Electrochemical synthesis of formic acid from CO2 catalyzed by Shewanella oneidensis MR-1 whole-cell biocatalyst

Metabolic engineering of Shewanella oneidensis to produce glutamate and itaconic acid

Shewanella oneidensis is a gram-negative bacterium known for its unique respiratory capabilities, which allow it to utilize a wide range of electron acceptors, including solid substrates such as electrodes. For a future combination of chemical production and electro-fermentation, the goal of this study was to expand its product spectrum. S. oneidensis was metabolically engineered to optimize its glutamate production and to enable production of itaconic acid. By deleting the glutamate importer gltS for a reduced glutamate uptake and pckA/ptA to redirect the carbon flux towards the TCA cycle, a ∆3 mutant was created. In combination with the plasmid pG2 carrying the glutamate dehydrogenase gdhA and a specific glutamate exporter NCgl1221 A111V, a 72-fold increase in glutamate concentration compared to the wild type was achieved. Along with overexpression of gdhA and NCgl1221 A111V, the deletion of gltS and pckA/ptA as well as the deletion of all three genes (∆3) was examined for their impact on growth and lactate consumption. This showed that the redirection of the carbon flux towards the TCA cycle is possible. Furthermore, we were able to produce itaconic acid for the first time with a S. oneidensis strain. A titer of 7 mM was achieved after 48 h. This suggests that genetic optimization with an expression vector carrying a cis-aconitate decarboxylase (cadA) and a aconitate hydratase (acnB) along with the proven redirection of the carbon flux to the TCA cycle enabled the production of itaconic acid, a valuable platform chemical used in the production of a variety of products. KEY POINTS: •Heterologous expression of gdhA and NCgl1221_A111V leads to higher glutamate production. •Deletion of ackA/pta redirects carbon flux towards TCA cycle. •Heterologous expression of cadA and acnB enables itaconic acid production.

Metabolic engineering strategies to enable microbial electrosynthesis utilization of CO2: recent progress and challenges

Microbial electrosynthesis (MES) is a promising technology that mainly utilizes microbial cells to convert CO2 into value-added chemicals using electrons provided by the cathode. However, the low electron transfer rate is a solid bottleneck hindering the further application of MES. Thus, as an effective strategy, genetic tools play a key role in MES for enhancing the electron transfer rate and diversity of production. We describe a set of genetic strategies based on fundamental characteristics and current successes and discuss their functional mechanisms in driving microbial electrocatalytic reactions to fully comprehend the roles and uses of genetic tools in MES. This paper also analyzes the process of nanomaterial application in extracellular electron transfer (EET). It provides a technique that combines nanomaterials and genetic tools to increase MES efficiency, because nanoparticles have a role in the production of functional genes in EET although genetic tools can subvert MES, it still has issues with difficult transformation and low expression levels. Genetic tools remain one of the most promising future strategies for advancing the MES process despite these challenges.

Application of dissimilatory iron-reducing bacteria for the remediation of soil and water polluted with chlorinated organic compounds: Progress, mechanisms, and directions

Chlorinated organic compounds are widely used as solvents, but they are pollutants that can have adverse effects on the environment and human health. Dissimilatory iron-reducing bacteria (DIRB) such as Shewanella and Geobacter have been applied to treat a wide range of halogenated organic compounds due to their specific biological properties. Until now, there has been no systematic review on the mechanisms of direct or indirect degradation of halogenated organic compounds by DIRB. This work summarizes the discussion of DIRB's ability to enhance the dechlorination of reaction systems through different pathways, both biological and biochemical. For biological dechlorination, some DIRB have self-dechlorination capabilities that directly dechlorinate by hydrolysis. Adjustment of dechlorination genes through genetic engineering can improve the dechlorination capabilities of DIRB. DIRB can also adjust the capacity for the microbial community to dechlorinate and provide nutrients to enhance the expression of dechlorination genes in other bacteria. In biochemical dechlorination, DIRB bioconverts Fe(III) to Fe(II), which is capable of dichlorination. On this basis, the DIRB-driven Fenton reaction can efficiently degrade chlorinated organics by continuously maintaining anoxic conditions to generate Fe(II) and oxic conditions to generate H2O2. DIRB can drive microbial fuel cells due to their electroactivity and have a good dechlorination capacity at low levels of energy consumption. The contribution of DIRB to the removal of pesticides, antibiotics and POPs is summarized. Then the DIRB electron transfer mechanism is discussed, which is core to their ability to dechlorinate. Finally, the prospect of future work on the removal of chlorine-containing organic pollutants by DIRB is presented, and the main challenges and further research directions are suggested.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.

Mechanism and applications of bidirectional extracellular electron transfer of Shewanella

Electrochemically active microorganisms (EAMs) play an important role in the fields of environment and energy. Shewanella is the most common EAM. Research into Shewanella contributes to a deeper comprehension of EAMs and expands practical applications. In this review, the outward and inward extracellular electron transfer (EET) mechanisms of Shewanella are summarized and the roles of riboflavin in outward and inward EET are compared. Then, four methods for the enhancement of EET performance are discussed, focusing on riboflavin, intracellular reducing force, biofilm formation and substrate spectrum, respectively. Finally, the applications of Shewanella in the environment are classified, and the restrictions are discussed. Potential solutions and promising prospects for Shewanella are also provided.

Bioelectrocatalytic Synthesis: Concepts and Applications

Bioelectrocatalytic synthesis is the conversion of electrical energy into value-added products using biocatalysts. These methods merge the specificity and selectivity of biocatalysis and energy-related electrocatalysis to address challenges in the sustainable synthesis of pharmaceuticals, commodity chemicals, fuels, feedstocks and fertilizers. However, the specialized experimental setups and domain knowledge for bioelectrocatalysis pose a significant barrier to adoption. This review introduces key concepts of bioelectrosynthetic systems. We provide a tutorial on the methods of biocatalyst utilization, the setup of bioelectrosynthetic cells, and the analytical methods for assessing bioelectrocatalysts. Key applications of bioelectrosynthesis in ammonia production and small-molecule synthesis are outlined for both enzymatic and microbial systems. This review serves as a necessary introduction and resource for the non-specialist interested in bioelectrosynthetic research.

Metabolic regulation of Shewanella oneidensis for microbial electrosynthesis: From extracellular to intracellular

Shewanella oneidensis MR-1 (S. oneidensis MR-1) has been shown to benefit from microbial electrosynthesis (MES) due to its exceptional electron transfer efficiency. In this study, genes involved in both extracellular electron uptake (EEU) and intracellular CO2 conversion processes were examined and regulated to enhance MES performance. The key genes identified for MES in the EEU process were mtrB, mtrC, mtrD, mtrE, omcA and cctA. Overexpression of these genes resulted in 1.5-2.1 times higher formate productivity than that of the wild-type strains (0.63 mmol/(L·μg protein)), as 0.94-1.61 mmol/(L·μg protein). In the intracellular CO2 conversion process, overexpression of the nadE, nadD, nadR, nadV, pncC and petC genes increased formate productivity 1.3-fold-3.4-fold. Moreover, overexpression of the formate dehydrogenase genes fdhA1, fdhB1 and fdhX1 in modified strains led to a 2.3-fold-3.1-fold increase in formate productivity compared to wild-type strains. The co-overexpression of cctA, fdhA1 and nadV in the mutant strain resulted in 5.59 times (3.50 mmol/(L·μg protein)) higher formate productivity than that of the wild-type strains. These findings revealed that electrons of MES derived from the electrode were utilized in the energy module for synthesizing ATP and NADH, followed by the synthesis of formate in formate dehydrogenase by the combinatorial effects of ATP, NADH, electrons and CO2. The results provide new insights into the mechanism of MES in S. oneidensis MR-1 and pave the way for genetic improvements that could facilitate the further application of MES.

Renewable Hydrogen Production and Storage Via Enzymatic Interconversion of CO2 and Formate with Electrochemical Cofactor Regeneration

The urgent need to reduce CO2 emissions has motivated the development of CO2 capture and utilization technologies. An emerging application is CO2 transformation into storage chemicals for clean energy carriers. Formic acid (FA), a valuable product of CO2 reduction, is an excellent hydrogen carrier. CO2 conversion to FA, followed by H2 release from FA, are conventionally chemically catalyzed. Biocatalysts offer a highly specific and less energy-intensive alternative. CO2 conversion to formate is catalyzed by formate dehydrogenase (FDH), which usually requires a cofactor to function. Several FDHs have been incorporated in bioelectrochemical systems where formate is produced by the biocathode and the cofactor is electrochemically regenerated. H2 production from formate is also catalyzed by several microorganisms possessing either formate hydrogenlyase or hydrogen-dependent CO2 reductase complexes. Combination of these two processes can lead to a CO2 -recycling cycle for H2 production, storage, and release with potentially lower environmental impact than conventional methods.

Structure and function relationship of formate dehydrogenases: an overview of recent progress

Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.

Direct Biocatalytic Processes for CO2 Capture as a Green Tool to Produce Value-Added Chemicals

Direct biocatalytic processes for CO₂ capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO₂ uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO₂ into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C₁-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO₂ uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes.

Recent Applications and Strategies to Enhance Performance of Electrochemical Reduction of CO2 Gas into Value-Added Chemicals Catalyzed by Whole-Cell Biocatalysts

Carbon dioxide (CO2) is one of the major greenhouse gases that has been shown to cause global warming. Decreasing CO2 emissions plays an important role to minimize the impact of climate change. The utilization of CO2 gas as a cheap and sustainable source to produce higher value-added chemicals such as formic acid, methanol, methane, and acetic acid has been attracting much attention. The electrochemical reduction of CO2 catalyzed by whole-cell biocatalysts is a promising process for the production of value-added chemicals because it does not require costly enzyme purification steps and the supply of exogenous cofactors such as NADH. This study covered the recent applications of the diversity of microorganisms (pure cultures such as Shewanella oneidensis MR1, Sporomusa species, and Clostridium species and mixed cultures) as whole-cell biocatalysts to produce a wide range of value-added chemicals including methane, carboxylates (e.g., formate, acetate, butyrate, caproate), alcohols (e.g., ethanol, butanol), and bioplastics (e.g., Polyhydroxy butyrate). Remarkably, this study provided insights into the molecular levels of the proteins/enzymes (e.g., formate hydrogenases for CO2 reduction into formate and electron-transporting proteins such as c-type cytochromes) of microorganisms which are involved in the electrochemical reduction of CO2 into value-added chemicals for the suitable application of the microorganism in the chemical reduction of CO2 and enhancing the catalytic efficiency of the microorganisms toward the reaction. Moreover, this study provided some strategies to enhance the performance of the reduction of CO2 to produce value-added chemicals catalyzed by whole-cell biocatalysts.

Versatile mechanisms and enhanced strategies of pollutants removal mediated by Shewanella oneidensis: A review

The removal of environmental pollutants is important for a sustainable ecosystem and human health. Shewanella oneidensis (S. oneidensis) has diverse electron transfer pathways and can use a variety of contaminants as electron acceptors or electron donors. This paper reviews S. oneidensis's function in removing environmental pollutants, including heavy metals, inorganic non-metallic ions (INMIs), and toxic organic pollutants. S. oneidensis can mineralize o-xylene (OX), phenanthrene (PHE), and pyridine (Py) as electron donors, and also reduce azo dyes, nitro aromatic compounds (NACs), heavy metals, and iodate by extracellular electron transfer (EET). For azo dyes, NACs, Cr(VI), nitrite, nitrate, thiosulfate, and sulfite that can cross the membrane, S. oneidensis transfers electrons to intracellular reductases to catalyze their reduction. However, most organic pollutants cannot be directly degraded by S. oneidensis, but S. oneidensis can remove these pollutants by self-synthesizing catalysts or photocatalysts, constructing bio-photocatalytic systems, driving Fenton reactions, forming microbial consortia, and genetic engineering. However, the industrial-scale application of S. oneidensis is insufficient. Future research on the metabolism of S. oneidensis and interfacial reactions with other materials needs to be deepened, and large-scale reactors should be developed that can be used for practical engineering applications.

Efficient imidazolium ionic liquid as a tri-functional robust catalyst for chemical fixation of CO2 into cyclic carbonates

The recent increase in CO₂ levels has had an extensive impact on the environment; hence an effective catalyst for chemical CO₂ fixation into value-added products is demanded. This work demonstrates a simple approach towards the chemical fixation of CO₂ to cyclic carbonates without solvent, metal and additives using one-pot synthesized tri-functional-imidazolium bromide ionic liquid. Herein, synthesized tri-functional-imidazolium-based ionic liquids, namely 3-(2-hydroxyethyl)-1-vinyl-1H-imidazole-3-ium bromide ([VIMEtOH][Br] (24 and 72 h)), 3-(2-hydroxyethyl)-1-vinyl-1H-imidazole-3-ium hydroxyl ([VIMEtOH][OH]) and poly 3-(2-hydroxyethyl)-1-vinyl-1H-imidazole-3-ium bromide (poly [VIMEtOH][Br]), were used for the comprehensive investigation of chemical fixation of CO₂ into cyclic carbonates and their physiochemical properties. In case of [VIMEtOH][Br] ionic liquid, it displayed time-dependent synthesis dissolution in the reaction system. This study found that [VIMEtOH][Br]-72 ionic liquid is not dissolved in the reaction system. The effect on the catalytic efficiency of the presence of functional groups in ionic liquids such as N-vinyl (-CC-N), acidic proton of imidazolium (-C (2)-H) and hydroxyl (-OH) along with bromide anion and the reaction conditions are systematically investigated. For CO₂ fixation, 99.6% conversion of propylene oxide with an excellent selectivity of propylene carbonate (≥99%) over [VIMEtOH][Br]-72 catalyst (at 120 °C, 2 MPa, 2 h) was observed without co-catalyst, metal and solvent. Also, it demonstrated an excellent wide substrates scope of epoxide and all reactions were performed on gram-scalable, which are potential prospects for industrial use.

Elucidation of the Roles of Ionic Liquid in CO2 Electrochemical Reduction to Value-Added Chemicals and Fuels

The electrochemical reduction of carbon dioxide (CO₂ER) is amongst one the most promising technologies to reduce greenhouse gas emissions since carbon dioxide (CO₂) can be converted to value-added products. Moreover, the possibility of using a renewable source of energy makes this process environmentally compelling. CO₂ER in ionic liquids (ILs) has recently attracted attention due to its unique properties in reducing overpotential and raising faradaic efficiency. The current literature on CO₂ER mainly reports on the effect of structures, physical and chemical interactions, acidity, and the electrode–electrolyte interface region on the reaction mechanism. However, in this work, new insights are presented for the CO₂ER reaction mechanism that are based on the molecular interactions of the ILs and their physicochemical properties. This new insight will open possibilities for the utilization of new types of ionic liquids. Additionally, the roles of anions, cations, and the electrodes in the CO₂ER reactions are also reviewed.

Local Acidification Limits the Current Production and Biofilm Formation of Shewanella oneidensis MR-1 With Electrospun Anodes

The anodic current production of Shewanella oneidensis MR-1 is typically lower compared to other electroactive bacteria. The main reason for the low current densities is the poor biofilm growth on most anode materials. We demonstrate that the high current production of Shewanella oneidensis MR-1 with electrospun anodes exhibits a similar threshold current density as dense Geobacter spp biofilms. The threshold current density is a result of local acidification in the biofilm. Increasing buffer concentration from 10 to 40 mM results in a 1.8-fold increase of the current density [(590 ± 25) μA cm⁻²] while biofilm growth stimulation by riboflavin has little effect on the current production. The current production of a reference material below the threshold did not respond to the increased buffer concentration but could be enhanced by supplemented riboflavin that stimulated the biofilm growth. Our results suggest that the current production with S. oneidensis is limited (1) by the biofilm growth on the anode that can be enhanced by the choice of the electrode material, and (2) by the proton transport through the biofilm and the associated local acidification.

Membrane Protein Modified Electrodes in Bioelectrocatalysis

Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.

Reversing an Extracellular Electron Transfer Pathway for Electrode-Driven Acetoin Reduction

Microbial electrosynthesis is an emerging technology with the potential to simultaneously store renewably generated energy, fix carbon dioxide, and produce high-value organic compounds. However, limited understanding of the route of electrons into the cell remains an obstacle to developing a robust microbial electrosynthesis platform. To address this challenge, we leveraged the native extracellular electron transfer pathway in Shewanella oneidensis MR-1 to connect an extracellular electrode with an intracellular reduction reaction. The system uses native Mtr proteins to transfer electrons from an electrode to the inner membrane quinone pool. Subsequently, electrons are transferred from quinones to NAD⁺ by native NADH dehydrogenases. This reverse functioning of NADH dehydrogenases is thermodynamically unfavorable; therefore, we added a light-driven proton pump (proteorhodopsin) to generate proton-motive force to drive this activity. Finally, we use reduction of acetoin to 2,3-butanediol via a heterologous butanediol dehydrogenase (Bdh) as an electron sink. Bdh is an NADH-dependent enzyme; therefore, observation of acetoin reduction supports our hypothesis that cathodic electrons are transferred to intracellular NAD⁺. Multiple lines of evidence indicate proper functioning of the engineered electrosynthesis system: electron flux from the cathode is influenced by both light and acetoin availability, and 2,3-butanediol production is highest when both light and a poised electrode are present. Using a hydrogenase-deficient S. oneidensis background strain resulted in a stronger correlation between electron transfer and 2,3-butanediol production, suggesting that hydrogen production is an off-target electron sink in the wild-type background. This system represents a promising step toward a genetically engineered microbial electrosynthesis platform and will enable a new focus on synthesis of specific compounds using electrical energy.

Recent Advances in Power-to-X Technology for the Production of Fuels and Chemicals

Environmental issues related to greenhouse gas emissions are progressively pushing the transition toward fossil-free energy scenario, in which renewable energies such as solar and wind power will unavoidably play a key role. However, for this transition to succeed, significant issues related to renewable energy storage have to be addressed. Power-to-X (PtX) technologies have gained increased attention since they actually convert renewable electricity to chemicals and fuels that can be more easily stored and transported. H2 production through water electrolysis is a promising approach since it leads to the production of a sustainable fuel that can be used directly in hydrogen fuel cells or to reduce carbon dioxide (CO2) in chemicals and fuels compatible with the existing infrastructure for production and transportation. CO2 electrochemical reduction is also an interesting approach, allowing the direct conversion of CO2 into value-added products using renewable electricity. In this review, attention will be given to technologies for sustainable H2 production, focusing on water electrolysis using renewable energy as well as on its remaining challenges for large scale production and integration with other technologies. Furthermore, recent advances on PtX technologies for the production of key chemicals (formic acid, formaldehyde, methanol and methane) and fuels (gasoline, diesel and jet fuel) will also be discussed with focus on two main pathways: CO2 hydrogenation and CO2 electrochemical reduction.

On-going applications of Shewanella species in microbial electrochemical system for bioenergy, bioremediation and biosensing

Microbial electrochemical system (MES) has attracted ever-growing interest as a promising platform for renewable energy conversion and bioelectrochemical remediation. Shewanella species, the dissimilatory metal reduction model bacteria with versatile extracellular electron transfer (EET) strategies, are the well-received microorganisms in diverse MES devices for various practical applications as well as microbial EET mechanism investigation. Meanwhile, the available genomic information and the unceasing established gene-editing toolbox offer an unprecedented opportunity to boost the applications of Shewanella species in MES. This review thoroughly summarizes the status quo of the applications of Shewanella species in microbial fuel cells for bioelectricity generation, microbial electrosynthesis for biotransformation of valuable chemicals and bioremediation of environment-hazardous pollutants with synoptical discussion on their EET mechanism. Recent advances in rational design and genetic engineering of Shewanella strains for either promoting the MES performance or broadening their applications are surveyed. Moreover, some emerging applications beyond electricity generation, such as biosensing and biocomputing, are also documented. The challenges and perspectives for Shewanella-based MES are also discussed elaborately for the sake of not only discovering new scientific lights on microbial extracellular respiratory but also propelling practical applications.