A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates. Bioelectrochemical techniques offer a promising method to alleviate redox imbalances during the synthesis of biochemicals. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell’s redox balance. The cellular response to such redox changes and the additional reducing can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can improve product yields and/or productivity. We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity.

A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates. Bioelectrochemical techniques offer a promising method to alleviate redox imbalances during the synthesis of biochemicals. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell’s redox balance. The cellular response to such redox changes and the additional reducing can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can improve product yields and/or productivity. We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity.

L’électrosynthèse microbienne est une technologie innovante qui permet de convertir le dioxyde de carbone en molécules organiques en utilisant une cathode comme source d’électrons de la réduction microbienne du CO2. Le procédé «Biorare» propose de coupler l’électrosynthèse microbienne avec l’oxydation de déchets à l’anode afin d’augmenter le rendement énergétique du procédé. Il devient ainsi possible de traiter un effluent à l’anode et de valoriser du CO2 à la cathode. La thèse a eu pour objectif d’améliorer les performances de la bioanode et de la biocathode séparément, afin de réaliser in fine un prototype de procédé «Biorare» à l’échelle du laboratoire. Parmi plusieurs types de déchets testés, les boues biologiques se sont avérées bien adaptées pour une utilisation à l’anode en assurant des densités de courant jusqu’à 10 A/m2. Toutefois, ces performances étant peu reproductibles, nous avons choisi d’exploiter des biodéchets, dont le gisement représente plus de 22 millions de tonnes en France et la valorisation est aujourd’hui obligatoire. Leur utilisation brute n’a pas permis de dépasser 1 A/m2 mais une méthode innovante de formation des bioanodes a permis d’augmenter les densités de courant jusqu’à 7 A/m2, de façon reproductible et dans des conditions extrapolables. Les travaux sur les biocathodes ont révélé que l’hydrogène est un intermédiaire réactionnel clé pour le transfert d’électrons de la cathode vers les microorganismes qui réduisent le CO2. Cela a conduit à découpler le procédé initial en deux étapes : l’hydrogène est produit dans une cellule d’électrolyse microbienne qui oxyde les biodéchets et, en aval, un bioréacteur gaz-liquide utilise l’hydrogène pour convertir le CO2 en acétate, éthanol, formiate, ou butyrate, suivant les systèmes microbiens. Cette stratégie permet d’augmenter les performances d’un facteur 24 avec une vitesse de production d’acétate de 376 mg/L/j et des concentrations jusqu’à 11 g/L. / Microbial electrosynthesis is an innovative technology to produce organic molecules from CO2, using a cathode as electron source for the microbial reduction of CO2. The Biorare process intends to associate the microbial electrosynthesis with the oxidation of organic wastes at the anode, in order to increase the energetic yield of the process. The system allows thus both the treatment of polluted effluents at the anode and CO2 valorization to organic molecules at the cathode. The purpose of the PhD work was to improve the bioanode and biocathode performance separately, to finally design a Biorare prototype at laboratory scale. Among the various wastes tested, biological sludge was a good substrate, which led to current densities up to 10 A/m2. However, the performance was not reproducible and it was decided to use food wastes, which constitute an abundant resource of 22 million tons in France that must be valorized. The use of raw food waste did not allow exceeding 1 A/m2, but a new method for bioanode formation improved the current density up to 7 A/m2 in a reproducible and close-to-industrial way. The study on biocathodes revealed hydrogen as a key intermediate in electron transfer from the cathode to the microbial cells that reduce CO2. This led to dissociate the initial process into two steps: hydrogen is produced in a microbial electrolysis cell that oxidizes food wastes and, downstream, a gas-liquid bioreactor uses hydrogen to convert CO2 to acetate, ethanol, formate or butyrate, depending on the microbial system. This strategy allowed increasing the performance by a factor 24 with a maximal acetate production rate of 376 mg/L/j and concentrations up to 11 g/L.

Microbial electrosynthesis (MES) has recently emerged as a novel biotechnology platform for value-added product generation from waste CO2 stream. Integrating MES technology with renewable energy sources for both CO2 valorization and renewable energy storage is regarded as one type of artificial photosynthesis and a perfect example of circular bioeconomy. However, several challenges remain to be addressed to scale-up MES as a feasible process for chemical production, which include enhanced production rate, reduced energy consumption and excellent resistance to external fluctuations. To fill these knowledge gaps, different in-depth approaches were proposed in this dissertation by optimizing the cathode architecture, CO2 flow rates and utilizing efficient photoelectrode to improve MES performance and stability. A novel cathode design, made of conductive hollow fiber membrane, was developed in this dissertation to improve CO2 availability at MES cathode surface via direct CO2 delivery to chemolithoautotrophs through the pores in the hollow fibers. By modifying the hollow fiber surface with carbon nanotubes (CNTs), higher bioproduct formation was achieved with excellent faradaic efficiencies, which could be attributed to the improved surface area for bacterial adhesion and the reduction of cathodic electron transfer resistance. Since CO2 flow rate from industrial facilities typically varies over time, this hollow-fiber architecture was also applied to test the resistance of MES systems to CO2 flow rate fluctuation. Stepwise increase of CO2 flow rates from 0.3 ml/min to 10 ml/min was tested and the effect of CO2 flow rate fluctuations was evaluated in terms of biochemical generation and microbial community. MES was further integrated with renewable energy supply for both energy storage and CO2 transformation into biofuels and biochemicals. Stable MES photoanode, based on molybdenum-doped bismuth vanadate deposited on fluorine-doped tin oxide glass (FTO/BiVO4/Mo), was prepared for efficient solar energy harvesting and overpotential reduction for oxygen evolution reaction (OER), which contributed to one of the highest solar-to-biochemical conversion efficiencies ever reported for photo-assisted MES systems. The applied nature of this dissertation with fundamental insights is of great importance to bring MES one step closer to full-scale applications and enable MES technology to be economically more viable for renewable energy storage and CO2 valorization.

Microbial electrosynthesis (MES) is an emerging biotechnology platform for the conversion of CO2 feedstocks into value-added chemical commodities. In MES, microbial catalysts use the cathode (electrons/ H2) as a sole source of energy for the reduction of CO2. Integrating MES technology with renewable energy sources, such as solar power, to convert CO2 to storable chemicals is an example of a perfect circular economy and a sustainable climate change mitigation strategy. However, many knowledge gaps need to be addressed to scale-up MES as an economically viable chemical production process. Therefore, different in-depth approaches were tested in this dissertation by optimizing the cathode architecture and exploring the saline application to enhance MES performance. A balance between various bio-physicochemical phenomena at the MES cathode, i.e., the three-phase interface between CO2 gas, cathodic-biofilm, and electrolyte, is desirable for efficient microbial electrochemical CO2 capture and utilization. To address this problem, this thesis investigated alternatives to the benchmark carbonbased plane cathode by applying a dual-functioning (cathode as well as a CO2 gas-transfer membrane) electrode architecture on MES performance. High Faradaic efficiencies for CO2 reduction were achieved with this novel cathode architecture. This hollow-fiber electrode architecture was also applied to MES operation in saline conditions (i.e., Saline-MES). Because seawater potentially acts as an endless source of saline electrolyte, and its high electrical conductivity useful to minimize the concentration overpotential losses occurs in MES. However, exploring robust halophilic microbial catalysts with high selectivity towards CO2 reduction to the desired end product(s) is necessary to develop the saline-MES process. Therefore, this thesis investigated natural saline habitats with hyper (Red sea brine pool) and moderate salinity (mangrove and salt marsh sediment) as a source of inoculum. Emphasis was placed on improving new knowledge in the direction of halophilic CO2 reducing communities enrichment using cathode selective pressure in the saline-MES. The fundamental insights demonstrated in this dissertation are useful for further development of MES technology, to bring MES one step closer to full-scale applications, for overcoming the bottlenecks associated with reactor scaling-up related to cathode architecture, strategies for the enrichment of halophilic CO2 reducing microbial communities, and saline-MES process optimization.

Les sources hydrothermales profondes sont des édifices géologiques formés par l’infiltration d’eau de mer dans la croûte océanique, formant un fluide chaud (>400 °C), riche en métaux qui précipite pour former des cheminées dans lesquelles circulent un courant électrique. Les travaux de recherche présentés ici avaient pour objectif de révéler la présence de microorganismes capable de participer à la production de ce courant électrique ou d’utiliser cette électricité pour vivre au sein de ces cheminées électriquement conductrices. Nous nous sommes focalisés sur les microorganismes capables de survivre à haute température (entre 60 et 95°C). Différentes communautés microbienne en interaction et électroactives ont pu être cultivées permettant de poser des hypothèses crédibles quant à la colonisation primaire de ces environnements extrêmes. Ces hypothèses pourraient également s’appliquer aux théories d’origine de la vie en contexte hydrothermal. / Deep hydrothermal vents are geologic structures formed by the infiltration of seawater into the oceanic crust, forming a hot metal-rich fluid (> 400 ° C) that precipitates to form chimneys in which an electric current flows. The purpose of the research presented here was to reveal the presence of microorganisms capable of participating in the production of this electric current or of using this electricity to live within these electrically conductive chimneys. We focused on microorganisms able to survive at high temperatures (between 60 and 95 ° C). Different interacting and electroactive microbial communities have been cultivated, allowing the building of credible hypotheses about the primary colonization of these extreme environments. These hypotheses could also be applied to theories of origin of life in a hydrothermal context.