A indústria sucroalcooleira nacional, fruto da política de autonomia energética da década de 70, busca no aumento de portifólio produtivo a melhora da eficiência produtiva e energética. A produção de hidrogênio e metabólitos dissolvidos por processo biológico é uma linha de pesquisa relativamente recente, porém, que pode representar uma alternativa para esse setor, maximizando a produção de energia e ampliando a produção de compostos de alto valor agregado. Partindo destes preceitos, o objetivo deste trabalho foi avaliar a produção de hidrogênio e ácidos orgânicos por meio da fermentação escura a partir de compostos da indústria sucroalcooleira; sacarose (RS), caldo (RC), melaço (RM) e vinhaça (RV) a 5.000 mg DQO L-1, em reatores anaeróbios de leito fluidificado termofílicos (55°C), submetidos a tempos de detenção hidráulica (TDH) de 8, 6, 4, 2 e 1h. O inóculo utilizado foi obtido a partir de lodo de reator de manta de lodo metanogênico empregado na biodigestão de vinhaça de cana-de-açúcar em faixa termofílica de temperatura (55°C). As produtividades volumétricas de hidrogênio (PVH) mais elevadas foram obtidas quando em operação em TDH de 1h, sendo 194,9; 501,4; 303,4 e 40,7 mL H2 h-1 L-1 para RS, RC, RM e RV, respectivamente. Os melhores rendimentos de hidrogênio (HY) foram logrados em distintos TDH; 1,97; 3,01; 2,5 e 0,65 mol H2 mol- 1 sacarose quando RS, RC, RM e RV foram operados em 4, 6, 2 e 1h, respectivamente. Na fase de maior PVH, os metabólitos dissolvidos predominantes resumiram-se a ácido lático, ácido acético, ácido butírico, ácido propiônico, ácido málico e etanol, condicionados ao substrato empregado em cada reator. Assim, evidenciou-se a possibilidade de produção de hidrogênio, ácidos orgânicos e etanol por meio da fermentação escura aplicada aos substratos desta indústria, confirmando que a produção de energia e produtos de elevado valor agregado pode ser uma aplicação alternativa para seus compostos. / The national sugarcane industry, coming from the energy policy autonomy of the 70s, seeks increase its portfolio productive improvement of productive and energy efficiency. Hydrogen and dissolved metabolites production by biological process is a relatively recent research line, however it, may represent an alternative for this sector, maximizing energy production and increasing the value-added compounds production. Based on these principles, the aim of this study was to evaluate the hydrogen and dissolved metabolites production by means of the dark fermentation from compounds of the sugarcane industry; sucrose (RS), sugarcane juice (RC), molasses (RM) and vinasse (RV) with 5,000 mg COD L- 1in thermophilic anaerobic fluidized bed reactor (55°C) submitted to hydraulic retention time (HRT) of 8, 6, 4, 2, and 1h. The inoculum was obtained from methanogenic upflow anaerobic sludge blanket reactor employed to digestion of sugarcane stillage in thermophilic temperature range (55°C). The highest hydrogen production rates (HPR) of these reactors were obtained when operating in HRT 1h, which were 194.9, 501.4, 303.4, and 40.7 mL H2 h-1 L-1 to RS, RC , RM, and RV respectively. The best hydrogen yield (HY) were duped in differents HRT; 1.97, 3.01, 0.65, and 2.5 mol H2 mol-1 sacarose when RS, RC , RM, and RV were operated in 4, 6, 2, and 1h , respectively. When were produced the biggest HPR, the predominant dissolved metabolites were lactic acid, acetic acid, butyric acid, propionic acid, malic acid and ethanol, dependent on the substrate used in each reactor. Therefore, evidence of the possibility of hydrogen, organic acids and ethanol production by dark fermentation applied to substrates that industry, confirming that the production of energy and high value-added products may be an alternative application for their compounds.

Um reator anaeróbio com biomassa imobilizada operado em bateladas sequenciais com recirculação da fase liquida (AnSBBR) foi aplicado à produção de biohidrogênio. Foram tratados 1.9 L de meio por ciclo, analisando a influência da variação da carga orgânica volumétrica (COAV) através da variação da concentração do afluente sintético a base de sacarose. A concentração afluente variou entre 3600 e 5400 mgDQO/L e os tempos de ciclo de 4, 3 e 2 horas obtendo, dessa maneira, as cargas orgânicas volumétricas de 9, 12, 13,5, 18 e 27 gDQO/L. O sistema foi inoculado com lodo proveniente de um UASB aplicado ao tratamento de águas residuárias de abatedouro de aves. Foram utilizados diferentes indicadores de rendimento para averiguar a estabilidade e o efeito da carga orgânica aplicada ao sistema sobre a produção de biohidrogênio. Os indicadores utilizados tiveram como base a quantidade de mols de \'H IND.2\' produzidos por dia em relação à massa de sólidos voláteis no interior do reator e às cargas orgânicas aplica e removida, tanto em termos de matéria orgânica (DQO) quanto de carboidratos (sacarose) aplicados. Os resultados mostraram estabilidade do sistema na produção de biohidrogênio e consumo de substrato. Em todas condições experimentais, em termos de cargas orgânicas aplicada e removida obteve-se comportamento análogo com uma redução deste indicador em função do aumento da carga orgânica. O melhor rendimento obtido foi de 4,16 mol-\'H IND.2\'/kg-SAC.d para a carga orgânica de 9 gDQO/L.d (concentração afluente de 3600 mgDQO/L e tempo de ciclo de 4 h), sendo a composição de \'H IND.2\' no biogás de 36% (64% de \'CO IND.2\' e 0% de \'CH IND.4\'). Os compostos metabólitos presentes de modo mais significativo foram o etanol, ácido acético e ácido butírico. A morfologia da microbiologia no interior do reator não apresentou variações significativas entre as diferentes condições experimentais, sendo composta por bacilos, endósporos e filamentos. / A reactor with immobilized biomass anaerobic sequencing batch operated with recirculation of the liquid phase (AnSBBR) was applied to the production of biohydrogen. The influence of the applied volumetric organic load was studied by varying the concentration of influent 3600 e 5400 mgDQO/L and cycle times of 4, 3 and 2 hours getting this way, the volumetric organic loads of 9, 12, 13.5, 18 and 27 gDQO/L. The system was inoculated with sludge from a UASB applied to the treatment of wastewater from poultry slaughterhouse. Different performance indicators were used to ascertain the stability and the effect of the organic load applied to the system on the production of biohydrogen. The indicators used were based on the number of moles of \'H IND.2\' produced per day on the mass of volatile solids inside the reactor and the organic loads applied and removed, both in terms of organic matter (COD) and carbohydrate (sucrose) applied. The results showed system stability in the production of bio-hydrogen and substrate consumption. In all experimental conditions in terms of organic loads applied and removed analogous behavior was obtained a reduction of the indicator as a function of the increase in organic load. The best yield was 4.16 mol-\'H IND.2\'/kg-SAC.d for the organic load of 9 gDQO/L.d (influent concentration of 3600 mgDQO/L and time cycle of 4 h), and the composition of \'H IND.2\' in the biogas 36% (64% 0% \'CO IND.2\' and \'CH IND.4\'). The compounds metabolites present more significantly were ethanol, acetic acid and butyric acid. The morphology of microbiology within the reactor showed no significant variations between different experimental conditions, consisting of bacilli, and filaments endospores.

O uso intensificado de combustíveis fósseis como fonte de energia, vê-se a necessidade do desenvolvimento de novas tecnologias, principalmente as renováveis, como o hidrogênio, que possui vantagens por ser elemento abundante no universo, ser renovável e não poluente. A utilização de microalgas e cianobactérias é uma alternativa para a produção de biohidrogênio a partir da quebra da água e de compostos orgânicos. De acordo com isso, nesta pesquisa foram testados diversos fatores físico-químicos e nutricionais nas condições de cultivo de cepas de Chlamydomonas spp. e Anabaena spp. Para tanto, cepas selecionadas foram cultivadas em duas fases experimentais, a primeira aeróbia e a segunda anaeróbia, para proporcionar produção de hidrogênio por biofotólise direta anaeróbia, via hidrogenase, sob privação de enxofre para a clorofícea, e de nitrogênio para a cianobactéria, estimulando para esta também a produção por biofotólise indireta, via nitrogenase. A cepa com melhor produtividade de hidrogênio, de cada gênero, foi selecionada para a etapa de otimização das fases experimentais de cultivo. Durante os ensaios foram realizadas análises de produção máxima, velocidade de produção, volume e produtividade de hidrogênio, além de análises de concentração de biomassa, físico-químicas, bioquímicas e geração de subprodutos. O método utilizado foi eficiente para produção de hidrogênio e ficou comprovada a diferença de produção de hidrogênio entre diferentes cepas. Anabaena sp. obteve produtividade média de hidrogênio quatro vezes maior, aproximadamente de 76,8 µmol.L-1.h-1, comparada a C. reinhardtii, com média de 18,6 µmol.L-1.h-1. / The intensifying use of fossil fuels as energy source, one sees the need to develop new technologies, especially renewable, such as hydrogen. This has advantages because hydrogen is an abundant element in the universe, be renewable and non-polluting. The use of microalgae and cyanobacteria is an alternative for the production of bio-hydrogen of breaking water and organic compounds. Accordingly, in this study were tested several physic-chemical factors and nutrition in growing conditions of Chlamydomonas spp. and Anabaena spp. strains. For this purpose, strains selected were cultured in two experimental phases, first aerobic and second anaerobic, to hydrogen production by direct biofotolise anaerobic, via hydrogenase, under sulfur deprived to chlorofycea, and nitrogen to cyanobacterium, for this also to production by indirect biofotolise, via nitrogenase. The strain with highest productivity of hydrogen, of each gender, was selected for the optimization of the experimental stages of cultivation. During the tests were analyzes of maximum production, velocity, volume and productivity of hydrogen, and analysis of biomass concentration, physic-chemical, biochemical and generation of by-products. The method used was efficient for the production of hydrogen and was different between strains. Anabaena sp. obtained average yield four times highest, approximately 76.8 µmol. L-1.h-1compared to C. reinhardtii, averaging 18.6 µmol. L-1.h-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.

This work focused a pH readjustment strategy has been applied for the enhancement ofbiohydrogen production form food waste hydrolysate in a semi-pilot scale bioreactor seededwith selectively enriched mixed microbial culture. Different initial pH (pH 6, pH 7, and pH8) was selected for biohydrogen production from FW. When hydrogen production was terminated due to the accumulation of volatile fatty acids in the bioreactor, then the pHof the bioreactor was again readjusted to its initial pH. Highest hydrogen production rate of1.13 L/h (CHP: 58.48 L) was achieved with pH 8 operation which was almost double thanpH 6 and pH 7 operation. Volatile fatty acids (VFA) production was also influenced by thisstrategy. Higher acetic and butyric acids (2471.4mg/L and 947.37mg/L) were observed. Highest buffering capacity (0.1ßmol) significantly contributed towards higher biohydrogenproduction via this pH adjustment strategy. This strategy not only enhanced H 2 productionbut it also increased the waste conversion efficiency towards other biobased productsproduction during acidogenesis of FW.

Hydrogen is re-emerging as a serious alternative to fossil fuels. It is a clean gas with high energy density and its combustion only generates water vapour. Nevertheless, the hydrogen industry has a significant carbon footprint since this gas is mostly derived from fossil fuels reforming processes. This project focusses on the development of sustainable alternatives to conventional hydrogen production, in which approaches based on dark fermentation (DF) using an inexpensive residue from the brewery industry as primary feedstock are presented. Firstly, a fungal pre-treatment (FT) was proposed to degrade a high-strength brewery waste slurry (BWS) to obtain an effluent with a lower concentration of chemical oxygen demand (COD) but rich in readily fermentable sugars for the ensuing DF, thus improving hydrogen yields (HY). Secondly, microbial electrolysis and fuel cells (MECs and MFCs) were proposed to assist DF, generating electricity in MFCs while improving HY by MECs. Coupling both microbial electrochemical technologies sequentially after DF did not show any advantage. However, promising results were obtained for electricity and hydrogen production when taking a single-staged approach. Treating BWS directly by MFCs produced 2.0 watts/g COD consumed, while the DF process assisted simultaneously by MECs (DF/MEC) produced 1.6 times more hydrogen than DF alone. An average HY of 2.32 ± 0.06 mol H₂/mol glucose was attained between both DF/MEC and DF after FT, hence approaching the theoretical value of 2.4 mol H₂/mol glucose, representing roughly a 50% improvement compared to DF alone. With an overall COD reduction above 76%, the DF after FT exhibited the highest energy conversion rate per substrate consumed (6.3 kJ/g COD). As valuable by-products obtained, up to 31 g/L of fungal biomass, which is appreciated in many state-of-the-art biomaterials applications, was produced by using BWS. While in the DF/MEC process, 18 g/L of butyric acid were generated, which is three times more than with DF alone. Butyric acid being the precursor to butanol and building block of biodegradable thermoplastics, this result is not without significance. The proposed approaches not only valorize BWS but also validate their economic and environmental attractiveness as promising alternative hydrogen production methods.

In order to meet the energy needs of a growing world in a sustainable manner, new high efficiency, carbon-neutral fuels and chemical feedstocks are required. An emerging approach that shows promise for high efficiency production of renewable fuels and chemicals is the use of purified enzymes combined in one pot to catalyze complex conversions: synthetic pathway biotransformations (SyPaB). An exemplary technology in this burgeoning field is the production of hydrogen from biomass sugars. Lignocellulosic biomass, which includes agricultural residues, energy crops, and industrial waste streams, is an ideal substrate for SyPaB conversion, as it is abundant and cheap, second only to untaxed coal on a $/energy content basis. But the structure of biomass is highly recalcitrant, making high-yield biological conversion difficult to achieve. In order to increase susceptibility to enzymatic digestion, thermochemical pretreatments are applied, with the goals of removing of lignin, the simplest example being soaking in aqueous ammonia (SAA); hemicellulose removal, most often using dilute acid (DA); and increasing cellulose accessibility by cellulose solvent-based pretreatments, such as cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF). In a comparison of the lignin removal (SAA) and accessibility increase (COSLIF) approaches, we found that certain levels of lignin removal (~15%) were important, but further lignin removal was less effective at achieving digestibility gains than increasing cellulose accessibility. Pretreated biomass forms an excellent substrate for SyPaB hydrogen generation, due to low cost and high sugar content. Following experiments demonstrating the high yield conversion of sucrose to hydrogen (97%) and SyPaB generation of hydrogen at a rate commensurate with the best biological rates achieved, 157 mmol/L/h. SyPaB was combined with enzymatic hydrolysis to enable the direct conversion of cellulosic biomass, including untreated, DA, and COSLIF corn stover. In addition, an updated kinetic model of the system was used to rationally increase the maximum hydrogen production rate by 70% while minimizing total enzyme loading and without increasing substrate concentration. Together, these results demonstrate the high level of engineering control in cell-free systems, which can enable conversion of a variety of substrates to hydrogen at the highest possible yield and rates as high as any biohydrogen production method. / Ph. D.

Wastewater treatment has developed as a mature technology over time. However, conventional wastewater treatment is a very energy-intensive process. Bioelectrochemical system (BES) is an emerging technology that can treat wastewater and also recover resources such as energy in the form of electricity/hydrogen gas and nutrients such as nitrogen and phosphorus compounds. Microbial electrolysis cell (MEC) is a type of BES that, in the presence of an additional voltage, can treat wastewater and generate hydrogen gas. This is a promising approach for wastewater treatment and value-added product generation, though it may not be sustainable in the long run, as it relies on fossil fuels to provide that additional energy. Thus, it is important to explore alternative renewable resources that can provide energy to power MEC. Waste heat is one such resource that has not been researched extensively, particularly at the low-temperature spectrum. This was utilized as a renewable resource by converting waste heat to electricity using a device called thermoelectric generator (TEG). TEG converted simulated waste heat from an anaerobic digester to power an MEC. The feasibility of TEG to act as a power source for an MEC was investigated and its performance compared to the external power source. Various cold sources were analyzed to characterize TEG performance. To explore this integrated TEG-MEC system further, a hydraulic connection was added between the two systems. Wastewater was used as a cold source for TEG and it was recirculated to the anode of the MEC. This system showed improved performance with both systems mutually benefitting each other. The operational parameters were analyzed for the optimization of the system. The integrated system could generate hydrogen at a rate of 0.36 ± 0.05 m3 m-3 d-1 for synthetic domestic wastewater treatment. For the practical application, it is necessary to estimate the cost and narrow the focus on the functions of the system. Techno-economic analysis was performed for MEC with cost estimation and net present value model to understand the economic viability of the technology. The application niche of the BES was described and directions for addressing the challenges towards a full-scale operation were discussed. The present system provides a sustainable method for wastewater treatment and resource recovery which can play an important role in human health, social and economic development and a strong ecosystem. / Doctor of Philosophy / An average person produces about 50-75 gallons of wastewater every day. In addition to the households, wastewater is generated from industries and agricultural practices. As the population increases, the quantity of wastewater production will inevitably increase. To keep our rivers and oceans clean and safe, it is essential to treat the wastewater before it is discharged to the water bodies. However, the conventional wastewater treatment is a very energy (and thus cost) intensive process. For low-income and developing parts of the world, it is difficult to adapt the technology everywhere in its present form. Furthermore, as the energy is provided mostly by fossil fuels, their limited reserves and harmful environmental effects make it critical to find alternative methods that can treat the wastewater at a much lower energy input. For a circular and sustainable economy, it is important to realize wastewater as a resource which can provide us energy, nutrients, and water, rather than discard it as a waste. Bioelectrochemical systems (BES) is an emerging technology that can simultaneously treat wastewater and recover resources in the form of electricity/hydrogen gas, and nitrogen and phosphorus compounds. Microbial electrolysis cell (MEC) is a type of BES that is used to treat wastewater and generate hydrogen gas. An additional voltage is supplied to the MEC for producing hydrogen. In the long run, this may not be sustainable as it relies on fossil fuels to provide that additional energy. Thus, it is important to explore alternative renewable resources that can provide energy to power MEC. Waste heat is a byproduct of many industrial processes and widely available. This was utilized as a renewable resource by converting waste heat to electricity using a device called thermoelectric generator (TEG). TEG converted simulated waste heat from an anaerobic digester to power an MEC. The mutual benefit for MEC and TEG was also explored by connecting the system electrically and hydraulically. Cost-estimation of the system was performed to understand the economic viability and functions of the system were developed. The present system provides a sustainable method for wastewater treatment and resource recovery which can play an important role in human health, social and economic development and a strong ecosystem.

Coenzyme nicotinamide adenine dinucleotide (NAD, including the oxidized form-- NAD+ and reduced form--NADH) and the phosphorylated form--nicotinamide adenine dinucleotide phosphate (NADP, including NADP+ and NADPH) are two of the most important biological electron carriers. Most NAD(P) dependent redox enzymes show a preference of either NADP or NAD as an electron acceptor or donor depending on their unique metabolic roles. In biocatalysis, the low enzymatic activities with unnatural coenzymes have made it difficult to replace costly NADP with economically advantageous NAD or other biomimetic coenzyme for catalysis. This is a significant challenge that must be addressed should in vitro biocatalysis be a viable option for the practical production of low-value biocommodities (i.e., biohydrogen). There is a significant need to first address the coenzyme selectivity of the NADP-dependent dehydrogenases and evolve mutated enzymes that accept biomimetic coenzymes. This is a major focus of this dissertation. Establishment of efficient screening methods to identify beneficial mutants from an enzymatic library is the most challenging task of coenzyme engineering of dehydrogenases. To fine tune the coenzyme preference of dehydrogenases to allow economical hydrogen production, we developed a double-layer Petri-dish based screening method to identify positive mutant of the Moorella thermoacetica 6PGDH (Moth6PGDH) with a more than 4,278-fold reversal of coenzyme selectivity from NADP+ to NAD+. This method was also used to screen the thermostable mutant of a highly active glucose 6-phosphate dehydrogenase from the mesophilic host Zymomonas mobilis. The resulting best mutant Mut 4-1 showed a more than 124-fold improvement of half-life times at 60oC without compromising the specific activity. The screening method was further upgraded for the coenzyme engineering of Thermotaga maritima 6PGDH (Tm6PGDH) on the biomimetic coenzyme NMN+. Through six-rounds of directed evolution and screening, the best mutant showed a more than 50-fold improvement in catalytic efficiency on NMN+ and a more than 6-fold increased hydrogen productivity rate from 6-phosphogluconate and NMN+ compared to those of wild-type enzyme. Together, these results demonstrated the effectiveness of screening methods developed in this research for coenzyme engineering of NAD(P) dependent dehydrogenase and efficient use of the less costly coenzyme in ivSB based hydrogen production. / Ph. D. / NADP and NAD are two of the most important electron carriers in cellular metabolism, and they play distinctive roles in anabolism and catabolism, respectively. Most NAD(P)-dependent dehydrogenases exhibit a strong preference for either NADP or NAD. This coenzyme preference, however, make it nearly impossible to replace the costly NADP with less costly NAD or biomimetic coenzymes in the biocatalysis application. How to engineer dehydrogenases through directed evolution and effective screening method to accept NAD or biomimetic coenzymes, is critical and the focus of this dissertation. The use of in vitro synthetic biosystem (ivSB) to produce hydrogen form starch, is one of the most important in vitro synthetic biology projects, and it depends on NADP coenzyme. With other issues in this system solved, the efficient use of dehydrogenases along with low cost and stable coenzyme is the last obstacle to hydrogen production through industrial biomanufacturing. However, the 6-phosphogluconate dehydrogenase (6PGDH), one of the rate-limiting enzymes in this biosystem, exhibits a strong coenzyme preference for NADP⁺ . For producing low-cost hydrogen, the coenzyme engineering of this dehydrogenase is urgently required. Its activity with less costly NAD or biomimetic coenzymes must be improved. The establishment of an effective screening method is the most challenging task for coenzyme engineering of dehydrogenases. In this research, we developed a Petri-dish double-layer based screening method for coenzyme engineering of thermophilic 6PGDH for activity for NAD⁺ . This screening method was also used to improve the thermostability of a highly active glucose 6-phosphate dehydrogenase from a mesophilic host, where the evolved mutant had a greatly improved thermostability without losing activity. The screening method was further upgraded to develop for coenzyme engineering on biomimetic coenzyme NMN⁺ . The engineered mutant showing a more than 50-fold increase in catalytic efficiency on NMN⁺ was used to develop the first biomimetic coenzyme dependent electron transfer chain for hydrogen production. This screening method is suitable to change the coenzyme selectivity of series of NAD(P)-dependent redox enzymes and show great potential in improving other properties, such as thermostability, substrate scope and optimal pH, of different dehydrogenases. With this method developed, we can efficiently use the low cost stable coenzyme in the biocatalysis, and break the last obstacle to industrial biomanufacturing of hydrogen production.

Cette étude vise à étudier l'effet de la composition de substrats organiques solides sur les performances de production d'hydrogène, les voies métaboliques associées et les changements des communautés microbiennes dans un réacteur discontinu (sCSTR). L'hydrogène est un vecteur énergétique idéal qui a gagné en intérêt scientifique au cours de la dernière décennie. L'H2 produit par voie biologique, ou biohydrogène, peut être produit par des procédés de fermentation sombre où les déchets organiques sont traités et avec la production de molécules à haute valeur ajoutée. Cependant, l'effet de la composition des déchets organiques solides sur la production de biohydrogène dans la fermentation sombre n'a pas encore été clairement élucidé. Au cours de cette étude, une revue bibliographique a été réalisée sur la production d'hydrogène à partir de déchets agricoles. Cette revue montre qu'une large gamme de performances en hydrogène peut être observée principalement en raison de la variabilité dans les compositions en même type de substrats et des conditions expérimentales appliquées. Après avoir optimisé un protocole de test de potentiel biohydrogène (BHP), une grande variété de substrats organiques solides visant à couvrir un grand panel de déchets a été testée pour fournir des données comparables à analyser. Les résultats d'une régression PLS ont montré que seuls les sucres solubles ou facilement disponibles éteint corrélaient avec la production d'hydrogène. En outre, les rendements d'hydrogène corrélaient aussi bien avec l'accumulation de butyrate, principale voie productrice de bioH2. Un modèle prédictif du rendement en hydrogène en fonction de la teneur en sucres a été proposé. Ensuite, des expériences ont été menées en réacteur semi-continu (sCSTR) avec le topinambour comme substrat solide. Il a été montré qu'une faible charge organique favorisait une production continue d'hydrogène tandis que l'accroissement de la charge organique introduisait la présence de voies concurrentes à la production d'hydrogène. De plus, les profils des empreintes moléculaires basées sur l'ADNr 16s ont montré que l'augmentation de la charge organique avait un impact significatif sur la diversité microbienne en favorisant l'implantation de microorganismes ne produisant pas d'hydrogène tels que des bactéries lactiques. / This study aims to investigate the effect of solid substrates composition on hydrogen production performances, metabolic pathways and microbial community changes in batch reactor and their dynamics in semi continuous reactors (sCSTR). Hydrogen is an ideal energy carrier which has gained scientific interest over the past decade. Biological H2, so-called biohydrogen, can especially be produced by dark fermentation processes concomitantly with value-added molecules (i.e. metabolic end-products), while organic waste is treated. However, the effect of solid organic waste composition on biohydrogen production in dark fermentation has not yet been clearly elucidated. In this study, a bibliographic review was made on hydrogen production from agricultural waste. This survey on literature showed that diverse performances were reported on hydrogen production due to the variability in substrate compositions and experimental conditions. After having optimized a protocol of biohydrogen potential test (BHP), a wide variety of organic solid substrates aiming to covering a large range of solid waste was tested to provide a comparable data analysis. The results of a PLS regression showed that only soluble carbohydrates or easily available carbohydrates correlated with hydrogen production. Furthermore, hydrogen yields correlated as well with butyrate H2-producing pathway which is consistent with the literature knowledge. A predictive model of hydrogen yield according to carbohydrate content was proposed. Then, experiments were carried out in sCSTR with Jerusalem artichoke tubers as a case study. It was shown that low organic loading rate favored continuous hydrogen production while higher organic loading introduced hydrogen competition pathways and decreased the overall hydrogen yields. Moereover, 16S rRNA gene based CE-SSCP profiles showed that increasing OLR had a significant effect on the microbial diversity by favoring the implementation of microorganisms not producing hydrogen, i.e. lactic acid bacteria.