A digestão anaeróbia termofílica é uma opção vantajosa para efluentes descartados a altas temperaturas, além de estimular rotas mais eficientes de produção de H2. No entanto, os resultados da literatura divergem bastante, os rendimentos de H2 são inferiores ao valor teórico possível e poucos estudos avaliaram diferentes configurações para indicar a mais eficiente. Assim, este estudo avaliou a produção de H2 a partir da sacarose em três tipos de reator: reator anaeróbio de fluxo ascendente e manta de lodo (UASB), reator tubular de fluxo ascendente com leito empacotado (TCS) e sem material suporte (TSS), operados a 55°C. Os tempos de detenção hidráulica (TDH) aplicados ao reator UASB foram 12, 6 e 2 h e aos reatores TCS e TSS foram 2 e 0,5 h. Pré-tratamento térmico (100°C por 15 min) foi aplicado ao inóculo metanogênico do UASB e TCS e TSS foram auto inoculados. O efeito de nutrientes e a concentração nutricional ótima para a produção de H2 foram investigados através de ensaios em batelada. Com TDH de 2 h, o material suporte afetou a transferência de massa, resultando em menor teor de H2 no biogás quando presente, porém, maior conversão de sacarose e produção de H2. O pré-tratamento térmico não inibiu a metanogênese, sendo as condições operacionais mais importantes para a seleção dos microrganismos. TCS e TSS com TDH de 0,5 h apresentaram produção de H2 similar e o material suporte afetou apenas as rotas metabólicas. Entre todas as operações, TCS e UASB com TDH de 2 h alcançaram os maiores valores de rendimento de H2 (YH2), respectivamente, 1,99 ± 0,36 e 2,56 ± 0,84 molH2.mol-sac-1, através da via metabólica do etanol. TCS2 também demonstrou estabilidade e, apesar de o U2 ter gerado maiores porcentagens de H2 no biogás, pode ser apontado como o mais eficiente para a produção de H2. A relação C:N:P, Fe+2 e Ni+2 tiveram efeito significativo sobre a produção de H2, e YH2 ótimo foi estimado para concentrações de 4,53 mgFe+2.L-1 e 0,045 mgNi+2.L-1. / The thermophilic anaerobic digestion is a suitable option for wastewater discharged at high temperatures; in addition, it is suitable for more efficient pathways for H2 production. However, the results found in literature have divergences; the H2 yields are lower than the theoretical possible value and only few studies evaluated different types of reactors and defined the more advantageous one. Therefore, this study evaluated H2 production from sucrose in three types of reactor: upflow anaerobic sludge blanket (UASB), upflow tubular reactor with packed-bed (TCS) and without support materials (TSS), operated at 55°C. The hydraulic retention time (HRT) applied to UASB reactor was 12, 6 and 2h and to TCS and TSS was 2 and 0.5h.Thermal pretreatment (at 100°C, for 15 min) was applied to the methanogenic inoculum of UASB and TCS and TSS was inoculated through natural fermentation process. The effect of nutrients and the optimal concentration of t nutrients for H2 production were evaluated through batch assays. At HRT of 2h, the support material affected the mass transferring, leading to lower content of H2 in the biogas when it is used; however, in this condition it was found higher sucrose conversion and H2 production. The operational conditions showed to be more efficient for methanogenesis than pretreatment. TCS and TSS at HRT of 0.5h presented similar H2 production and the support material affected only the metabolic pathways. Among all the conditions assessed, TCS and UASB at HRT of 2h reached the highest values of H2 yield highest YH2, respectively, 1.99 ± 0.36 and 2.56 ± 0.84 molH2.mol-sac-1, through ethanol pathway. TCS2 demonstrated stability production also and, despite the U2 have achieved higher percentage of H2 in biogas, it can be pointed out as more efficient for H2 production. The ratio C:N:P, Fe+2 and Ni+2 showed significant effect on H2 production, and the optimal YH2 was estimated for 4.53 mgFe+2.L-1 e 0.045 mgNi+2.L-1.

A digestão anaeróbia termofílica é uma opção vantajosa para efluentes descartados a altas temperaturas, além de estimular rotas mais eficientes de produção de H2. No entanto, os resultados da literatura divergem bastante, os rendimentos de H2 são inferiores ao valor teórico possível e poucos estudos avaliaram diferentes configurações para indicar a mais eficiente. Assim, este estudo avaliou a produção de H2 a partir da sacarose em três tipos de reator: reator anaeróbio de fluxo ascendente e manta de lodo (UASB), reator tubular de fluxo ascendente com leito empacotado (TCS) e sem material suporte (TSS), operados a 55°C. Os tempos de detenção hidráulica (TDH) aplicados ao reator UASB foram 12, 6 e 2 h e aos reatores TCS e TSS foram 2 e 0,5 h. Pré-tratamento térmico (100°C por 15 min) foi aplicado ao inóculo metanogênico do UASB e TCS e TSS foram auto inoculados. O efeito de nutrientes e a concentração nutricional ótima para a produção de H2 foram investigados através de ensaios em batelada. Com TDH de 2 h, o material suporte afetou a transferência de massa, resultando em menor teor de H2 no biogás quando presente, porém, maior conversão de sacarose e produção de H2. O pré-tratamento térmico não inibiu a metanogênese, sendo as condições operacionais mais importantes para a seleção dos microrganismos. TCS e TSS com TDH de 0,5 h apresentaram produção de H2 similar e o material suporte afetou apenas as rotas metabólicas. Entre todas as operações, TCS e UASB com TDH de 2 h alcançaram os maiores valores de rendimento de H2 (YH2), respectivamente, 1,99 ± 0,36 e 2,56 ± 0,84 molH2.mol-sac-1, através da via metabólica do etanol. TCS2 também demonstrou estabilidade e, apesar de o U2 ter gerado maiores porcentagens de H2 no biogás, pode ser apontado como o mais eficiente para a produção de H2. A relação C:N:P, Fe+2 e Ni+2 tiveram efeito significativo sobre a produção de H2, e YH2 ótimo foi estimado para concentrações de 4,53 mgFe+2.L-1 e 0,045 mgNi+2.L-1. / The thermophilic anaerobic digestion is a suitable option for wastewater discharged at high temperatures; in addition, it is suitable for more efficient pathways for H2 production. However, the results found in literature have divergences; the H2 yields are lower than the theoretical possible value and only few studies evaluated different types of reactors and defined the more advantageous one. Therefore, this study evaluated H2 production from sucrose in three types of reactor: upflow anaerobic sludge blanket (UASB), upflow tubular reactor with packed-bed (TCS) and without support materials (TSS), operated at 55°C. The hydraulic retention time (HRT) applied to UASB reactor was 12, 6 and 2h and to TCS and TSS was 2 and 0.5h.Thermal pretreatment (at 100°C, for 15 min) was applied to the methanogenic inoculum of UASB and TCS and TSS was inoculated through natural fermentation process. The effect of nutrients and the optimal concentration of t nutrients for H2 production were evaluated through batch assays. At HRT of 2h, the support material affected the mass transferring, leading to lower content of H2 in the biogas when it is used; however, in this condition it was found higher sucrose conversion and H2 production. The operational conditions showed to be more efficient for methanogenesis than pretreatment. TCS and TSS at HRT of 0.5h presented similar H2 production and the support material affected only the metabolic pathways. Among all the conditions assessed, TCS and UASB at HRT of 2h reached the highest values of H2 yield highest YH2, respectively, 1.99 ± 0.36 and 2.56 ± 0.84 molH2.mol-sac-1, through ethanol pathway. TCS2 demonstrated stability production also and, despite the U2 have achieved higher percentage of H2 in biogas, it can be pointed out as more efficient for H2 production. The ratio C:N:P, Fe+2 and Ni+2 showed significant effect on H2 production, and the optimal YH2 was estimated for 4.53 mgFe+2.L-1 e 0.045 mgNi+2.L-1.

Genome-scale modeling and new strategies for constraining these models were applied in this research to find new insights into cellular metabolism and identify potential metabolic engineering strategies. A newly updated genome-scale model for Clostridium acetobutylicum, iMM864, was constructed, largely based on the previously published iRS552 model. The new model was built using a newly developed genome-scale model database, and updates were derived from new insights into clostridial metabolism. Novel methods of proton-balancing and setting flux (defined as reaction rate (mmol/g biomass/hr)) ratio constraints were applied to create simulations made with the iMM864 model approximate observed experimental results. It was determined that the following constraints must be applied to properly model C. acetobutylicum metabolism: (1) proton-balancing, (2) constraining the specific proton flux (SPF), and (3) installing proper flux ratio constraints. Simulations indicate that the metabolic shift into solventogenesis is not due to optimizing growth at different pH conditions. However, they provide evidence that C. acetobutylicum has developed strictly genetically regulated solventogenic metabolic pathways for the purpose of increasing its surrounding pH to decrease the toxic effects of high proton concentrations. Applying a ratio constraint for the P/O ratio (a measure of aerobic respiratory efficiency) to the iAF1260 genome-scale model of E. coli K12 MG1655 was explored. Relationships were found between: (1) the P/O ratio, (2) the SPF, (3) the growth rate, and (4) the production of acetate. As was expected, higher acetate production correlates with lower P/O ratios, while higher growth correlates with higher P/O ratios. For the first time, a genome-scale model was able to quantify this relationship and targeting both the P/O ratio and the SFP is required to produce an E. coli K12 strain with either (i) maximized growth rate (and minimized acetate production) or (ii) maximized acetate production (at the expense of cell growth). A gene knockout mutant, Î ndh, was created with E. coli BL-21 to study the effects of forcibly higher P/O ratios on growth. The results suggest that a metabolic bottleneck lies with the NADH-1 complex, the NADH dehydrogenase that contributes to the generation of a proton motive force. / Master of Science

Le phosphore est un élément crucial pour la vie sur Terre, de par son implication dans les processus bioénergétiques, le stockage et le traitement de l'information génétique. C'est également l'un des nutriments limitants en agriculture, aux côtés de l'azote et du potassium. Depuis la révolution verte au milieu du 20ième siècle, le monde agricole est dépendant des engrais phosphorés à bas coûts, fabriqués à partir d'une ressource fossile et nécessaires à l'amélioration des rendements des cultures à même de répondre aux besoins en nourriture d'une population en forte croissance. Cependant cette ressource, la roche phosphatée, s'épuise progressivement. De plus, son utilisation est très peu efficiente : moins de 20% du phosphore extrait se retrouve effectivement dans la nourriture consommée. L'une des raisons de cette faible efficience est la spécialisation de régions entières dans des productions agricoles spécifiques. Ainsi, les régions spécialisées dans les cultures à hauts rendements ont besoin de grandes quantités d'engrais minéraux alors que les régions d'élevage intensif ont des excédents de lisier sans terres agricoles suffisamment grandes et proches pour servir de zones d'épandage. L'épandage excessif de lisier en Bretagne est la cause première d'eutrophisation des cours d'eau. Le phosphore contenu dans le lisier porcin pourrait être recyclé sous forme de struvite (MgNH4PO4,6H2O), un engrais phosphaté à dissolution lente, très concentré et facilement transportable vers les régions de cultures végétales nécessitant une fertilisation phosphatée importante. Le phosphore du lisier porcin étant initialement présent sous une forme minérale solide, il est nécessaire de le dissoudre avant de le précipiter en struvite. Parce-que la dissolution par acidification chimique est trop chère et implique un mauvais bilan environnemental, le procédé développé lors de cette thèse utilise l'acidogénèse, un procédé biologique au cours duquel la matière organique est convertie en acides organiques en absence d'oxygène, acidifiant naturellement le lisier porcin. Différents déchets organiques ont été testés en tant que co-substrats dans du lisier porcin brut ou digéré, provoquant une fermentation de type lactique lorsque le co-substrat possédait une forte teneur en glucides facilement biodégradables, et une fermentation avec de nombreux acides organiques produits lorsque la teneur en glucides facilement biodégradables était faible. Il a pu être démontré que la fermentation lactique était le fait de bactéries appartenant au genre Lactobacillus, alors que divers Clostridiales dominaient lors des autres fermentations avec la production d'acétate, propionate, butyrate et valérate. Un réacteur en semi continu alimenté d'un mélange de lisier brut de petit pois et de carottes a permis la dissolution de 50% du phosphore total soit 750 mg-P/L. Après centrifugation, 3.4 g d'hydroxyde de magnésium par litre de surnageant a été ajouté afin d'élever le pH à 8 et ainsi précipiter la struvite. 99% du phosphore dissous a alors été abattu. Le solide obtenu contenait 70% de struvite, un léger excès de phosphore et de magnésium, ainsi que de la matière organique. L'acidogénèse permet l'hydrolyse de la matière organique complexe et la formation d'acides organiques. De ce fait, ce procédé de recyclage du phosphore contenu dans le lisier porcin pourrait être implémenté dans les nombreuses unités de méthanisation présentes en Bretagne et qui traitent des effluents animaux ainsi que des déchets organiques d'origine agricole, industrielle et municipale. La struvite obtenue pourrait être vendue dans les régions ayant besoin de fertilisation phosphatée alors que la matière organique du digestat pourrait être maintenue en Bretagne. Un tel procédé réduirait significativement l'eutrophisation due à l'épandage excessif du lisier tout en diminuant les besoins en fertilisants minéraux fossiles grâce à une source alternative aux performances fertilisantes équivalentes. / Phosphorus is a crucial nutrient for life, implicated in cellular bioenergetics as well as storage and processing of genetic information. It is also one of the limiting nutrients in agriculture with nitrogen and potassium. Since the green revolution in the middle of the 20th century, agriculture has relied on increasing amounts of cheap mineral P-fertilizers produced from a fossil resource to improve crop yields and sustain population growth. However, the resource is depleting and its use efficiency is poor: less than 20% of extracted P is actually consumed in food. One of the reasons for this is the specialization of entire regions into on type of agricultural production or another. Thus, regions focusing on high yield crops require large applications of fossil mineral fertilizers while intensive livestock breeding areas cannot find an output for their P-rich manure due to the distance with crop fields in need of P fertilization. Over application of animal manure in Brittany is the main cause of eutrophication in the region. Phosphorus could be recovered from pig manure as struvite, a concentrated, slow-release mineral fertilizer easily transported to crop-oriented regions in need of P fertilization. P in pig slurry is mostly under a solid inorganic form, requiring dissolution prior to precipitation as struvite. Because chemical acidification is too expensive and harmful to the environment, the process developed in this PhD relied on acidogenesis, a biological process in which organic matter is converted to organic acids under anaerobic conditions, thus naturally acidifying the swine slurry. Various organic wastes were tested as organic co-substrates on raw and digested pig slurry, leading to lactic acid fermentation when the co-substrate had a high content in easily biodegradable carbohydrates and a fermentation with diverse organic acids produced at low content in easily biodegradable carbohydrates. Lactobacillus was the genus responsible for lactic acid fermentation and various Clostridiales dominated otherwise, producing acetate, propionate, butyrate and valerate. A reactor was operated with semi-continuous feeding of raw swine slurry and carrot/pea, leading to the dissolution of 50% total-phosphorus or 750 mg-P/L. After centrifugation, struvite was precipitated in the supernatant by adding magnesium hydroxide to increase the pH to 8. 99% of dissolved P precipitated. The solid recovered contained 70% of struvite, a slight excess of P and Mg as well as organic matter. Because hydrolysis of organic matter and production of organic acids occurs during acidogenesis, the process could be implemented in the many anaerobic digestion units installed in Brittany treating animal manure and agricultural, industrial and municipal organic waste. The struvite recovered could be sold to regions in need while the digestate impoverished in P and rich in organic matter could be kept locally. Such process would reduce eutrophication due to over application of pig manure and also reduce the reliance on fossil P fertilizer by offering an alternative source with equivalent fertilizing performances.

The objective of this study is to illustrate that phase separation improves the efficiency of an anaerobic system which digests semi-solid organic wastes. Organic fraction of municipal solid waste (OFMSW) was the semi-solid organic waste investigated. In the first part of the study, the optimum operational conditions for acidified reactor were determined by considering the volatile solid (VS) reductions and average acidification percentages at the end of two experimental sets conducted. Organic loading rate (OLR) of 15 g VS/L.day, pH value of 5.5 and hydraulic retention time (HRT) of 2 days were determined to be the optimum operational conditions for the acidification step. Maximum total volatile fatty acid and average acidification percentage were determined as 12405 mg as HAc/L and 28%, respectively in the reactor operated at optimum conditions. In the second part, an acidification reactor was operated at the optimum conditions determined in the first part. The effluents taken from this reactor as well as the waste stock used to feed this reactor were used as substrate in the biochemical methane potential (BMP) test. The results of BMP test revealed that the reactors fed by acidified samples indicated higher total chemical oxygen demand (tCOD) removals (39%), VS reductions (67%) and cumulative gas productions (265 mL). The result of this study indicated that the separation of the reactors could lead efficiency enhancement in the systems providing that effective control was achieved on acidified reactors.

Ce travail de thèse a eu pour objectif principal l'étude thermodynamique des changements métaboliques dans l'acidogénèse. L'acidogénèse est un procédé anaérobie à double intérêt qui en traitant des résidus organiques, permet de produire des composés chimiques comme l'hydrogène, l'éthanol et les acides organiques. Par conséquent, l'acidogénèse se place comme un procédé biotechnologique dans le concept de bioraffinerie. En outre, ce processus n'a pas besoin de conditions stériles d'opération et fonctionne sur une large gamme de pH. Ces changements métaboliques sont dépendants des modifications dans les conditions opératoires. Afin d'étudier ces changements métaboliques, des expériences basées sur des modifications du ciel gazeux du réacteur par introduction d'azote et sur des changements du pH, ont été menées. Un des résultats les plus intéressants a été l'augmentation du rendement de production d'hydrogène de 1 à 3,2 molH2/molglucose à pH 4,5 et débit de N2 de 58,4 L/d. Ce rendement est proche de la valeur théorique (4 molH2/molglucose). L'étude thermodynamique a permis d'expliquer les mécanismes métaboliques concernant l'hydrogène, dont la production importante, représentée par le rendement de 3,2 molH2/molglucose, est due à la réaction inverse H2/NAD+, qui est thermodynamiquement faisable à faibles pressions partielles d'hydrogène (par exemple 0,02 bar). En outre, les bas rendements en hydrogène ont été expliqués par l'action consommatrice d'hydrogène par la réaction d'homoacetogénèse. Cependant, le modèle n'a pas été capable d'expliquer les changements métaboliques de l'acétate, du butyrate et de l'éthanol lors de la fermentation acidogénique du glucose. / This thesis deals with thermodynamic based modelling of metabolic shifts during acidogenic fermentation. Acidogenic fermentation is an anaerobic process of double purpose: while treating organic residues, it produces chemical compounds, such as hydrogen, ethanol and organic acids. Therefore, acidogenic fermentation arises as an attractive biotechnology process towards the biorefinery concept. Moreover, this process does not need sterile operating conditions and works under a wide range of pH.Changes of operating conditions produce metabolic shifts, inducing variability on acidogenic product yields. In order to study these metabolic shifts, an experiment design was based on reactor headspace N2-flushing (gas phase) and pH step changes (liquid phase). A major result was the hydrogen yield increase from 1 to 3.2 (molH2/molglucose) at pH 4.5 and N2-flushing of 58.4 L/d. This yield is close to the theoretical acidogenic value (4 molH2/molglucose).The thermodynamic model, based on the assumption that acidogenic fermentation is characterised by limited energy available for biological process, allowed to explain the mechanisms that govern hydrogen metabolic shifts, showing that the synthesis of extra hydrogen, i.e. yield of 3.2 (molH2/molglucose), was due to reverse H2/NAD+ redox reaction, which is thermodynamically feasible at low hydrogen partial pressures (e.g. 0.02 bar). Moreover, low hydrogen yields were explained by the action of homoacetogenesis hydrogen consuming reaction. However, the model was not capable to explain the metabolic shifts of acetate, butyrate and ethanol on acidogenic glucose fermentation.