Resíduos celulósicos por erem ricos em celulose e hemicelulose estão sendo apontados como promissoras fontes para a produção de etanol. Com isso, este trabalho tem como objetivo hidrolisar e fermentar resíduos celulósicos visando a produção de etanol. Para estudo da hidrólise do bagaço de cana-de-açúcar, foram isolados 22 fungos da cidade de Araras-SP e estes testados para produção de endoglucanases (EG). Foram testadas temperatura e pH ótimos, diferentes tampões, estabilidade do coquetel e influência de sais, EDTA e ?-mercaptoetanol para lacase, xilanase, endo-?-1,4-glucanase, celobiohidrolase I, ?-glucosidase e glucoamilase. As condições padronizadas para aplicação do coquetel enzimático foi 55ºC, tampão citrato de sódio 50 mM e pH 5,0. Para elaboração do coquetel enzimático foi realizado um Plackett-Burman seguido de um delineamento composto central rotacional, em que as condições padronizadas para aplicação foram (U/g de bagaço de cana-deaçúcar): 0,122 de lacase; 7 de xilanase; 5 de endoglucanase; 14 de celobiohidrolase e 9 de ?-glucosidase. Foram liberados 4,405 µmol de açúcares redutores por mL, após 48 horas de hidrólise do bagaço a 55ºC, em tampão citrato de sódio 50 mM (7 mL), pH 5,0, agitação de 110 rpm. O hidrolisado obtido foi fermentado pelas leveduras Saccharomyces cerevisiae PE-2 e Meyerozyma guilliermondii 311 (CCT7783), separadamente e em cultivo misto, averiguando a necessidade de suplementação do meio, para a produção de etanol. Os resultados mostraram a necessidade de suplementação para aumento da viabilidade das leveduras. Observou-se que a suplementação manteve a viabilidade acima de 90%. A fermentação com Meyerozyma guilliermondii 311 (CCT7783), sem a necessidade de suplementação, possibilitou a produção de 12,66% de etanol; com a Saccharomyces cerevisiae a produção de etanol foi de 7,03%, quando o meio foi suplementado com 3 g/L de extrato de levedura. A fermentação com cultura mista produziu 0,53% e 1,18% de etanol em 24 e 48 horas de cultivo, respectivamente. Para aplicação enzimática na hidrólise do lodo branco foram utilizadas amilase de Aspergillus carbonarius e celulase comercial. Os produtos de hidrólise enzimática do lodo branco detectados HPLC mostraram a formação de glicose, xilose e traços de maltose. A viabilidade celular da levedura Saccharomyces cerevisiae durante a fermentação se manteve bastante elevada, acima de 95 %. A fermentação do lodo branco, quando o meio foi suplementado com 3g/L de extrato de levedura, foi considerada satisfatória, com 2,37 g/L de etanol. Foram realizadas análise de superfície por ion-tof e microscopia eletrônica de varredura nos resíduos celulósicos. Desta maneira, com este trabalho foi possível estudar a importância da aplicação de enzimas fúngicas para degradação de biomassa lignocelulósica para produção de etanol de segunda geração. / As cellulosic wastes are rich in cellulose and hemicellulose they have been pointed as promising sources for ethanol production. Thereby, this work aimed to hydrolyze and ferment cellulosic residues to produce ethanol. In order to study the hydrolyzes of sugar-cane bagasse and ferment the sugars obtained from this process, twenty-two fungi were isolated in the city of Araras-SP and tested for endoglucanase (EG) production. Aiming to optmize an enzyme cocktail, variables as temperature, optimum pH, different buffers, stability, salt influence, EDTA and ?-mercaptoethanol were tested for laccase, xylanase, endo- ?-1,4-glucanase, cellobiohydrolase I, ?-glucosidase and glucoamylase. The standard conditions for applying the enzyme cocktail were 55°C, sodium citrate buffer 50 mM pH 5.0. For the preparation of the enzyme cocktail a Plackett-Burman was made followed by a central composite design, in which the standard conditions for application were (U/g of sugarcane bagasse): 0.122 of laccase; 7 of xylanase; 5 of endoglucanase; 14 of cellobiohydrolase and 9 of ?-glucosidase per gram of sugarcane bagasse. After 48 hours of hydrolyzes in the following conditions, 55ºC, sodium citrate buffer 50 mM (7 mL), pH 7.0, 110 rpm, 4.405 µmol of reducing sugar per mL were released. The hydrolyzate obtained was separately fermented by the yeasts Saccharomyces cerevisiae PE-2, Meyerozyma guilliermondii 311 (CCT7783) and with both yeasts in a mixed cultivation, in order to investigate the need of medium supplementation for ethanol production. The results showed the need of supplementation to increase the viability of the yeasts. It was observed that this procedure kept the viability over 90%. The fermentation with Meyerozyma guilliermondii 311 (CCT7783), without supplementation, allowed the production of 12.66% of ethanol and with Saccharomyces cerevisiae the production was 7.03% with a supplementation of 3 g/L of yeast extract. The fermentation with mixed cultivation produced 0.53% and 1.18% in 24 and 48 hours of cultivation, respectively. Another objective of this work was the hydrolysis of paper sludge which was obtained by using amylases from Aspergillus carbonarius and commercial cellulases. The products of enzymatic hydrolysis of the white sludge detected in HPLC showed the formation of glucose, xylose and maltose traits. Cell viability counting of the yeast, analyzes of pH, reducing sugar and alcohol content were carried out. Cellular viability of Saccharomyces cerevisiae along the fermentation was kept over 95%. Paper sludge fermentation using Saccharomyces cerevisiae, in medium supplemented with yeast extract 3 g/L, was considered satisfactory, showing 2.37 g/L of ethanol. Surface analysis was performed by Ion-tof and scanning electron microscopy in the cellulosic waste. Thus, this work made possible to study the importance of fungal enzymes application in lignocellulosic biomass degradation for the production of second generation ethanol.

Resíduos celulósicos por erem ricos em celulose e hemicelulose estão sendo apontados como promissoras fontes para a produção de etanol. Com isso, este trabalho tem como objetivo hidrolisar e fermentar resíduos celulósicos visando a produção de etanol. Para estudo da hidrólise do bagaço de cana-de-açúcar, foram isolados 22 fungos da cidade de Araras-SP e estes testados para produção de endoglucanases (EG). Foram testadas temperatura e pH ótimos, diferentes tampões, estabilidade do coquetel e influência de sais, EDTA e ?-mercaptoetanol para lacase, xilanase, endo-?-1,4-glucanase, celobiohidrolase I, ?-glucosidase e glucoamilase. As condições padronizadas para aplicação do coquetel enzimático foi 55ºC, tampão citrato de sódio 50 mM e pH 5,0. Para elaboração do coquetel enzimático foi realizado um Plackett-Burman seguido de um delineamento composto central rotacional, em que as condições padronizadas para aplicação foram (U/g de bagaço de cana-deaçúcar): 0,122 de lacase; 7 de xilanase; 5 de endoglucanase; 14 de celobiohidrolase e 9 de ?-glucosidase. Foram liberados 4,405 µmol de açúcares redutores por mL, após 48 horas de hidrólise do bagaço a 55ºC, em tampão citrato de sódio 50 mM (7 mL), pH 5,0, agitação de 110 rpm. O hidrolisado obtido foi fermentado pelas leveduras Saccharomyces cerevisiae PE-2 e Meyerozyma guilliermondii 311 (CCT7783), separadamente e em cultivo misto, averiguando a necessidade de suplementação do meio, para a produção de etanol. Os resultados mostraram a necessidade de suplementação para aumento da viabilidade das leveduras. Observou-se que a suplementação manteve a viabilidade acima de 90%. A fermentação com Meyerozyma guilliermondii 311 (CCT7783), sem a necessidade de suplementação, possibilitou a produção de 12,66% de etanol; com a Saccharomyces cerevisiae a produção de etanol foi de 7,03%, quando o meio foi suplementado com 3 g/L de extrato de levedura. A fermentação com cultura mista produziu 0,53% e 1,18% de etanol em 24 e 48 horas de cultivo, respectivamente. Para aplicação enzimática na hidrólise do lodo branco foram utilizadas amilase de Aspergillus carbonarius e celulase comercial. Os produtos de hidrólise enzimática do lodo branco detectados HPLC mostraram a formação de glicose, xilose e traços de maltose. A viabilidade celular da levedura Saccharomyces cerevisiae durante a fermentação se manteve bastante elevada, acima de 95 %. A fermentação do lodo branco, quando o meio foi suplementado com 3g/L de extrato de levedura, foi considerada satisfatória, com 2,37 g/L de etanol. Foram realizadas análise de superfície por ion-tof e microscopia eletrônica de varredura nos resíduos celulósicos. Desta maneira, com este trabalho foi possível estudar a importância da aplicação de enzimas fúngicas para degradação de biomassa lignocelulósica para produção de etanol de segunda geração. / As cellulosic wastes are rich in cellulose and hemicellulose they have been pointed as promising sources for ethanol production. Thereby, this work aimed to hydrolyze and ferment cellulosic residues to produce ethanol. In order to study the hydrolyzes of sugar-cane bagasse and ferment the sugars obtained from this process, twenty-two fungi were isolated in the city of Araras-SP and tested for endoglucanase (EG) production. Aiming to optmize an enzyme cocktail, variables as temperature, optimum pH, different buffers, stability, salt influence, EDTA and ?-mercaptoethanol were tested for laccase, xylanase, endo- ?-1,4-glucanase, cellobiohydrolase I, ?-glucosidase and glucoamylase. The standard conditions for applying the enzyme cocktail were 55°C, sodium citrate buffer 50 mM pH 5.0. For the preparation of the enzyme cocktail a Plackett-Burman was made followed by a central composite design, in which the standard conditions for application were (U/g of sugarcane bagasse): 0.122 of laccase; 7 of xylanase; 5 of endoglucanase; 14 of cellobiohydrolase and 9 of ?-glucosidase per gram of sugarcane bagasse. After 48 hours of hydrolyzes in the following conditions, 55ºC, sodium citrate buffer 50 mM (7 mL), pH 7.0, 110 rpm, 4.405 µmol of reducing sugar per mL were released. The hydrolyzate obtained was separately fermented by the yeasts Saccharomyces cerevisiae PE-2, Meyerozyma guilliermondii 311 (CCT7783) and with both yeasts in a mixed cultivation, in order to investigate the need of medium supplementation for ethanol production. The results showed the need of supplementation to increase the viability of the yeasts. It was observed that this procedure kept the viability over 90%. The fermentation with Meyerozyma guilliermondii 311 (CCT7783), without supplementation, allowed the production of 12.66% of ethanol and with Saccharomyces cerevisiae the production was 7.03% with a supplementation of 3 g/L of yeast extract. The fermentation with mixed cultivation produced 0.53% and 1.18% in 24 and 48 hours of cultivation, respectively. Another objective of this work was the hydrolysis of paper sludge which was obtained by using amylases from Aspergillus carbonarius and commercial cellulases. The products of enzymatic hydrolysis of the white sludge detected in HPLC showed the formation of glucose, xylose and maltose traits. Cell viability counting of the yeast, analyzes of pH, reducing sugar and alcohol content were carried out. Cellular viability of Saccharomyces cerevisiae along the fermentation was kept over 95%. Paper sludge fermentation using Saccharomyces cerevisiae, in medium supplemented with yeast extract 3 g/L, was considered satisfactory, showing 2.37 g/L of ethanol. Surface analysis was performed by Ion-tof and scanning electron microscopy in the cellulosic waste. Thus, this work made possible to study the importance of fungal enzymes application in lignocellulosic biomass degradation for the production of second generation ethanol.

Les cocktails enzymatiques tels que Rovabio® sont utilisés en nutrition animale comme complément alimentaire pour aider les animaux à mieux assimiler les fibres présentes dans leur ration alimentaire composée principalement de blé en Europe. Le mécanisme de déconstruction enzymatique du son de blé, partie du grain majoritairement composée de fibres, considérées comme difficilement hydrolysables et donc assimilables reste encore incompris, c’est pourquoi ces travaux de thèse s’appuient sur l’utilisation d’un bioréacteur instrumenté combinant des analyses physiques in-situ et biochimiques ex-situ afin d’avoir un point de vue global de ce phénomène. Cette approche multi-échelle est originale car rarement considérée en nutrition animale où les études in-vivo sont privilégiées. Cos travaux ont ainsi permis de mettre en évidence que l’action de Rovabio® se caractérise par une première phase de fragmentation notamment des grosses particules concomitante avec une forte solubilisation. La déconstruction du son de blé se poursuit ensuite par une fragmentation mais cette fois sans aucune solubilisation de polysaccharides. L’ajout d’une xylanase seule, en tant qu’enzyme la plus active du cocktail, solubilise la même quantité d’arabinoxylane mais ne permet pas une fragmentation importante des particules, contrairement au Rovabio®. Ces résultats confirment donc l’importance de la richesse et de la diversité d’un cocktail enzymatique pour déconstruire efficacement des structures aussi complexe que le son de blé. Cependant, en dépit de cela, seulement 37%w/w de matière sèche est solubilisée, même en excès de Rovabio®. Cette incapacité du cocktail enzymatique à dégrader complètement ces fibres semblerait provenir d’une inaccessibilité des enzymes à leur substrat. Nous avons ainsi montré que le rendement d’hydrolyse enzymatique est amélioré en augmentant la surface spécifique des particules (traitement mécanique) et/ ou en désorganisant l’architecture de la structure des fibres par l’ajout d’un complexe enzymatique particulièrement riche en pectinases. Néanmoins, si ces deux voies améliorent les performances du cocktail, elles ne permettent toujours pas une hydrolyse totale du son de blé. Finalement ce travail souligne l’intérêt d’enzymes ou de protéines actives capables d’attaquer les structures minoritaires du réseau lignocellulosique assurant sa résistance et sa cohésion, ce qui permet ainsi aux enzymes d’avoir un meilleur accès à leurs substrats. / Enzyme cocktails, such as Rovabio®, which is rich of hydrolytic enzymes are used as feed additives to favor degradation of non-starch polysaccharides present in wheat, a major feed in poultry industry. The deconstruction mechanism of wheat bran, part of the seed mainly composed of fiber, is still fairly unclear. This PhD aims to highlight these mechanisms using a multi-instrumented bioreactor that allowed to combine in-situ physical and ex-situ biochemical analyses. This multiscale approach stands as an alternative and original approach which is rarely considered in animal nutrition. This work highlights that Rovabio® action occurred in two concurrent process, namely fragmentation and solubilization phenomena which take place within the first 2 h after addition of the enzyme cocktail. It is then followed by a particle fragmentation which was not accompanied by any sugars solubilization. Thus, in spite of the abundant and very active hydrolytic enzyme activities in Rovabio®, the deconstruction of destarched wheat bran was however limited to 37% of w/w. At variance to Rovabio®, xylanase added alone was capable of solubilization activity (same final release of xylose and arabinose) but the fragmentation was much weaker by only disorganizing the fibrous network and hence led to particle disaggregation. Altogether, these results confirmed the importance of the enzyme mixtures which act in a synergistic manner to readily solubilize wheat bran. Our results also indicated that the limitation of Rovabio® action upon wheat bran degradation may come from physical inaccessibility of the substrate as it could be partially overcome by enhancing the substrate specific surface by a mechanical treatment and/or due to some missing or limiting enzyme activity as shown by a slight increase in solubilization following addition of some pectinases cocktails that are poorly represented in Rovabio®. Nevertheless, these complementary actions were still insufficient for complete hydrolysis of wheat bran. To conclude, this work draws attention to plant cell wall-deconstructing enzymes or active proteins which are able to attack the biomass minor structures and disorganize its network in order to increase substrate accessibility to enzymes that cleave backbone structures.

Ph. D. (Department of Biotechnology, Faculty of Applied and Computer Sciences), Vaal University of Technology. / Hydrocarbon pollution is becoming a growing environmental concern in South Africa and globally. This inadvertently supports the need to identify enzymes for their targeted degradation. The search for novel biocatalysts such as monooxygenases, alcohol dehydrogenases and aldehyde dehydrogenases, have relied on conventional culture-based techniques but this allows sourcing of the biomolecules from only 1-10 % of the microbial population leaving the majority of the biomolecules unaccounted for in 90-99 % of the microbial community. The implementation of a metagenomics approach, a culture-independent technique, ensures that more or less than 100 % of the microbial community is assessed. This increases the chance of finding novel enzymes with superior physico-chemical and catalytic traits. Hydrocarbon polluted soils present a rich environment with an adapted microbial diversity. It was thus extrapolated that it could be a potential source of novel monooxygenases, alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (ALDH) involved in hydrocarbon degradation pathways. Therefore, the aim of the study was to extract metagenomic DNA from hydrocarbon contaminated soils and construct a metagenomic fosmid library and screen the library for monooxygenases, alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (ALDH). Accordingly, the fosmid library was constructed from metagenome of hydrocarbon-contaminated soil. Then the library was functionally screened using hexadecane, octadecene and cyclohexane as substrates and fifteen positive clones were selected. The fosmid constructs of the positive clones were sequenced using PacBio next generation sequencing platform. The sequences were de novo assembled and analysed using CLC Genomic Workbench. The open reading frames (ORF) of the contigs were identified by blasting the contigs against uniport database. Accordingly, four novel genes namely amo-vut1, aol-vut3, dhy-sc-vut5 and dhy-g-vut7 that showed close similarity with our target enzymes were further analysed in silico and codon-optimized as per Escherichia coli codon preference. The codon adjusted sequences were synthesised and cloned into pET30a(+) expression vector. However, it is worth noting that expression of amo-vut1 was not successful since it was later identified to be a multi-pass member protein, which made it insoluble despite the use of detergent to the effect. There is a need to meticulously genetically engineer amo-vut1 to remove the signal and other membrane-bound peptides while maintaining its activity. Yet the other three constructs were successfully transformed and expressed in E. coli BL21 (DE3). The enzymes were purified and characterized and cocktail for hydrolysis of hexanol was succesfully engineered based on AOL-VUT3, DHY-SC-VUT5 and DHY-G-VUT7. Therefore, novel enzymes were mined from metagenome of fossil-oil contaminated soil and effective hydrocarbon-degrading enzyme cocktails containing their combination were successfully engineered.

La biomasse lignocellulosique comprend les sous-produits agricoles et industriels pouvant être utilisés comme matière première dans des bioprocédés variés destinés à produire des molécules d'intérêt énergétique ou chimique. Ces ressources lignocellulosiques, peuvent notamment être fournies par l'industrie papetière qui est particulièrement adaptée pour les bio-raffineries modernes car elle est en capacité de produire en grande quantité un substrat ayant une faible teneur en lignine et sans composés inhibiteurs. La bagasse de canne à sucre est également un substrat prometteur par sa composition chimique simple et son abondance dans les pays tropicaux. Lors de l'utilisation de ces substrats, l'hydrolyse enzymatique constitue une étape cruciale permettant la transformation des fibres de cellulose en une source de carbone fermentescible. Si les aspects biochimiques de cette étape d'hydrolyse font l'objet de nombreuses recherches et de développements, les réactions sous haute teneur en matière sèche font apparaître des limitations physiques qui sont beaucoup moins étudiées et analysées mais constituent des verrous scientifiques et technologiques qui freinent actuellement l'utilisation de cette ressource abondante et durable. Ce travail s'inscrit dans ce contexte et propose l'étude de cette étape d'hydrolyse enzymatique de la lignocellulose en s'intéressant conjointement aux aspects biochimiques et physiques de façon à aller vers une compréhension et une maîtrise des transferts (de masse, de chaleur) dans les réactions à forte concentration en substrat. La stratégie adoptée a consisté à réaliser et analyser des réactions d'hydrolyse sous différentes conditions opératoires en travaillant dans un premier temps sur des concentrations intermédiaires (suspension semi-diluée), c'est-à-dire en introduisant, mais de façon limitée, les complexités dues aux interactions entre particules/fibres de lignocellulose. Les résultats obtenus sont ensuite utilisés pour élaborer une stratégie adaptée aux fortes concentrations. Les aspects physiques analysés sont essentiellement le comportement rhéologique du milieu réactionnel ainsi que la morpho-granulométrie des objets en suspension. Différentes métrologies, tant in-situ que ex-situ, ont été mises en œuvre et apportent des résultats complémentaires. Les études ont été menées sur un substrat de référence, le papier Whatman, et deux substrats à vocation industrielle: la pâte à papier et la bagasse de canne à sucre. La stratégie d'étude porte sur les aspects suivants: (i) le suivi de l'évolution des comportements rhéologiques et des propriétés morphologiques des suspensions au cours de l'hydrolyse, (ii) l'étude des mécanismes d'hydrolyse lors de la dégradation des substrats, (iii) l'étude de l'impact de la composition et de la structure des substrats sur les cinétiques de solubilisation et d'hydrolyse, (iv) la quantification de la contribution des différentes activités enzymatiques, seules ou en mélange par une approche physique multi-échelle et (v) le contrôle et l'optimisation des conditions d'alimentation dans un procédé discontinu alimenté (fed-batch) afin d'atteindre des conditions de milieu concentré. Les chapitres 1 et 2 de ce document sont consacrés à une étude bibliographique du sujet et à la présentation des matériels et méthodes mis en œuvre. Le troisième chapitre présente les résultats obtenus et leur analyse. Il est constitué de trois sections: tout d'abord une étude des propriétés des différents enzymes ou cocktail d'enzymes utilisés, des substrats retenus et des suspensions avec, notamment, la détermination des régimes semi-dilués et concentrés. Ensuite sont présentées et analysées les hydrolyses effectuées en milieu semi-dilué. Les mécanismes d'hydrolyse (fragmentation, solubilisation, hydratation et séparation des agglomérats) sont étudiés pour diverses concentrations et divers enzymes/cocktails. Enfin les résultats en milieu concentré sont présentés dans une dernière section. / Lignocellulosic biomass consists of several agriculture and industrial by-products that can be used as raw material for several bioprocesses to obtain range of products. Among lignocellulosic sources, the pulp & paper industry is appropriated for modern bio-refining thank to pulp with low lignin content and free of inhibitory compounds. Besides, sugarcane bagasse is a very promising feedstock because of its simple chemical composition and its abundancy especially in tropical countries. In the bioconversion of lignocellulose, enzymatic hydrolysis is a crucial step that allows the transformation of cellulosic and hemicellulosic fibers into fermentable carbon sources. The lack of knowledge about physical limitations and hydrolysis mechanisms, especially at high dry matter content, stands as the main barrier which forbids the scale-up of bio-refinery processes. Thus, the efficient and sustainable use of lignocellulosic resources is currently a major challenge and need to be investigated. In this context, this PhD focused on the enzymatic hydrolysis of lignocellulose by both physical and biochemical approaches. The strategy consisted in carrying out and in analyzing the hydrolysis reactions under different operating conditions with semi-dilute suspensions. Then, obtained results were used to develop a hydrolysis strategy for concentrated suspensions. Different methodologies, in- and ex-situ analyses, were implemented and provided complementary results. From physical approach, analyses consisted in rheological behavior of suspensions as well as the morpho-granulometry of particles. The study was carried out on a reference substrate, Whatman paper, and on two industrial substrates, paper pulp and sugarcane bagasse. The strategy aimed to investigate different stakes: (i) evolution of rheological behaviors and the morphological properties of suspensions, (ii) hydrolysis mechanisms during the degradation of substrates, (iii) impact of substrate composition and structure on solubilization and hydrolysis kinetics, (iv) quantification of the contribution of single enzyme and enzyme mixture activities by multi-scale physical approaches and (v) control and optimization of feeding parameters for fed-batch process in order to access to concentrated suspension. Chapters 1 and 2 of this document are devoted to a research bibliographic and presentation of materials and methods. The third chapter presents obtained results and discussion in three sections. The first one is a study of the properties of different enzymes and substrates, in particular, the determination of semi-dilute and concentrated regime. Subsequently the enzymatic hydrolysis at semi-dilute regime is presented to highlight the hydrolysis mechanisms (fragmentation, solubilization, solvation and agglomerate separation) in relationship with enzyme mixtures and dosages. Finally, results in concentrated regime are discussed in the final section.