen zur korrespondierenden, verzweigten Säure 2-HIBA gewandelt. Zum 2-HIBA-Abbau gibt es, basierend auf bekannten Enzymreaktionen, diverse Hypothesen. Anhand einer weiteren Tn5-Mutation konnte jetzt bestätigt werden, dass in den genannten beta-Proteobacteria die neuartige Mutase HcmAB wirksam ist, welche 2-HIBA abhängig von Cobalamin und Coenzym A (CoA) zu 3-Hydroxybuttersäure (3-HB) linearisiert. Sequenzvergleiche ergaben, dass Stamm L108 die Schlüsselenzyme des Etherabbaus, EthABCD, MdpJ und HcmAB, durch horizontalen Gentransfer erworben hat. Für TAME und TAEE wurde ein völlig neuer Abbauweg gefunden. In Stamm L108 wird der beim Abbau dieser Ether entstehende tert-Amylalkohol (TAA) wie TBA ebenfalls exklusiv durch MdpJ oxidiert. Durch die Tn5-Deletionsstudien und durch Analyse der Metabolite konnte allerdings keine Hydroxylierung nachgewiesen werden. TAA wird durch MdpJ vielmehr desaturiert. Somit entstehen im Abbauweg keine zu MPD und 2-HIBA analogen Diole und Säuren, sondern TAA wird zunächst durch MdpJ zu einem ungesättigten tertiären Alkohol, dem Hemiterpen 2-Methyl-3-buten-2-ol, abgebaut. Prenol (3-Methyl-2-buten-2-ol), Prenal (3-Methyl-2-buten-2-al) und 3-Methylcrotonsäure wurden als weitere Metabolite des TAA-Stoffwechsels detektiert. Somit spielt eine Isomerisierung einer tertiär verzweigten Säure durch HcmAB im TAA-Abbauweg offensichtlich keine Rolle. Entsprechend konnte gezeigt werden, dass Deletionsmutanten für hcmAB zwar nicht mehr auf TBA, aber immer noch auf TAA wachsen können, und das genauso schnell, wie der Wildtyp. Der tertiäre Alkohol 2-Methyl-3-buten-2-ol wird wahrscheinlich durch eine andere Isomerase zum primären Alkohol Prenol umgewandelt und dieser dann durch Dehydrogenasen zur Methylcrotonsäure oxidiert. Dies würde dem bereits in anderen Bakterien beobachteten Abbauweg des Monoterpens Linalool entsprechen. Die in Stamm L108 dafür verantwortlichen Enzyme wurden aber noch nicht identifiziert. Neben diesem grundsätzlichen Erkenntnisgewinn zum Abbau der xenobiotischen Etherverbindungen und der Evolution degradativer Mikroorganismen, können die hier bestätigten Schlüssel-enzyme EthABCD, MdpJ und HcmAB bzw. deren codierende Gene als spezifische Marker zum Monitoring natürlicher Abbauprozesse für in-situ-Untersuchungen genutzt werden. Auf dieser Basis kann auf die Anwesenheit aktiver Mikroorganismen und zudem noch - abgeleitet aus der Präsenz der einzelnen Schlüsselenzyme - auf einen potenziell kompletten Abbau geschlossen werden. Darauf aufbauend kann die natürliche mikrobiologische Aktivität durch nachfolgende biotechnologische Maßnahmen stimuliert werden, zum Beispiel durch eine Bioaugmentation mit Abbauspezialisten. Des weiteren können mögliche limitierende Schritte hinsichtlich des potenziellen Verlaufs der Sanierungsmaßnahme über Präsenztiter der betreffenden Marker gezielter verfolgt und als etwaige Ursachen defizitärer Abbauleistungen eingegrenzt werden. Voraussetzung für dieses funktionsbasierte Monitoring ist allerdings der spezifische Nachweis. Somit sollte in nachfolgenden Studien analysiert werden, ob es bei den drei Schlüsselenzymen eine Sequenzdiversität gibt. Die bisherigen Sequenzvergleiche lassen zumindest vermuten, dass bis etwa 60% Übereinstimmung der Proteinsequenzen bei Homologen von MdpJ und HcmA noch mit der gleichen Enzymfunktion zu rechnen ist. Diese Diversität sollte bei der Entwicklung von spezifischen Sonden berücksichtigt werden.

L’éthyl tert-butyl éther (ETBE) et le méthyl tert-butyl éther (MTBE) sont des éthers carburants utilisés comme additifs dans les essences sans plomb. Du fait de leur utilisation massive, de nombreux cas de pollutions d’aquifères ont été répertoriés, en particulier pour le MTBE, et ces composés représentent donc un risque sanitaire potentiel. Des travaux récents ont permis de mettre en évidence différents micro-organismes capables de dégrader ces composés malgré leur faible biodégradabilité dans l'environnement. Néanmoins, une meilleure compréhension de l'écologie et de la régulation de ces capacités de dégradation permettrait une meilleure gestion de la bioremédiation de sites contaminés par l'ETBE ou le MTBE.L’objectif de la thèse, réalisée dans le cadre d'un projet ANR Blanc (MiOxyFun), est de mieux comprendre l'écologie des communautés microbiennes impliquées dans la dégradation de ces éthers et leur relation avec la régulation ainsi qu'avec les cinétiques de dégradation de ces composés par des membres spécifiques de ces communautés. Ainsi, à partir de différents échantillons environnementaux venant de sites pollués par l'ETBE ou le MTBE, des enrichissements ont pu être réalisés en laboratoire afin d'étudier leurs microflores. Ces enrichissements ont été étudiés notamment pour leurs cinétiques de dégradation, la composition de leurs communautés bactériennes, et pour l'isolement de souches bactériennes directement impliquées dans la dégradation de ces composés. L'étude des cinétiques de dégradation de l'ETBE ou du MTBE par différents enrichissements obtenus sur ETBE (cinq) et sur MTBE (six) a permis de montrer des profils de dégradation très différents. La dégradation était généralement lente et s'accompagnait d'un faible rendement en biomasse avec parfois accumulation transitoire de tert-butanol (TBA). Les capacités de dégradation d'autres composés des essences (BTEXs et n-alcanes) étaient aussi différentes d'un enrichissement à l'autre, le benzène, entre autres, étant dégradé par 10/11 enrichissements. Des techniques d'empreinte moléculaire (RISA, DGGE) ont permis de constater que les communautés bactériennes présentes dans les cinq enrichissements sur ETBE étaient différentes de celles sur les enrichissements sur MTBE. Les enrichissements sur ETBE ont fait spécifiquement l'objet d'une étude par analyse de banques de clones réalisées à partir des gènes codant l'ARNr 16S de ces enrichissements. Cette étude a montré la prédominance des Proteobacteria dans trois enrichissements, la prédominance des Acidobacteria dans un autre ainsi qu'une composition plus héterogène dans le cinquième. De plus, des Actinobacteria ont été détectées dans les 5 enrichissements.En parallèle, plusieurs souches possédant des capacités de dégradation ont été isolées des enrichissements: Rhodococcus sp. IFP 2040, IFP 2041, IFP 2042, IFP 2043 (dégradant l'ETBE jusqu'au TBA), une Betaproteobacteria IFP 2047 (dégradant l'ETBE), Bradyrhizobium sp. IFP 2049 (dégradant le TBA), Pseudonocardia sp. IFP 2050 (dégradant l'ETBE et le MTBE), Pseudoxanthomonas sp. IFP 2051 et une Proteobacteria IFP 2052 (dégradant le MTBE). Une étude par qPCR sur les gènes codant l'ARNr 16S a montré la prédominance de certaines souches isolées dans les enrichissements ETBE. Enfin, plusieurs gènes connus comme étant impliqués dans la dégradation des éthers carburants ont pu être mis en évidence dans les enrichissements et dans certaines des souches isolées. / ETBE and MTBE are fuel oxygenates added to unleaded gasoline to improve combustion. Due to their extensive use, numerous aquifers have been contaminated, particularly by MTBE. The use of ETBE and MTBE is considered to represent an environmental risk. Recent research has uncovered a range of microorganisms capable of degrading these compounds, even though their environmental half-lives are long. Improved understanding of the ecology and regulation of this degradative ability could improve the management of the ETBE and MTBE contaminated site remediation. The aim of this work, taking place in the framework of the ANR project MiOxyFun was to investigate the ecology of ETBE- and MTBE-degrading microbial communities and their relationship to the regulation and kinetics of ETBE- and MTBE-degradation by specific members of these communities. Several ETBE- and MTBE-degrading microbial communities were enriched in the laboratory from environmental samples from contaminated sites throughout the world. These enrichments were examined for their degradation kinetics, microbial community structure, and used to isolate specific community members actively degrading ETBE and/or MTBE. The ETBE or MTBE biodegradation kinetics of the five ETBE- and six MTBE- degrading enrichments demonstrated a diversity of biodegradation rates. Overall, biodegradation was generally slow and associated to a low biomass yield. Tert-butanol (TBA) was transiently produced in several cases. Biodegradation of other gasoline compounds (BTEXs and n-alkanes) was tested and varied among the enrichments studied. Benzene, however, was degraded in 10 out of the 11 enrichments. DNA fingerprinting techniques (RISA, DGGE) showed that the microflora present in the five ETBE enrichments were different from those of the MTBE enrichments. The ETBE enrichments were studied further by sequencing the 16S rRNA genes extracted, amplified and cloned from these enrichments. Proteobacteria dominated three of the ETBE enrichments, Acidobacteria in another one, and a more heterogeneous composition was found in the fifth ETBE enrichment. Actinobacteria were detected in all five enrichments. Several strains with ETBE or MTBE degradation capacities were isolated: Rhodococcus sp. IFP 2040, IFP 2041, IFP 2042, IFP 2043 (degrading ETBE to TBA),a Betaproteobacteria IFP 2047 (degrading ETBE), Bradyrhizobium sp. IFP 2047 (degrading TBA), Pseudonocardia sp. IFP 2050 (degrading ETBE and MTBE), Pseudoxanthomonas sp. IFP 2051 and a Proteobacteria IFP 2052 (degrading MTBE). Quantification of the 16S rRNA gene confirmed the relatively high number of these isolates in some of the ETBE enrichments. Several genes involved in ETBE and/or MTBE biodegradation were detected in some of the enrichments and in some of the isolated strains.

The switch to unleaded fuels in the 1970s and the high air pollution in areas of high population density due to traffic particularly since the 1990s required the use of alternative fuel additives to achieve an improvement of the combustion. The utilization of oxygenated hydrocarbons as antiknock additives and so-called oxygenates provided a more complete and efficient combustion with simultaneously less harmful and polluting emissions. These include the synthetic ethers methyl tert-butyl ether (MTBE), ethyl tert-butyl ether (ETBE), tert-amyl methyl ether (TAME) and tert-amyl ethyl ether (TAEE). MTBE has a particular position as within some years it became the dominant oxygenate worldwide. Since then, over 100.000 leakages, most often in close proximity to gas stations, resulted in just as many oxygenate-contaminated sites of soil and groundwater within few years. The high water solubility of these ethers leads to an especially fast and extensive spread of the contamination plumes. Ether-contaminated groundwater has a turpentine-like taste that is noticed already in really low concentrations. Thus, such water can no longer serve as drinking water and requires a counter-measure. The chemical parameters of oxygenates decrease the efficiency of otherwise successfully applied techniques such as adsorption or aeration. In addition the ethers proved recalcitrant against microbial attack. The search for microorganisms that could degrade these synthetic oxygenates indeed resulted in the enrichment of many isolates. The majority of these isolates oxidize the ethers in a cometabolic manner either partially or completely to CO2. However, only few cultures are capable of independent growth on these oxygenates. These include the beta-proteobacteria Methylibium petroleiphilum PM1 and Aquincola tertiaricarbonis L108, of which the latter is of particular interest for the present work. Strain L108 is characterized by good growth on MTBE and is presently the only known isolate which is able to mineralize ETBE, TAME and TAEE at similar rates. This work examined the seemingly particularly well adapted oxygenate ether metabolism of strain L108, that was formerly isolated from an aquifer highly contaminated with MTBE. Via diverse deletion studies key enzymes of the degradative metabolism and their genetic background were clearly identified. Hence, the results of this work contribute to verify so far just hypothesized metabolic steps by detailed enzymatic and genetic studies. Based on detected metabolites, first studies on MTBE biodegradation already postulated an oxidative pathway via TBA, 2-methyl-1,2-propane-diol (MPD) and 2-HIBA. In case of a monoxygenatic hydroxylation of the methoxy group of MTBE a hemiacetale results as reaction product, from which the tertiary alcohol TBA can be formed easily in subsequent reactions. By comparing wild type strain L108 with the spontaneous mutant strain L10, we were now able to clearly show that the cytochrome P-450 monoxygenase system EthABCD accounts solely for this MTBE-oxidizing activity. It is also the only enzyme catalyzing the corresponding hydroxylation of ETBE, TAME and TAEE. In strain L108 this enzyme complex is expressed constitutively. TBA, which is also generated from hydroxylation of ETBE, is, as postulated and verified by this study, degraded by a different monoxygenase resulting in MPD. Via Tn5-mediated mutations this enzyme was confirmed as Rieske non-heme mononuclear iron monooxygenase MdpJ. MPD is further altered to the corresponding branched acid 2-HIBA, presumably by two dehydrogenation reactions. For the degradation of 2-HIBA, diverse hypotheses exist on the basis of known enzymatic reactions. Another Tn5 mutation now gave evidence, that in the mentioned beta-proteobacteria the novel mutase HcmAB linearizes 2-HIBA to 3-hydroxybutyric acid (3-HB) dependent on cobalamin and coenzyme A (CoA). Sequence comparison revealed, that strain L108 acquired all three key enzyme complexes, EthABCD, MdpJ and HcmAB via horizontal gene transfer (HGT). For TAME and TAEE a completely new degradation pathway was found. In strain L108, the resulting degradation product tert-amyl alcohol (TAA) of these ethers is, like TBA, also specifically oxidized by MdpJ. In Tn5-deletion studies and metabolite analyzes, however, no hydroxylation could be detected. Instead, TAA is rather desaturated. Therefore within the metabolism no diols or acids analogue to MPD or 2-HIBA were formed. Instead, via MdpJ TAA is initially degraded to the unsaturated tertiary alcohol and hemiterpene 2-methyl-3-butene-2-ol. Prenol (3-methyl-2-buten-2-ol), prenal (3-methyl-2-buten-2-al) and 3-methyl crotonic acid were detected as additional metabolites. Hence, an isomerization of the branched acid by HcmAB is apparently irrelevant in TAA biodegradation. Accordingly it could be shown, that deletion mutants for HcmAB indeed could not grow on TBA, but are still able to grow on TAA, just as fast as the wild type, in fact. The tertiary alcohol 2-methyl-3-butene-2-ol is presumably transformed via another isomerase resulting in the primary alcohol prenol. Prenol is further oxidized by postulated dehydrogenases to 3-methyl crotonic acid. This would also be in correlation to the already observed degradation pathway of the monoterpene linalool in other bacteria. However, the responsible enzymes in strain L108 are not yet identified. Besides this principal gain of knowledge in the degradation of xenobiotic ether structures and the evolution of degradative microorganism, the now confirmed key enzymes EthB, MdpJ and HcmAB, respectively their coding genes, can be used as specific markers to monitor natural degradation processes in in situ studies. On this basis, the presence of active microorganisms and additionally - derived from the confirmed single key enzymes - a potentially complete degradation can be concluded. In the long run, it might be possible to stimulate the natural microbiological activity, e.g. via bioaugmentation with degradation specialists. Furthermore, regarding the potential progress of remediation procedures, potentially limiting steps can be distinguished via respective markers and narrowed down as possible cause of deficient degradation activity. However, such function-based monitoring requires specific verification. Therefore, subsequent studies have to analyze, if there is a sequence diversity among these three key enzymes. Previous sequence comparisons hypothesize that up to 60% accordance in the protein sequence in homologues of MdpJ and HcmA they can still be assumed to possess the same enzymatic function. This diversity has to be considered in the development of specific probes.:Bibliographische Darstellung Eidesstattliche Erklärung Danksagung Abstract Kurzfassung Abkürzungsverzeichnis 1. Einleitung 1.1. Tertiäre Ether als Benzin-Oxygenate - Hintergrund und Umweltproblematik 1.2. Mikrobiologischer Abbau tertiärer Ether 1.3. Postulierter Abbauweg 1.4. Monitoring-Tools für biologischen Abbau 1.5. Ziel dieser Arbeit 1.6. Referenzen der Einleitung 2. Die initiale Etherspaltung des Stammes L108 2.1. Die Ethermonooxygenase EthB 2.2. Supplemental Material 3. Die spezifische Alkoholmonooxygenase MdpJ 3.1. Die Alkoholmonooxygenase MdpJ als Hydroxylase und Reduktase 3.2. Supplemental Material 4. Die 2-HIBA-Mutase HcmAB des Stammes L108 4.1. Die 2-HIBA-Mutase HcmAB 4.2. Supplemental Material 5. Der TAA-Abbau des Stammes L108 5.1. Der TAA-Abbau des Stammes L108 5.2. Supplemental Material 6. Diskussion 6.1. Nachweis der Schlüsselenzyme in Stamm L108 durch Mutation 6.2. Nutzen für den Nachweis natürlichen Abbaus 6.3. Der TAA-Metabolismus als neuartiger Abbauweg 6.4. Mikrobiologische Anpassung an Xenobiotika am Beispiel MTBE 6.5. Ausblick 6.6. Referenzen der Diskussion Anhang Curriculum Vitae Publikationsverzeichnis Tagungsbeiträge Nachweis über Anteile der Co-Autoren / Die Einführung bleifreien Benzins in den 1970er-Jahren und die hohe Emissionsbelastung von Ballungszentren durch den Straßenverkehr insbesondere seit den 1990er-Jahren erforderte den Einsatz alternativer Benzinadditive, um eine Verbesserung der Verbrennung zu erreichen. Die Nutzung sauerstoffhaltiger Kohlenwasserstoffe als Antiklopfmittel und als sogenannte Oxygenate bot sich an, da diese eine effizientere Verbrennung mit gleichzeitig niedrigeren gesundheits- und umweltschädigenden Emissionen fördern. Zu den Oxygenaten gehören die synthetischen Ether Methyl-tert-butylether (MTBE), Ethyl-tert-butylether (ETBE), tert-Amylmethylether (TAME) und tert-Amylethylether (TAEE). Eine herausragende Stellung nimmt MTBE ein. Innerhalb weniger Jahre wurde es zum hauptsächlich verwendeten Oxygenat weltweit. Seitdem führten jedoch über 100.000 Leckagen, zumeist in Tankstellennähe, innerhalb weniger Jahre zu ebenso zahlreichen Kontaminationen des Grundwassers mit Oxygenaten. Aufgrund der hohen Wasserlöslichkeit kommt es dabei zu einer besonders schnellen und großflächigen Ausbreitung der Ether. Derart belastetes Grundwasser weist schon bei geringsten Etherkonzentrationen einen als terpentinartig wahrgenommenen Geruch und Geschmack auf und kann daher nicht mehr als Trinkwasserzufuhr genutzt werden. Es bedarf einer Lösung dieses Problems. Die chemischen Parameter der Ether senken allerdings die Effizienz anderweitig erfolgreich genutzter technischer Sanierungsverfahren auf Basis von z. B. Adsorption oder Aerisierung. Auch gegenüber mikrobiellen Abbau erweisen sie sich als rekalzitrant. Die Suche nach oxygenatabbauenden Mikroorganismen führte zwar zur Anreicherung vieler Isolate, welche die Oxygenate cometabolisch partiell oder sogar komplett oxidieren, nur sehr wenige Kulturen sind aber zu autarkem Wachstum auf diesen Ethern fähig. Dazu gehören die Beta-Proteobacteria Methylibium petroleiphilum PM1 und der dieser Arbeit zugrunde liegende Aquincola tertiaricarbonis L108. Der Stamm L108 zeichnet sich durch ein vergleichsweise gutes Wachstum auf MTBE aus und ist als bisher einzig bekanntes Isolat in der Lage, auch ETBE, TAME und TAEE ähnlich schnell zu mineralisieren. Die vorliegende Arbeit handelt von dem scheinbar besonders gut an den Oxygenatabbau adaptierten Stoffwechsel des ursprünglich aus MTBE-kontaminiertem Grundwasser angereicherten Stammes L108. Durch verschiedene Deletionsstudien wurden Schlüsselenzyme des Abbaus und deren genetischer Hintergrund eindeutig identifiziert. Die Ergebnisse der genetischen, enzymatischen und physiologischen Studien des Wildtyps im Vergleich zu den erzeugten Deletionsstämmen tragen dazu bei, bisher nur postulierte Reaktionsschritte zu verifizieren. Schon seit den ersten Studien zum MTBE-Abbau wird anhand markanter Metabolite ein oxidativer Abbau via TBA, 2-Methyl-1,2-propandiol (MPD) und 2-Hydroxyisobuttersäure (2-HIBA) vermutet. Im Fall einer Hydroxylierung der Methoxygruppe von MTBE wird ein Hemiacetal als Reaktionsprodukt erzeugt, aus dem nachfolgend leicht der tertiäre Alkohol TBA entstehen kann. Durch den Vergleich des Wildtyps mit der Spontanmutante Stamm L10 konnte jetzt gezeigt werden, dass hierfür allein das Cytochrom-P450-Monooxygenasesystem EthABCD verantwortlich ist. Dieses katalysiert auch exklusiv die entsprechende Hydroxylierung von ETBE, TAME und TAEE. In Stamm L108 wird das Enzym konstitutiv exprimiert. TBA, das auch aus der Hydroxylierung von ETBE resultiert, wird, wie postuliert und in dieser Arbeit verifiziert, durch eine weitere Monooxygenase zu MPD abgebaut. Durch eine Tn5-Transposon-vermittelte Mutation konnte verifiziert werden, dass es sich bei diesem Enzym um die Rieske-nicht-Häm-Monooxygenase MdpJ handelt. MPD wird im weiteren Verlauf voraussichtlich durch zwei Dehydrogenierungen zur korrespondierenden, verzweigten Säure 2-HIBA gewandelt. Zum 2-HIBA-Abbau gibt es, basierend auf bekannten Enzymreaktionen, diverse Hypothesen. Anhand einer weiteren Tn5-Mutation konnte jetzt bestätigt werden, dass in den genannten beta-Proteobacteria die neuartige Mutase HcmAB wirksam ist, welche 2-HIBA abhängig von Cobalamin und Coenzym A (CoA) zu 3-Hydroxybuttersäure (3-HB) linearisiert. Sequenzvergleiche ergaben, dass Stamm L108 die Schlüsselenzyme des Etherabbaus, EthABCD, MdpJ und HcmAB, durch horizontalen Gentransfer erworben hat. Für TAME und TAEE wurde ein völlig neuer Abbauweg gefunden. In Stamm L108 wird der beim Abbau dieser Ether entstehende tert-Amylalkohol (TAA) wie TBA ebenfalls exklusiv durch MdpJ oxidiert. Durch die Tn5-Deletionsstudien und durch Analyse der Metabolite konnte allerdings keine Hydroxylierung nachgewiesen werden. TAA wird durch MdpJ vielmehr desaturiert. Somit entstehen im Abbauweg keine zu MPD und 2-HIBA analogen Diole und Säuren, sondern TAA wird zunächst durch MdpJ zu einem ungesättigten tertiären Alkohol, dem Hemiterpen 2-Methyl-3-buten-2-ol, abgebaut. Prenol (3-Methyl-2-buten-2-ol), Prenal (3-Methyl-2-buten-2-al) und 3-Methylcrotonsäure wurden als weitere Metabolite des TAA-Stoffwechsels detektiert. Somit spielt eine Isomerisierung einer tertiär verzweigten Säure durch HcmAB im TAA-Abbauweg offensichtlich keine Rolle. Entsprechend konnte gezeigt werden, dass Deletionsmutanten für hcmAB zwar nicht mehr auf TBA, aber immer noch auf TAA wachsen können, und das genauso schnell, wie der Wildtyp. Der tertiäre Alkohol 2-Methyl-3-buten-2-ol wird wahrscheinlich durch eine andere Isomerase zum primären Alkohol Prenol umgewandelt und dieser dann durch Dehydrogenasen zur Methylcrotonsäure oxidiert. Dies würde dem bereits in anderen Bakterien beobachteten Abbauweg des Monoterpens Linalool entsprechen. Die in Stamm L108 dafür verantwortlichen Enzyme wurden aber noch nicht identifiziert. Neben diesem grundsätzlichen Erkenntnisgewinn zum Abbau der xenobiotischen Etherverbindungen und der Evolution degradativer Mikroorganismen, können die hier bestätigten Schlüssel-enzyme EthABCD, MdpJ und HcmAB bzw. deren codierende Gene als spezifische Marker zum Monitoring natürlicher Abbauprozesse für in-situ-Untersuchungen genutzt werden. Auf dieser Basis kann auf die Anwesenheit aktiver Mikroorganismen und zudem noch - abgeleitet aus der Präsenz der einzelnen Schlüsselenzyme - auf einen potenziell kompletten Abbau geschlossen werden. Darauf aufbauend kann die natürliche mikrobiologische Aktivität durch nachfolgende biotechnologische Maßnahmen stimuliert werden, zum Beispiel durch eine Bioaugmentation mit Abbauspezialisten. Des weiteren können mögliche limitierende Schritte hinsichtlich des potenziellen Verlaufs der Sanierungsmaßnahme über Präsenztiter der betreffenden Marker gezielter verfolgt und als etwaige Ursachen defizitärer Abbauleistungen eingegrenzt werden. Voraussetzung für dieses funktionsbasierte Monitoring ist allerdings der spezifische Nachweis. Somit sollte in nachfolgenden Studien analysiert werden, ob es bei den drei Schlüsselenzymen eine Sequenzdiversität gibt. Die bisherigen Sequenzvergleiche lassen zumindest vermuten, dass bis etwa 60% Übereinstimmung der Proteinsequenzen bei Homologen von MdpJ und HcmA noch mit der gleichen Enzymfunktion zu rechnen ist. Diese Diversität sollte bei der Entwicklung von spezifischen Sonden berücksichtigt werden.:Bibliographische Darstellung Eidesstattliche Erklärung Danksagung Abstract Kurzfassung Abkürzungsverzeichnis 1. Einleitung 1.1. Tertiäre Ether als Benzin-Oxygenate - Hintergrund und Umweltproblematik 1.2. Mikrobiologischer Abbau tertiärer Ether 1.3. Postulierter Abbauweg 1.4. Monitoring-Tools für biologischen Abbau 1.5. Ziel dieser Arbeit 1.6. Referenzen der Einleitung 2. Die initiale Etherspaltung des Stammes L108 2.1. Die Ethermonooxygenase EthB 2.2. Supplemental Material 3. Die spezifische Alkoholmonooxygenase MdpJ 3.1. Die Alkoholmonooxygenase MdpJ als Hydroxylase und Reduktase 3.2. Supplemental Material 4. Die 2-HIBA-Mutase HcmAB des Stammes L108 4.1. Die 2-HIBA-Mutase HcmAB 4.2. Supplemental Material 5. Der TAA-Abbau des Stammes L108 5.1. Der TAA-Abbau des Stammes L108 5.2. Supplemental Material 6. Diskussion 6.1. Nachweis der Schlüsselenzyme in Stamm L108 durch Mutation 6.2. Nutzen für den Nachweis natürlichen Abbaus 6.3. Der TAA-Metabolismus als neuartiger Abbauweg 6.4. Mikrobiologische Anpassung an Xenobiotika am Beispiel MTBE 6.5. Ausblick 6.6. Referenzen der Diskussion Anhang Curriculum Vitae Publikationsverzeichnis Tagungsbeiträge Nachweis über Anteile der Co-Autoren

Oxidation reactions are of prime importance at an industrial level and correspond to a huge market. Oxidation reactions are widely practiced in industry and are thoroughly studied in academic and industrial laboratories. Achievements in oxidation process resulted in the development of many new selective oxidation processes. Environmental protection also relies mainly on oxidation reactions. Remarkable results obtained in this field contributed to promote the social image of chemistry which gradually changes from being the enemy of nature to becoming its friend and savior. This study dealt with two aspects regarding oxidation process. The first aspect represented an experimental study for the partial oxidation of benzene to phenol using Pd membrane in the gaseous phase. The second part was a theoretical study for some of the advanced oxidation process (AOPs) which are applied for contaminant destructions in polluted waters. Niwa and coworkers reported a one step catalytic process to convert benzene to phenol using Pd membrane. According to their work, this technique will produce a higher yield than current cumene and nitrous oxide based industrial routes to phenol. A similar system to produce phenol from benzene in one step was studied in this work. Results at low conversion of benzene to phenol were obtained with a different selectivity from the reported work. High conversion to phenol was not obtained using the same arrangement as the reported one. High conversion to phenol was obtained using a scheme different from the one reported by Niwa et al1. It was found that producing phenol from benzene is not related to Pd-membrane since phenol was produced by passing all reactants over a Pd catalyst. Within the studied experimental conditions, formation of phenol was related to Pd catalyst since Pt catalyst was not capable of activating benzene to produce phenol. Other evidence was the result of a blank experiment, where no catalyst was used. From this experiment no phenol was produced. A kinetic model for the advanced oxidation process using ultraviolet light and hydrogen peroxide (UV/H2O2) in a completely mixed batch reactor has been tested for the destruction of humic acid in aqueous solutions. Known elementary chemical reactions with the corresponding rate constants were taken from the literature and used in this model. Photochemical reaction parameters of hydrogen peroxide and humic acid were also taken from the literature. Humic acid was assumed to be mainly destroyed by direct photolysis and radicals. The rate constant for the HA- reaction was optimized from range of values in the literature. Other fitted parameters were the rate constant of direct photolysis of hydrogen peroxide and humic acid. A series of reactions were proposed for formation of organic byproducts of humic acid destruction by direct photolysis and radicals. The corresponding rate constants were optimized based on the best fit within the range of available published data. This model doesn't assume the net formation of free radicals species is zero. The model was verified by predicting the degradation of HA and H2O2 for experimental data taken from the literature. The kinetic model predicted the effect of initial HA and H2O2 concentration on the process performance regarding the residual fraction of hydrogen peroxide and nonpurgeable dissolved organic carbon (NPDOC). The kinetic model was used to study the effect of the presence of carbonate/bicarbonate on the rate of degradation of NPDOC using hydrogen peroxide and UV (H2O2/UV) oxidation. Experimental data taken from literature were used to test the kinetic model in the presence of carbonate/bicarbonate at different concentrations. The kinetic model was able to describe the trend of the experimental data. The kinetic model simulations, along with the experimental data for the conditions in this work, showed a retardation effect on the rate of degradation of NPDOC due to the presence of bicarbonate and carbonate. This effect was attributed to the scavenging of the hydroxyl radicals by carbonate and bicarbonate. A kinetic model for the degradation of methyl tert-butyl ether (MTBE) in a batch reactor applying Fenton's reagent (FeII/ H2O2) and Fenton-like reagent (Feo/ H2O2) in aqueous solutions was proposed. All of the rate and equilibrium constants for hydrogen peroxide chemistry in aqueous solutions were taken from the literature. Rate and equilibrium constants for ferric and ferrous ions reactions in this model were taken from the reported values in the literature, except for the rate constant for the reaction of ferric ions with hydrogen peroxide where it was fitted within the range that was reported in the literature. Rate constant for iron dissolution was also a fitted parameter. The mechanism of MTBE degradation by the hydroxyl radicals was proposed based on literature studies. The kinetic model was tested on available experimental data from the literature which involved the use of Fenton's reagent and Fenton-like reagent for MTBE degradation. The degradation of MTBE in Fenton's reagent work was characterized to proceed by two stages, a fast one which involved the reaction of ferrous ions with hydrogen peroxide (FeII/H2O2 stage) and another, relatively, slower stage which involved the reaction of ferric ions with hydrogen peroxide (FeIII/H2O2 stage). The experimental data of MTBE degradation in the FeII/H2O2 stage were not sufficient to validate the model, however the model predictions of MTBE degradation in the FeIII/H2O2 stage was good. Also, the model was able to predict the byproducts formation from MTBE degradation and their degradation especially methyl acetate, and tert-butyl alcohol. The effect of each proposed reaction on MTBE degradation and the byproducts formation and degradation was elucidated based on a sensitivity analysis. The kinetic model predicted the degradation of MTBE for Fenton-like reagent for the tested experimental data. Matlab (R13) was used to solve the set of ordinary nonlinear stiff differential equations that described rate of species concentrations in each advanced oxidation kinetic model. Niwa, S. et al., Science 295 (2002) 105