ENGINEERING BIOLOGICAL SYSTEMS TO ADVANCE ELECTROMICROBIAL PRODUCTION
The biological fixation of CO2 by plants/algae takes place naturally on a massivescale. However, photosynthetic carbon fixation is challenging to harness due to multiple constraints, including difficulties processing lignocellulosic biomass and the low efficiency by which phototrophs use sunlight. Alternatively, CO2 can be upgraded electrochemically. However, such processes rely on extreme conditions and suffer from a narrow product spectrum and low product selectivity. My Ph.D. projects primarily focus on increasing CO2 fixation efficiency to bioproducts such as biofuel and bioplastics. I work on designing and developing engineered electroactive microorganisms that can absorb electricity, fix CO2, and synthesize energy storage molecules (food, biofuels, and bioplastics) in a process called electromicrobial production (EMP). To do this, I have been synthesizing the existing knowledge base on engineering microorganisms, specifically electroactive organisms, building predictive models of electrically driven metabolism, and discovering new genes into new engineered microorganisms. There are many possible variations of CO2 fixation, and it is far from clear which is the best approach. In a first for the field, I compiled quantitative data on all known methods for natural and synthetic carbon fixation mechanisms and powering microbial metabolism with electricity. Next, I used this compiled data to build a comprehensive theoretical model of electromicrobial production technology. This model predicts the efficiency of electromicrobial production systems that absorb electricity with extracellular electron uptake (EEU) mechanism or by hydrogen-oxidation; fix CO2 with any known carbon fixation systems, and store this electricity and carbon as a wide variety of biofuels, and energy storage polymers. Also, this model evaluates and compares the many different variants of electromicrobial production technology and predicts which has the most potential to scale up. I further demonstrated that EEU mechanisms are just as efficient as hydrogen-oxidation at the lab scale and, most importantly, could scale up much better. But the genetic basis of extracellular electron uptake was missing for implanting EEU-based electrosynthesis. Therefore I used genomic engineering techniques such as homologous recombination gene knockout and insertion, CRISPR, and protein tagging/expression to identify essential genes involved in extracellular electron uptake in Shewanella oneidensis. We have shown that EEU enables extracellular electron uptake into microbial metabolism, allowing cells to be independent of any carbon source as an energy carrier. This started a roadmap for decoupling the carbon and energy source in microbial metabolism, increasing the biofuel production efficiency, and bringing flexibility in feedstock primary CO2 fixation selection. One of the main promising primary fixation products of CO2 is formate, with more than 90% electrochemical Faradaic efficiency. Formate is mainly used as an electron source, whereas S. oneidensis uses formate dehydrogenase (fdh) to catalyze the oxidation of formate to CO2 and NADH. Therefore cell adaptation to utilize formate as a sole carbon source, not an electron source, is required to have efficient electromicrobial productivity. We designed and built a homemade bioreactor with an embedded electrochemical cell to reconstruct central metabolic activity in S. oneidensis bypassing the need for CO2 fixation pathways and assimilating formate in a C1 pathway such as the reductive glycine (rGly) pathway. Electrons were provided via electrochemical reduction of AQDS, and formate was tracked using the carbon labeling technique to ensure carbon was utilized through rGly pathway. The LC/MS and formate consumption assays confirm the activity of the rGly pathway in S. oneidensis. This technology integrates abiotic and biotic processes, stitching together electrochemistry with biology, and harnessing advantages while avoiding their drawbacks. Electromicrobial production technology increases bioproduction efficiency by decoupling the carbon and energy source in microbial metabolism. This can produce a large set of fuel molecules at room temperature and pressure, including branched-chain alcohols and medium-chain fatty acids.