Improving electron trans-inner membrane movements in microbial electrocatalysts

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.

Enhanced depolluting capabilities of microbial bioelectrochemical systems by synthetic biology

Microbial bioelectrochemical system (BES) is a promising sustainable technology for the electrical energy recovery and the treatment of recalcitrant and toxic pollutants. In microbial BESs, the conversion of harmful pollutants into harmless products can be catalyzed by microorganisms at the anode (Type I BES), chemical catalysts at the cathode (Type II BES) or microorganisms at the cathode (Type III BES). The application of synthetic biology in microbial BES can improve its pollutant removing capability. Synthetic biology techniques can promote EET kinetics, which is helpful for microbial anodic electro-respiration, expediting pollutant removing not only at the anode but also at the cathode. They offer tools to promote biofilm development on the electrode, enabling more microorganisms residing on the electrode for subsequent catalytic reactions, and to overexpress the pollutant removing-related genes directly in microorganisms, contributing to the pollutant decomposition. In this work, based on the summarized aspects mentioned above, we describe the major synthetic biology strategies in designing and improving the pollutant removing capabilities of microbial BES. Lastly, we discuss challenges and perspectives for future studies in the area.

Systematic Full-Cycle Engineering Microbial Biofilms to Boost Electricity Production in Shewanella oneidensis

Electroactive biofilm plays a crucial rule in the electron transfer efficiency of microbial electrochemical systems (MES). However, the low ability to form biofilm and the low conductivity of the formed biofilm substantially limit the extracellular electron transfer rate of microbial cells to the electrode surfaces in MES. To promote biofilm formation and enhance biofilm conductivity, we develop synthetic biology approach to systematically engineer Shewanella oneidensis, a model exoelectrogen, via modular manipulation of the full-cycle different stages of biofilm formation, namely, from initial contact, cell adhesion, and biofilm growth stable maturity to cell dispersion. Consequently, the maximum output power density of the engineered biofilm reaches 3.62 ± 0.06 W m-2, 39.3-fold higher than that of the wild-type strain of S. oneidensis, which, to the best our knowledge, is the highest output power density that has ever been reported for the biofilms of the genetically engineered Shewanella strains.

Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems

Bioelectrochemical systems (BESs) based on Shewanella oneidensis MR-1 offer great promise for sustainable energy/chemical production, but the low rate of electron generation remains a crucial bottleneck preventing their industrial application. Here, we reconstructed a genome-scale metabolic model of MR-1 to provide a strong theoretical basis for novel BES applications. The model iLJ1162, comprising 1,162 genes, 1,818 metabolites and 2,084 reactions, accurately predicted cellular growth using a variety of substrates with 86.9% agreement with experimental results, which is significantly higher than the previously published models iMR1_799 and iSO783. The simulation of microbial fuel cells indicated that expanding the substrate spectrum of MR-1 to highly reduced feedstocks, such as glucose and glycerol, would be beneficial for electron generation. In addition, 31 metabolic engineering targets were predicted to improve electricity production, three of which have been experimentally demonstrated, while the remainder are potential targets for modification. Two potential electron transfer pathways were identified, which could be new engineering targets for increasing the electricity production capacity of MR-1. Finally, the iLJ1162 model was used to simulate the optimal biosynthetic pathways for six platform chemicals based on the MR-1 chassis in microbial electrosynthesis systems. These results offer guidance for rational design of novel BESs.

NADH dehydrogenases Nuo and Nqr1 contribute to extracellular electron transfer by Shewanella oneidensis MR-1 in bioelectrochemical systems

Shewanella oneidensis MR-1 is quickly becoming a synthetic biology workhorse for bioelectrochemical technologies due to a high level of understanding of its interaction with electrodes. Transmembrane electron transfer via the Mtr pathway has been well characterized, however, the role of NADH dehydrogenases in feeding electrons to Mtr has been only minimally studied in S. oneidensis MR-1. Four NADH dehydrogenases are encoded in the genome, suggesting significant metabolic flexibility in oxidizing NADH under a variety of conditions. A strain lacking the two dehydrogenases essential for aerobic growth exhibited a severe growth defect with an anode (+0.4 V_SHE) or Fe(III)-NTA as the terminal electron acceptor. Our study reveals that the same NADH dehydrogenase complexes are utilized under oxic conditions or with a high potential anode. Our study also supports the previously indicated importance of pyruvate dehydrogenase activity in producing NADH during anerobic lactate metabolism. Understanding the role of NADH in extracellular electron transfer may help improve biosensors and give insight into other applications for bioelectrochemical systems.

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.

Shewanella oneidensis as a living electrode for controlled radical polymerization

Metabolic engineering has facilitated the production of pharmaceuticals, fuels, and soft materials but is generally limited to optimizing well-defined metabolic pathways. We hypothesized that the reaction space available to metabolic engineering could be expanded by coupling extracellular electron transfer to the performance of an exogenous redox-active metal catalyst. Here we demonstrate that the electroactive bacterium Shewanella oneidensis can control the activity of a copper catalyst in atom-transfer radical polymerization (ATRP) via extracellular electron transfer. Using S. oneidensis, we achieved precise control over the molecular weight and polydispersity of a bioorthogonal polymer while similar organisms, such as Escherichia coli, showed no significant activity. We found that catalyst performance was a strong function of bacterial metabolism and specific electron transport proteins, both of which offer potential biological targets for future applications. Overall, our results suggest that manipulating extracellular electron transport pathways may be a general strategy for incorporating organometallic catalysis into the repertoire of metabolically controlled transformations.