La pollution des eaux superficielles et souterraines par des composés organiques est bien connue comme une préoccupation majeure de l'environnement dans de nombreux pays. Si les polluants prioritaires sont actuellement surveillés par la directive cadre européenne sur l'eau, il est désormais urgent de prendre en considération les nouveaux polluants dérivés de principes actifs des produits pharmaceutiques et d'identifier leurs produits de transformation à risque. Ce travail de thèse propose une étude globale sur l'état et l'avenir des produis pharmaceutiques dans l'environnement, sur l'exemple de deux pharmaceutiques choisis, dans le cadre de cette importante problématique environnementale. Nous avons donc appliqué les procédés électrochimiques d'oxydation avancée, électro-Fenton (EF), oxydation anodique(OA) et photoélectro-Fenton solaire (PEFS), ainsi que le couplage électro-Fenton/traitement biologique pour une élimination effective des polluants médicamenteux furosémide et ranitidine. Les résultats obtenus confirment l'efficacité de ces technologies électrochimiques pour la minéralisation quasi-totale des produits pharmaceutiques étudiés. En outre, l'utilisation du pré-traitement par EF suivi d'un procédé biologique confirme la capacité de l'EF de transformer les polluants organiques en produits biodégradables qui peuvent être consommés par des microorganismes lors d'un traitement biologique, démontrant ainsi l'applicabilité potentiel de cette technique combinée, en termes d'une consommation énergétique réduite. L'identification des produits de transformation (PTs) des pharmaceutiques étudiés par voie électrochimique (électro-oxydation) et biologique (bioconversion) a été effectuée par différentes techniques d'analyse physico-chimiques. La biotransformation du FRSM a conduit à la formation de trois PT principales; saluamide, pyridinium et un dérivé céto-alcool. Les deux premiers ont aussi été détectés lors du traitement électrochimique, ce qui suggère la probabilité de les trouver dans l'environnement comme les produits de transformation les plus plausibles par des différentes conditions de dégradation. Les tests de toxicité basés sur l'inhibition de la bioluminescence des bactéries marines Vibrio fischeri ont montré que certains PT formés lors de traitement électrochimiques sont plus toxique que la molécule mère, car une augmentation de la toxicité globale de la solution a été observée au début des électrolyses. Néanmoins, la toxicité de la solution est complètement éliminée à la fin des traitements électrochimiques, ce qui indique l'efficacité de ces technologies aussi pour la détoxification des solutions des médicaments traités. Par conséquent, cette étude constitue une contribution importante à l'évaluation des risques environnementaux des produits pharmaceutiques / The present project contributes with valuable data for a better fundamental understanding on the fate of pharmaceutical residues in the environment, dealing with the main challenges concerning this increasingly worrying environmental issue. The used Electrochemical Advanced Oxidation Processes (EAOPs), electro-Fenton (EF) and anodic oxidation (AO), showed to be a very efficient alternative for the mineralization of acid solutions of the pharmaceuticals RNTD and FRSM, attaining almost complete mineralization of the drugs after 6h of electrolysis. A comparative study on the mineralization of RNTD solutions by EF and SPEF processes in a 2.5 L capacity pre-pilot flow plant demonstrates the higher oxidation capacity of SPEF, achieving very good mineralization rates, thus evidencing the potentiality of this technology at greater scale for the treatment of wastewaters containing pharmaceutical products. The application of an EF pre-treatment coupled with a biological process for the degradation of both drugs was conducted. EF pre-pretreatment was capable of enhancing the solution biodegradability envisaging a biological treatment, which efficiently removed the short-chain carboxylic acids that had been formerly generated during the pre-applied electrolysis. In this way, the combination of both processes was confirmed as a very promising technology for the treatment of pharmaceuticals-containing wastewater. Several transformation products (TPs) were detected and identified during the electrochemical oxidation of the studied drugs. Toxicity tests based on the bioluminescence of the marine bacteria V. fischeri. evidenced the toxicity some of these oxidation by-products, since the toxicity of the solution increased on the first stages of the electrolysis. However, the abatement of the toxicity in the final stages of the electrochemical treatments, demonstrated the effectiveness of these technologies for both the mineralization and detoxification of the RNTD and FRSM solutions. The use of the fungi Cunninghanella echinulate for the bioconversion of FRSM led to the formation of three main bio-transofrmation products: the previously identified saluamide and pyridinium, and the new detected keto-alcohol derivate. These TPs were generated by both, biological and electrochemical approches, evidencing their high probability to be found in environmental compartments as the most likely TPs of FRSM by different oxidation conditions. This study is thus presented as a very useful alternative for the assessment of the fate of pharmaceutical residues in the environment

2-phenylethanol (2PE) is a valuable fragrance compound which gives a rose-like aroma. As such 2PE is one the highest used fragrances globally. While 2PE is predominantly produced from petrochemical resources, there is a growing market for a naturally derived alternative for food products. 2PE from natural sources is priced so highly due to limited supply from rose petals. Recently, a few reports have demonstrated the production in yeasts through both the de novo production from glucose and ex novo biosynthesis with L-phenylalanine as a precursor. While these are promising most of the yeasts used can only produce low titres under optimal conditions, and the fermentation still appears to be too expensive. In this investigation the wine yeast M. pulcherrima was selected to be assessed for 2PE production. M. pulcherrima is known to produce 2PE in small titres in wine production though has yet to be explored as a platform for this product. M. pulcherrima has several advantages as a yeast platform, in that it produces a range of antimicrobials which can ward off invasive species, allowing for less sterile control in any large scale fermentation. M. pulcherrima was demonstrated to be able to produce 2PE in high titres in the batch mode through de novo synthesis of glucose, producing up to 1 g/L in shake flasks on the lab scale. Arabitol was also observed in the fermentation broth and was produced up to 20 g/L. The fermentation was then scaled up to 2L in batch mode. From these experiments, up to 700 mg/L of 2PE was produced. This is substantially more than any other yeast in the literature to date. Though when xylose or glycerol was present then 2PE production was severely limited. M. pulcherrima was also demonstrated to be able to produce 2PE by bioconversion from phenylalanine up to 1.5 g/L. This 2PE concentration is suggested to be threshold of toxicity to M. pulcherrima by the toxicity study. The production of 2PE could be increased substantially by introducing an absorbent into the process. Liquid solvents and solid adsorbents were assessed to increase 2PE production, used as in-situ 2PE adsorbents. Oleyl alcohol was found to be a good solvent for in-situ extractive solvent in M. pulcherrima culture and increase the production to 3.3 g/L which is higher than 2PE tolerance threshold of the yeast. Activated carbon was also found to be an excellent 2PE adsorbents, with maximum Langmuir adsorption capacity up to 0.807 g/g. 2PE synthesis with activated carbon as an in-situ adsorbent can increase 2PE production to 14 g 2PE/L. Finally, the process was scaled to 2L and run in batch, continuous and semi-continuous modes. This study demonstrates that not only is M. pulcherrima a viable organism to produce 2PE but it has the potential to be scaled up and run in a more cost effective semi-continuous mode when coupled to a continuous extraction technique.

Cost-effective processing of dairy whey permeates is important to the environment and economics of the agriculture industry in Canada. Bioconversion of whey permeates is an attractive means of obtaining value-added adjuncts with improved nutritional and functional properties. In the past, cost-effective technologies to recover additional value from whey permeates at a low cost were lacking. Currently, such a technological platform is now feasible with the introduction of new modern bioconversion technologies that incorporate batch or continuous bioreactors, and use ultra- and nano-filtration membranes for the separation of whey permeate components. In this dissertation, a novel processing methodology is described. This methodology, which is a desirable configuration for food manufacturers includes a stirred batch nanomembrane bioreactor equipped with a crossflow nanomembrane and offers lactose bioconversion with an immobilized biocatalyst, product separation, and biocatalyst recovery in a batch operation. The major focus of this research was on: a) the development of a new analytical methodology for carbohydrate measurement during the lactose bioconversion process, b) the selection, testing and integration of highly selective nanomembranes to separate the desired substrates, whey permeate carbohydrates, from the reaction mixture, and c) the production of a stable and highly active and specific immobilized biocatalyst. Noticeably, this methodology was designed, developed and tested for the bioconversion of lactose, but could also be used for the bioconversion of other carbohydrate feedstocks. The food industry in Canada needs an integrated approach to achieve complete lactose reclamation and use. This research project offers such a solution. The research described in this dissertation presents an integrated model of a stirred batch bioreactor that may support not only current, but also future research, and may economically impact the development and bioconversion of whey permeates containing lactose. This may lead to the development of a continuous processing methodology for low cost recovery of lactose from whey permeates and simultaneous conversion to value-added products. / Bioresource and Food Engineering

Benzoin is an important a-hydroxy ketone which can be used as chiral intermediate for the synthesis of several drugs. In this study, it was aimed to synthesize this compound by high stereoslectivity and yield by the use of fungal bioconversions. For this purpose, whole cells of four different Fusarium spp. (F. anguoides, F. roseum, F. solanii, F.bulbigenum) were used for reduction of readily available achiral compound benzil. The reaction conditions were optimized as glucose peptone broth consisting of 30g/L glucose and 10 g/L peptone, inoculum size as 20 mg/L and substrate concentration as 200 mg/L. A complete set of derivatives substituted with electron donating and electron withdrawing groups of the benzils were also reduced to the corresponding benzoin derivatives with the same optimized condition with up to 98% ee.

Pretreatment of recalcitrant lignocellulosic biomass to release sugars for bioconversion into ethanol produces fermentation inhibitors. Increasing yeast inhibitor tolerance should reduce production time and cost. UV mutagenesis followed by genome shuffling using cross mating was performed on Scheffersomyces stipitis strain GS301, a genome shuffled strain with increased tolerance to spent sulphite liquor (SSL). The main fermentation inhibitors in SSL are acetic acid, hydroxymethylfurfural (HMF), and various phenolics. UV mutagenesis resulted in acetic acid tolerant mutants, but they were phenotypically unstable. However, two rounds of UV mutagenesis followed by five rounds of genome shuffling resulted in strains EVB105, EVB205 and EVB505 with increased SSL tolerance and improved acetic acid and HMF tolerance. When fermenting undiluted SSL at pH 5.5, the three strains utilized sugars faster producing higher maximum ethanol than GS301. This study demonstrates that UV mutagenesis with genome shuffling can significantly improve inhibitor tolerance and fermentation performance of yeast. / NSERC Bioconversion Network

No description available.

Increased world-wide interest in reducing the carbon-footprint of human activities has driven the coal-fueled energy industry to transition to a natural gas fueled future. Coupled with the continually increasing energy demand, the interest in alternate sources of natural gas has gained momentum. Microbially enhanced coalbed methane (MECBM), which aims at microbially converting in situ coal to methane provides one such alternate source of natural gas. Feasibility of MECBM as a viable technology is two-pronged, focusing on associated microbiology, and flow-governing reservoir response. The general advance of research in this area has thus far been from a microbial perspective, where coal-to-methane bioconversion has been successfully reported for several coal types worldwide. However, insights into reservoir properties governing flow and transport of fluids in a MECBM reservoir is missing. Given that coal is both the source and reservoir rock of the produced biogenic methane, a sound knowledge of the effect of bioconversion on flow governing properties of coal is decisive from a production perspective. Evaluating the flow governing reservoir response of a MECBM reservoir is the focus of the work presented in this dissertation. In order to investigate the effect of bioconversion on the Darcian flow regime existing in the natural fractures in coal, two experimental studies were undertaken. First, variation in coal’s flow governing micro- and macro- porosity was investigated using high-resolution scanning electron microscopy. The observed changes were quantified and the expected change in permeability of coal post-bioconversion was estimated. In the second set of experiments, the sorption-induced-strain response of coal pre- and post-bioconversion was studies. Finally, the experimental data was used to model and predict the geomechanical-coupled flow behavior of a MECBM reservoir during bioconversion and production of the produced biogenic methane. Experimental results from the imaging study revealed that bioconversion results in swelling of the coal matrix. This reduces the cleat (macroporous fracture) aperture post-bioconversion, reducing the permeability of the coal significantly. This validated the recently reported results, where measured permeability of coal packs and coal cores dropped by ~70% post-bioconversion. Bioconversion, however, resulted in increase in the cleat width of fractures greater than 5 microns wide, which constituted <5% of the fractures imaged. This is indicative of the possibility of enhanced reservoir performance in artificially fractured coal formations or, ones with wide-aperture fractures, like depleted coalbed methane (CBM) reservoirs and abandoned mines. Investigation into the sorption-induced-strain response of coal revealed suppression of the strain response post-bioconversion. Results from helium and methane flooding revealed that bioconversion softens the coal matrix, reducing the Langmuir pressure and strain constants post-bioconversion. The modeling exercise revealed that the depletion induced the permeability increase commonly associated with producing CBM will be suppressed post-bioconversion. Detailed analysis of the behavioral variation in multiple reservoir parameters was used to define the ideal condition, beyond which the reservoir flow during biogenic methane production improved. Additionally, a rating system is proposed, which can be used to rank coal deposits to rate their suitability for bioconversion from a flow perspective.

L’hydroperoxyde lyase (HPL) est une enzyme issue de la voie de la lipoxygénase, voie métabolique très représentée chez les végétaux, impliquée dans la production de composés aromatisants (l’hexanal, le 3Z-hexenal et le 2E-hexenal). Ces composés sont responsables de l’odeur fraîche de l’herbe coupée dite « note verte » et sont très utilisés par les industries cosmétiques et agroalimentaires. Leur biosynthèse résulte de l’oxydation des acides gras polyinsaturés en hydroperoxydes par la lipoxygénase, puis de leur clivage par l’hydroperoxyde lyase (HPL). Les procédés actuels de production de ces composés présentent certains inconvénients, ils sont notamment très polluants et peu performants, aussi l’utilisation d’enzymes recombinantes dans de tels procédés permettrait d’obtenir ces molécules de manière plus efficace tout en bénéficiant du label "naturel". L’ADNc codant pour l’hydroperoxyde lyase (HPLwt) a été isolé au laboratoire à partir d’olives noires. Afin d’améliorer la solubilité de l’enzyme, une HPL dépourvue de son peptide de transit chloroplastique (HPLdel) a également été produite. Les deux enzymes ont été exprimées chez E.coli, purifiées par chromatographie d’affinité puis caractérisées biochimiquement. Elles agissent exclusivement sur les 13-hydroperoxydes (13-HPL) à un pH et une température optimum de 7,5 et 25°C. De plus l’évaluation des paramètres cinétiques de l’enzyme montre qu’elles ont une meilleure efficacité catalytique (kcat/Km) sur les 13-hydroperoxydes d’acide linolénique (3,68 s-1.µM-1) que sur les 13-hydroperoxydes d’acide linoléique (0,54 s-1.µM-1). La bioconversion des 13-hydroperoxydes d’acide linoléique et linolénique en hexanal et 3Z-hexénal par l’action de l’HPLwt et l’HPLdel a été étudiée. Des taux de conversion maximum atteignant 93 % et 68 % pour la production d’hexanal et 73 % et 45% pour la production d’3Z-hexénal ont été obtenus quand l’HPLwt et l’HPLdel sont utilisées respectivement. La stabilité de l’enzyme a ensuite été étudiée. Des essais de conservation montrent que l’utilisation de glycérol à 10% (v/v) permet le maintien de la totalité de l’activité de l’HPLwt et de l’HPLdel durant cinq semaines de stockage à -80°C. De plus, l’ajout de composés chimiques tels que le KCl, le NaCl, le Na2SO4, la glycine et le glycérol permettent d’augmenter l’activité enzymatique des deux enzymes et d’améliorer les conditions de synthèse de l’hexanal et du 3Z-hexénal en diminuant la quantité d’enzyme nécessaire à leur production. / The hydroperoxide lyase (HPL) derives from a metabolic pathway named lipoxygenase pathway widely represented in plants and involved in the production of flavoring compounds (hexanal, 3Z-hexenal and 2E-hexenal). These volatile compounds are responsible for the fresh odor of cut grass known as "green note" and have a particularly interest for flavor and food industries. Their biosynthesis results from the oxygenation of linoleic and linolenic acids by lipoxygenase action to form fatty acid hydroperoxides, then of their cleavage by hydroperoxide lyase action. The processes of production currently used are highly polluting or lead to a low yield. To overcome these drawbacks, the use of recombinant enzymes in such processes constitutes an attractive alternative because they would allow producing these molecules in a more effective way, while benefiting from the "natural" label.A cDNA encoding for HPL (HPLwt) from black olive fruit was isolated, and in order to improve the enzyme solubility, the HPL deleted of its chloroplast transit peptide (HPLdel) was then produced. Both enzymes were expressed into E. coli (M15), purified by affinity chromatography, and characterized. They act exclusively on 13-hydroperoxide (13-HPL) and display an optimum pH at 7.5 and an optimum temperature at 25 °C. The bioconversion of 13-hydroperoxides of linoleic and linolenic acids in hexanal and 3Z-hexenal respectively, using HPLwt or HPLdel was studied. Conversion yields reach a maximum of 93 % and 68 % for hexanal production, and 73 % and 45 % for 3Z-hexenal when reactions were performed by HPLwt and HPLdel respectively.The enzyme stability was then studied. Conservations tests using 10 % glycerol (v/v) allows the maintenance of the entire activity of HPLwt and HPLdel during five weeks of storage at -80°C. Furthermore, the addition of chemical compounds such as KCl, NaCl, Na2SO4, glycine, and glycerol can increase the efficiency of both enzymes and improve the synthesis of hexanal and 3Z-hexenal by decreasing the amount of enzyme required to produce them.

Les chimistes organiciens disposent à l'heure actuelle des outils de la biocatalyse afin d'accéder aux produits de la chimie fine et en particulier à des synthons et des molécules optiquement enrichies. Dans ce cadre, le travail de thèse présenté dans ce mémoire a été conduit afin d'enrichir notre connaissance sur une époxyde hydrolase (EH) découverte après analyse métagénomique d'un bio-filtre. Afin de pouvoir mener une étude de mutagénèse dirigée de sorte à améliorer certaines propriétés de cette enzyme appelée Kau2-EH, un modèle de l'enzyme a été élaboré sur la base de la structure tridimensionnelle de l'EH de souris. Le choix de cette matrice fait suite à des études d'inhibition comparées visant à déterminer laquelle des trois EHs, dont la structure tridimensionnelle était connue (pomme de terre, souris, homme) et dont la séquence était proche de celle de Kau2-EH, présentait l’inhibition la plus proche de celle observée pour Kau2-EH. Il avait été montré précédemment que Kau2-EH présentait un intérêt en biocatalyse permettant une résolution cinétique quasi-parfaite de l'oxyde de trans-méthyl-styrène et une transformation énantioconvergente, elle aussi quasi-parfaite, de l'oxyde de cis-méthyl-styrène. Ainsi des études de bioconversion dédiées à l'évaluation de la diversité des substrats de Kau2-EH ont été réalisées. Cette enzyme se révéla être particulièrement performante lors de l'utilisation d'époxydes cis- et trans-1,2-disubstitués portant sur un des atomes de carbone de la fonction époxyde un groupement phényle ou p-méthoxy-phényle et sur l'autre un groupement variable (méthyl- ou éthyl-ester, cyano, bromo- ou chloro-méthyle, phényle). Pour neuf des dix substrats testés des énantiosélectivités très élevées ont été trouvées permettant des résolutions cinétiques quasi-parfaites de huit d'entre eux et la désymétrisation quasi-parfaite du neuvième. Seul le cis-méthyl-glycidate ne fut pas un substrat de Kau2-EH. Dans les neufs cas précédents une réaction préparative à l'échelle du gramme a pu être conduite à très haute concentration en substrat (de 25 à 75 g/L) et sur une courte période de temps (de 1 à 4h) sauf pour l'oxyde de cis-stilbène (24 h). Finalement et afin d'accéder aux constantes cinétiques fondamentale, une étude préliminaire de « stopped-flow » du comportement de Kau2-EH a été réalisée en utilisant l'oxyde de trans-stilbène comme substrat. / Biocatalysis is nowadays an important tool available to organist chemist to get access to fine chemicals and especially enantiomerically enriched synthons and molecules. Within this framework, the PhD work described in this dissertation was conducted in order to get insights about a newly discovered epoxide hydrolase (EH) from a metagenomic analysis of a biofilter. In order to conduct directed mutagenesis on the so-called Kau2-EH, a model of the enzyme was constructed based on the 3D structure of murine EH. The choice of this template was dictated by comparative inhibition studies aimed at differentiating three otherwise closely Kau2-sequence-related EHs with known crystal structure (potato-, murine- and human-EHs) and showing inhibition behavior the closest to the one found for Kau2. The enzyme was previously shown to display interesting biocatalytic properties such a nearly perfect kinetic resolution of trans-methyl-styrene-oxide and a nearly perfect enantioconvergent transformation of cis-methyl-styrene-oxide. Thus, bioconversion studies dedicated to the evaluation Kau2-EH substrate chemical space were undertaken. The enzyme proved to be particularly useful when using 1,2-disubstituted cis- or trans-aromatic epoxides bearing an aromatic ring (phenyl, p-methoxy-phenyl) on one of the epoxide-bearing carbon atom and various chemical groups (methyl- or ethyl-esters, cyano, chloro- or bromo-methyl or phenyl) on the second carbon atom. For nine of the ten tested substrates very high enantioselectivities were observed allowing nearly perfect kinetic resolutions of eight of them and a nearly perfect desymmetrization of the ninth. Only cis-methyl-glycidate proved to be not a substrate of Kau2-EH. In the all other nine cases a preparative scale reaction could be conducted on the 1g scale, at high to very high substrate concentration (25 to 75 g/L) and in short periods of time (1 to 4h) except for cis-stilbene-oxide (24 h). Finally and in order to get access to fundamental kinetic constants, a preliminary stopped-flow analysis of Kau2-EH behavior was undertaken using trans-stilbene-oxide as substrate.

Une part importante de la production mondiale de vecteurs énergétiques et de produits chimiques provient de la raffinerie de combustibles fossiles. En raison de l'augmentation du prix du pétrole et de son impact environnemental, la recherche de solutions alternatives, écologiques et économiques constitue l’un des enjeux de notre siècle. Le remplacement du pétrole par de la biomasse en tant que matière première pour la production de carburants et de produits chimiques constitue la force motrice dans le développement de complexes de bioraffinerie.Cette étude fait partie d’un projet de bioraffinerie visant la valorisation de biomasse lignocellulosique par la production d’hydrogène et de lipides microbiens précurseurs de biodiesel. Ce travail se concentre en particulier sur l’étape de production de biomasse et de lipides par la levure oléagineuse Cryptococcus curvatus à partir d’acides gras volatils (AGVs) synthétisés au cours de la fermentation anaérobie productrice d’hydrogène. Les cultures ont dans un premier temps été réalisées à partir d’un substrat modèle, l’acétate, en fed-batch et en continu. La détermination de l’influence de différents paramètres opératoires sur la production de biomasse et de lipides à partir d’acétate a permis de mettre au point des cultures en fed-batch dont les cinétiques, les productivités et les rendements finaux étaient compétitifs avec ceux rapportés dans la littérature pour des cultures sur substrats simples. Un modèle de croissance et de production de lipides a été construit à partir de ces données afin de prédire le comportement de la souche lors de cultures continues, permettant d’obtenir des productivités en lipides et en biomasse élevées. Enfin, des cultures ont été menées à partir d’AGVs issus de surnageant de fermentation anaérobie. Les résultats ont confirmé la croissance de ces levures sur ce substrat particulier et la production de lipides dont la composition en acides gras estérifiés était compatible avec une utilisation comme biodiesel. / A great part of the global production of energy vectors and chemicals comes from fossil fuels refinery. Because of the increase in oil price and their environmental impacts, the search for alternative, ecological and economic solutions is a current challenge. The replacement of oil with biomass as raw material for the production of fuels and chemicals is the driving force for the development of biorefinery complexes.This study is part of a project aiming at the biorefinery of lignocellulosic biomass for hydrogen and microbial lipids as biodiesel precursors. This work focuses on the biomass and lipids production step by the oleaginous yeast Cryptococcus curvatus using volatile fatty acids (VFAs) as carbon sources, which are synthesized during the anaerobic fermentation step. Yeast cultures have initially been realized using a model substrate, acetate, and fed-batch and continuous modes. The determination of the influence of different operating parameters on the biomass and lipids production led to the development of fed-batch cultures which kinetics, productivities and yields were competitive with those reported in the literature for cultures on simple substrates. A growth and lipid production model was built from these data to predict the behavior of the strain during continuous cultures and to obtain high lipid and biomass productivities. Finally, cultures were conducted using VFAs from anaerobic fermentation supernatant. The results confirmed the growth of these yeasts on this particular substrate and the production of lipids which composition was compatible with use as biodiesel.