Towards development of electrogenetics using electrochemically active bacteria

Redox mediators stimulated chain elongation process in fluidized cathode electro-fermentation systems for caproate production

Medium chain fatty acids (MCFAs), the secondary products of traditional anaerobic fermentation, can be produced via chain elongation (CE), a process often retarded due to the difficulty during interspecies electron transfer (IET). This study employed redox mediators, neutral red (NR), methyl viologen (MV), and methylene blue (MB) as electron shuttles to expedite the electro-fermentation for caproate production by improving IET. Results showed that MV increased the MCFAs production by promoting acetate to ethanol conversion, leading to the highest MCFAs selectivity of 68.73%. While NR was indicated to improve CE by encouraging H2 production, and the biocathode had the highest electrical activity due to the smallest internal resistance and largest capacitance increase of 96% than the control. A higher proportion of Sutterella, Prevotella, and Hydrogenophaga, linked with the H2 mediated interspecies electron transfer (MIET) during CE process, was observed across redox mediators supplied groups compared to the control. The presence of mediators led to an elevated abundance of key enzymes for enhanced CE process and electron transfer. This study provided the perspective of the stimulated electron transfer for improved MCFAs production in electro-fermentation systems.

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.

Living electrochemical biosensing: Engineered electroactive bacteria for biosensor development and the emerging trends

Bioelectrical interfaces made of living electroactive bacteria (EAB) provide a unique opportunity to bridge biotic and abiotic systems, enabling the reprogramming of electrochemical biosensing. To develop these biosensors, principles from synthetic biology and electrode materials are being combined to engineer EAB as dynamic and responsive transducers with emerging, programmable functionalities. This review discusses the bioengineering of EAB to design active sensing parts and electrically connective interfaces on electrodes, which can be applied to construct smart electrochemical biosensors. In detail, by revisiting the electron transfer mechanism of electroactive microorganisms, engineering strategies of EAB cells for biotargets recognition, sensing circuit construction, and electrical signal routing, engineered EAB have demonstrated impressive capabilities in designing active sensing elements and developing electrically conductive interfaces on electrodes. Thus, integration of engineered EAB into electrochemical biosensors presents a promising avenue for advancing bioelectronics research. These hybridized systems equipped with engineered EAB can promote the field of electrochemical biosensing, with applications in environmental monitoring, health monitoring, green manufacturing, and other analytical fields. Finally, this review considers the prospects and challenges of the development of EAB-based electrochemical biosensors, identifying potential future applications.

Engineering Outer Membrane Vesicles to Increase Extracellular Electron Transfer of Shewanella oneidensis

Outer membrane vesicles (OMVs) of Gram-negative bacteria play an essential role in cellular physiology. The underlying regulatory mechanism of OMV formation and its impact on extracellular electron transfer (EET) in the model exoelectrogenShewanella oneidensis MR-1 remain unclear and have not been reported. To explore the regulatory mechanism of OMV formation, we used the CRISPR-dCas9 gene repression technology to reduce the crosslink between the peptidoglycan (PG) layer and the outer membrane, thus promoting the OMV formation. We screened the target genes that were potentially beneficial to the outer membrane bulge, which were classified into two modules: PG integrity module (Module 1) and outer membrane component module (Module 2). We found that downregulation of the penicillin-binding protein-encoding gene pbpC for peptidoglycan integrity (Module 1) and the N-acetyl-d-mannosamine dehydrogenase-encoding gene wbpP involved in lipopolysaccharide synthesis (Module 2) exhibited the highest production of OMVs and enabled the highest output power density of 331.3 ± 1.2 and 363.8 ± 9.9 mW m-2, 6.33- and 6.96-fold higher than that of the wild-typeS. oneidensis MR-1 (52.3 ± 0.6 mW m-2), respectively. To elucidate the specific impacts of OMV formation on EET, OMVs were isolated and quantified for UV-visible spectroscopy and heme staining characterization. Our study showed that abundant outer membrane c-type cytochromes (c-Cyts) including MtrC and OmcA and periplasmic c-Cyts were exposed on the surface or inside of OMVs, which were the vital constituents responsible for EET. Meanwhile, we found that the overproduction of OMVs could facilitate biofilm formation and increase biofilm conductivity. To the best of our knowledge, this study is the first to explore the mechanism of OMV formation and its correlation with EET of S. oneidensis, which paves the way for further study of OMV-mediated EET.

Electrogenetic control of gene expression in Shewanella oneidensis MR-1 using Arc-dependent transcriptional promoters

Electrochemically active bacteria (EAB) are capable of electrically interacting with electrodes, enabling their application in bioelectrochemical systems (BESs). As the performance of BES is related to the metabolic activities of EAB, the development of methods to control their metabolic activities is important to facilitate BES applications. A recent study found that the EAB Shewanella oneidensis MR-1 uses the Arc system to regulate the expression of catabolic genes in response to electrode potentials, suggesting that a methodology for electrical control of gene expression in EAB, referred to as electrogenetics, can be developed by using electrode potential-responsive, Arc-dependent transcriptional promoters. Here, we explored Arc-dependent promoters in the genomes of S. oneidensis MR-1 and Escherichia coli to identify electrode potential-responsive promoters that are differentially activated in MR-1 cells exposed to high- and low-potential electrodes. LacZ reporter assays using electrode-associated cells of MR-1 derivatives revealed that the activities of promoters located upstream of the E. coli feo gene (P_feo) and the MR-1 nqrA2 (SO_0902) gene (P_nqr2) were significantly increased when S. oneidensis cells were exposed to electrodes poised at +0.7 V and -0.4 V (versus the standard hydrogen electrode), respectively. Additionally, we developed a microscopic system for in situ monitoring of promoter activity in electrode-associated cells and found that P_nqr2 activity was persistently induced in MR-1 cells associated with an electrode poised at -0.4 V. Our results indicate that these electrode potential-responsive promoters enable efficient regulation of gene expression in EAB, providing a molecular basis for the development of electrogenetics.

Industrial bioelectrochemistry for waste valorization: State of the art and challenges

Bioelectrochemistry has gained importance in recent years for some of its applications on waste valorization, such as wastewater treatment and carbon dioxide conversion, among others. The aim of this review is to provide an updated overview of the applications of bioelectrochemical systems (BESs) for waste valorization in the industry, identifying current limitations and future perspectives of this technology. BESs are classified according to biorefinery concepts into three different categories: (i) waste to power, (ii) waste to fuel and (iii) waste to chemicals. The main issues related to the scalability of bioelectrochemical systems are discussed, such as electrode construction, the addition of redox mediators and the design parameters of the cells. Among the existing BESs, microbial fuel cells (MFCs) and microbial electrolysis cells (MECs) stand out as the more advanced technologies in terms of implementation and R&D investment. However, there has been little transfer of such achievements to enzymatic electrochemical systems. It is necessary that enzymatic systems learn from the knowledge reached with MFC and MEC to accelerate their development to achieve competitiveness in the short term.

On-site determination of water toxicity based on freeze-dried electrochemically active bacteria

Our previous studies have reported water toxicity determination with a fresh electrochemically active bacteria (EAB) suspension as the sensing element, which exhibits high sensitivity and has great prospects in providing early warning about water pollution. However, because the preparation of fresh EAB suspensions is time-consuming, these studies are not suitable for the on-site determination of water toxicity. To solve this problem, this study investigated the rapid preparation of an EAB suspension by the rehydration of freeze-dried EABs and established a novel method for the on-site determination of water toxicity based on the freeze-dried EAB model strain Shewanella oneidensis MR-1. The results demonstrate that the optimal cryoprotectant for S. oneidensis MR-1 freeze drying is 7.5 % (w/v) skimmed milk powder. Compared with fresh S. oneidensis MR-1, freeze-dried S. oneidensis MR-1 exhibits similar extracellular electron transfer (EET) performance (74.7 % ± 0.3 %) and slightly lower sensitivity for water toxicity determination (65.8 % ± 2.2 %) with the optimal cryoprotectant. On-site determination of water toxicity was realized by using freeze-dried S. oneidensis MR-1, and the detection limits of five common toxic pollutants (Cd²⁺, Pb²⁺, Cu²⁺, phenol and dichlorophenol) reached 0.5 mg/L. Water toxicity determination is capable of resisting common interferences, e.g., glucose, lactate, nitrate and nitrite, and shows high accuracy in practical applications.

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.

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.

Unveiling the bioelectrocatalyzing behaviors and microbial ecological mechanisms behind caproate production without exogenous electron donor

Bioelectrochemical systems were proposed as a promising approach for the efficient valorization of biomass into 6-8 carbon atom medium-chain fatty acids (MCFAs), the precursors for high value-added chemicals or renewable energy, via acetyl-CoA-mediated chain elongation (CE). To achieve CE processes, exogenous electron donors (EDs), e.g., ethanol or lactic acid, were normally prerequisites. This research built a microbial electrolysis cell (MEC) for MCFAs biosynthesis from acetate without exogenous EDs addition. A wide range of applied voltages (0.6-1.2 V) was first employed to investigate the bioelectrocatalyzing response. The results show that caproate and butyrate were the main products formed from acetate under different applied voltages. Maximum caproate concentration (501 ± 12 mg COD/L) was reached at 0.8 V on day 3. Under this applied voltage, hydrogen partial pressure stabilized at about 0.1 bar, beneficial for MCFA production. Electron and carbon balances revealed that the electron-accepting capacity achieved 32% at 0.8 V, showing the highest interspecies electron transfer efficiency. Most of the carbon was recovered in the form of caproate (carbon loss was 9%). MiSeq sequencing revealed Rhodobacter and Clostridium_sensu_stricto playing the crucial role in the biosynthesis of caproate, while Acetobacterium, Acetoanaerobium, and Acetobacter represented the main ED contributors. Four available flora, i.e., homo-acetogen, anaerobic fermentation bacteria, electrode active bacteria, and nitrate-reducing bacteria, interacted and promoted caproate synthesis by molecular ecological network analysis.

Simultaneous Anaerobic Ammonium Oxidation and Electricity Generation in Microbial Fuel Cell: Performance and Electrochemical Characteristics

In this study, a microbial fuel cell (MFC) that can achieve simultaneous anode anaerobic ammonium oxidation (anammox) and electricity generation (anode anammox MFC) by high-effective anammox bacteria fed with purely inorganic nitrogen media was constructed. As the influent concentrations of ammonium (NH4+-N) and nitrite (NO2−-N) gradually increased from 25 to 250 mg/L and 33–330 mg/L, the removal efficiencies of NH4+-N, NO2−-N and TN were over 90%, 90% and 80%, respectively, and the maximum volumetric nitrogen removal rate reached 3.01 ± 0.27 kgN/(m3·d). The maximum voltage and maximum power density were 225.48 ± 10.71 mV and 1308.23 ± 40.38 mW/m3, respectively. Substrate inhibition took place at high nitrogen concentrations (NH4+-N = 300 mg/L, NO2−-N = 396 mg/L). Electricity production performance significantly depended upon the nitrogen removal rate under different nitrogen concentrations. The reported low coulombic efficiency (CE, 4.09–5.99%) may be due to severe anodic polarization. The anode charge transfer resistance accounted for about 90% of the anode resistance. The anode process was the bottleneck for energy recovery and should be further optimized in anode anammox MFCs. The high nitrogen removal efficiency with certain electricity recovery potential in the MFCs suggested that anode anammox MFCs may be used in energy sustainable nitrogen-containing wastewater treatment.

Advances in microbial electrochemistry-enhanced constructed wetlands

Constructed wetland (CW) is an effective ecological technology to treat water pollution and has the significant advantages of high impact resistance, simple construction process, and low maintenance cost. However, under extreme conditions such as low temperature, high salt concentration, and multiple types of pollutants, some bottlenecks exist, including the difficulty in improving operating efficiency and the low pollutant removal rate. Microbial electrochemical technology is an emerging clean energy technology and has the similar structure and pollutant removal mechanism to CW. Microbial electrochemistry combined with CW can improve the overall removal effect of pollutants in wetlands. This review summarizes characterization methods of microbial electrochemistry-enhanced constructed wetland systems, construction methods of different composite systems, mechanisms of single and composite systems, and removal effects of composite systems on different pollutants in water bodies. Based on the shortcomings of existing studies, the potential breakthroughs in microbial electrochemistry-enhanced constructed wetlands are proposed for developing the optimization solution of constructed wetlands.

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.

Recent advances in electro-fermentation technology: A novel approach towards balanced fermentation

Biotransformation of organic substrates via acidogenic fermentation (AF) to high-value products such as C1-C6 carboxylic acids and alcohol serves as platform chemicals for various industrial applications. However, the AF technology suffers from low product titers due to thermodynamic constraints. Recent studies suggest that augmenting AF redox potential can regulate the metabolic pathway and provide seamless electron flow by lowering the activation energy barrier, thus positively influencing the substrate utilization rate, product yield, and speciation. Hence, the augmented AF system with an exogenous electricity supply is termed as electro-fermentation (EF), which has enormous potential to strengthen the fermentation technology domain. Therefore, this critical review systematically discusses the current understanding of EF with a special focus on the extracellular electron transfer mechanism of electroactive bacteria and provides perspectives and research gaps to further improve the technology for green chemical synthesis, sustainable waste management, and circular bio-economy.

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.

Synthetic biology and bioelectrochemical tools for electrogenetic system engineering

Synthetic biology research and its industrial applications rely on deterministic spatiotemporal control of gene expression. Recently, electrochemical control of gene expression has been demonstrated in electrogenetic systems (redox-responsive promoters used alongside redox inducers and electrodes), allowing for the direct integration of electronics with biological processes. However, the use of electrogenetic systems is limited by poor activity, tunability, and standardization. In this work, we developed a strong, unidirectional, redox-responsive promoter before deriving a mutant promoter library with a spectrum of strengths. We constructed genetic circuits with these parts and demonstrated their activation by multiple classes of redox molecules. Last, we demonstrated electrochemical activation of gene expression under aerobic conditions using a novel, modular bioelectrochemical device. These genetic and electrochemical tools facilitate the design and improve the performance of electrogenetic systems. Furthermore, the genetic design strategies used can be applied to other redox-responsive promoters to further expand the available tools for electrogenetics.

Two key Geobacter species of wastewater-enriched electroactive biofilm respond differently to electric field

Electroactive biofilms have attracted increasing attention due to their unique ability to exchange electrons with electrodes. Geobacter spp. are widely found to be dominant in biofilms in acetate-rich environments when an appropriate voltage is applied, but it is still largely unknown how these bacteria are selectively enriched. Herein, two key Geobacter spp. that have been demonstrated predominant in wastewater-enriched electroactive biofilm after long-term operation, G. sulfurreducens and G. anodireducens, responded to electric field (EF) differently, leading to a higher abundance of EF-sensitive G. anodireducens in the strong EF region after cocultivation with G. sulfurreducens. Transcriptome analysis indicated that two-component systems containing sensor histidine kinases and response regulators were the key for EF sensing in G. anodireducens rather than in G. sulfurreducens, which are closely connected to chemotaxis, c-di-GMP, fatty acid metabolism, pilus, oxidative phosphorylation and transcription, resulting in an increase in extracellular polymeric substance secretion and rapid cell proliferation. Our data reveal the mechanism by which EF select specific Geobacter spp. over time, providing new insights into Geobacter biofilm formation regulated by electricity.

Towards Application of Electro-Fermentation for the Production of Value-Added Chemicals From Biomass Feedstocks

According to recent social demands for sustainable developments, the value of biomass as feedstocks for chemical industry is increasing. With the aid of metabolic engineering and genome editing, microbial fermentation has been developed for producing value-added chemicals from biomass feedstocks, while further improvements are desired for producing more diverse chemicals and increasing the production efficiency. The major intrinsic limitation in conventional fermentation technologies is associated with the need for balancing the net redox equivalents between substrates and products, resulting in limited repertories of fermentation products. One solution for this limitation would be “electro-fermentation (EF)” that utilizes bioelectrochemical systems for modifying the intracellular redox state of electrochemically active bacteria, thereby overcoming the redox constraint of fermentation. Recent studies have attempted the production of chemicals based on the concept of EF, while its utility has not been sufficiently demonstrated in terms of low production efficiencies. Here we discuss EF in terms of its concept, current status and future directions, which help us develop its practical applications to sustainable chemical industries.

Engineering Wired Life: Synthetic Biology for Electroactive Bacteria

Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.

Enhanced Bioreduction of Radionuclides by Driving Microbial Extracellular Electron Pumping with an Engineered CRISPR Platform

Dissimilatory metal-reducing bacteria (DMRB) with extracellular electron transfer (EET) capability show great potential in bioremediating the subsurface environments contaminated by uranium through bioreduction and precipitation of hexavalent uranium [U(VI)]. However, the low EET efficiency of DMRB remains a bottleneck for their applications. Herein, we develop an engineered CRISPR platform to drive the extracellular electron pumping of Shewanella oneidensis, a representative DMRB species widely present in aquatic environments. The CRISPR platform allows for highly efficient and multiplex genome editing and rapid platform elimination post-editing in S. oneidensis. Enabled by such a platform, a genomic promoter engineering strategy (GPS) for genome-widely engineering the EET-encoding gene network was established. The production of electron conductive Mtr complex, synthesis of electron shuttle flavin, and generation of NADH as intracellular electron carrier are globally optimized and promoted, leading to a significantly enhanced EET ability. Applied to U(VI) bioreduction, the edited strains achieve up to 3.62-fold higher reduction capacity over the control. Our work endows DMRB with an enhanced ability to remediate the radionuclides-contaminated environments and provides a gene editing approach to handle the growing environmental challenges of radionuclide contaminations.

Mediated electrochemistry for redox-based biological targeting: entangling sensing and actuation for maximizing information transfer

Biology and electronics are both expert at receiving, analyzing, and responding to information, yet they use entirely different information processing paradigms. Biology processes information using networks that are intrinsically molecular while electronics process information through circuits that control the flow of electrons. There is great interest in coupling the molecular logic of biology with the electronic logic of technology, and we suggest that redox (reduction-oxidation) is a uniquely suited modality for interfacing biology with electronics. Specifically, redox is a native biological modality and is accessible to electronics through electrodes. We summarize recent advances in mediated electrochemistry to direct information transfer into biological systems intentionally altering function, exposing it for more advanced interpretation, which can dramatically expand the biotechnological toolbox.

Shewanella oneidensis MR-1 as a bacterial platform for electro-biotechnology

The genus Shewanella comprises over 70 species of heterotrophic bacteria with versatile respiratory capacities. Some of these bacteria are known to be pathogens of fishes and animals, while many are non-pathogens considered to play important roles in the global carbon cycle. A representative strain is Shewanella oneidensis MR-1 that has been intensively studied for its ability to respire diverse electron acceptors, such as oxygen, nitrate, sulfur compounds, metals, and organics. In addition, studies have been focused on its ability as an electrochemically active bacterium that is capable of discharging electrons to and receiving electrons from electrodes in bioelectrochemical systems (BESs) for balancing intracellular redox states. This ability is expected to be applied to electro-fermentation (EF) for producing value-added chemicals that conventional fermentation technologies are difficult to produce efficiently. Researchers are also attempting to utilize its electrochemical ability for controlling gene expression, for which electro-genetics (EG) has been coined. Here we review fundamental knowledge on this bacterium and discuss future directions of studies on its applications to electro-biotechnology (EB).

Bioelectronic control of a microbial community using surface-assembled electrogenetic cells to route signals

We developed a bioelectronic communication system that is enabled by a redox signal transduction modality to exchange information between a living cell-embedded bioelectronics interface and an engineered microbial network. A naturally communicating three-member microbial network is 'plugged into' an external electronic system that interrogates and controls biological function in real time. First, electrode-generated redox molecules are programmed to activate gene expression in an engineered population of electrode-attached bacterial cells, effectively creating a living transducer electrode. These cells interpret and translate electronic signals and then transmit this information biologically by producing quorum sensing molecules that are, in turn, interpreted by a planktonic coculture. The propagated molecular communication drives expression and secretion of a therapeutic peptide from one strain and simultaneously enables direct electronic feedback from the second strain, thus enabling real-time electronic verification of biological signal propagation. Overall, we show how this multifunctional bioelectronic platform, termed a BioLAN, reliably facilitates on-demand bioelectronic communication and concurrently performs programmed tasks.

Food Waste Biorefinery: Pathway towards Circular Bioeconomy

Food waste biorefineries for the production of biofuels, platform chemicals and other bio-based materials can significantly reduce a huge environmental burden and provide sustainable resources for the production of chemicals and materials. This will significantly contribute to the transition of the linear based economy to a more circular economy. A variety of chemicals, biofuels and materials can be produced from food waste by the integrated biorefinery approach. This enhances the bioeconomy and helps toward the design of more green, ecofriendly, and sustainable methods of material productions that contribute to sustainable development goals. The waste biorefinery is a tool to achieve a value-added product that can provide a better utilization of materials and resources while minimizing and/or eliminating environmental impacts. Recently, food waste biorefineries have gained momentum for the production of biofuels, chemicals, and bio-based materials due to the shifting of regulations and policies towards sustainable development. This review attempts to explore the state of the art of food waste biorefinery and the products associated with it.

Molecular mechanisms regulating the catabolic and electrochemical activities of Shewanella oneidensis MR-1

Electrochemically active bacteria (EAB) interact electrochemically with electrodes via extracellular electron transfer (EET) pathways. These bacteria have attracted significant attention due to their utility in environmental-friendly bioelectrochemical systems (BESs), including microbial fuel cells and electrofermentation systems. The electrochemical activity of EAB is dependent on their carbon catabolism and respiration; thus, understanding how these processes are regulated will provide insights into the development of a more efficient BES. The process of biofilm formation by EAB on BES electrodes is also important for electric current generation because it facilitates physical and electrochemical interactions between EAB cells and electrodes. This article summarizes the current knowledge on EET-related metabolic and cellular functions of a model EAB, Shewanella oneidensis MR-1, focusing specifically on regulatory systems for carbon catabolism, EET pathways, and biofilm formation. Based on recent developments, the author also discusses potential uses of engineered S. oneidensis strains for various biotechnological applications.

Cytochromes in Extracellular Electron Transfer in Geobacter

Extracellular electron transfer (EET) is an important biological process in microbial physiology as found in dissimilatory metal oxidation/reduction and interspecies electron transfer in syntrophy in natural environments. EET also plays a critical role in microorganisms relevant to environmental biotechnology in metal-contaminated areas, metal corrosion, bioelectrochemical systems, and anaerobic digesters. Geobacter species exist in a diversity of natural and artificial environments. One of the outstanding features of Geobacter species is the capability of direct EET with solid electron donors and acceptors, including metals, electrodes, and other cells. Therefore, Geobacter species are pivotal in environmental biogeochemical cycles and biotechnology applications. Geobacter sulfurreducens, a representative Geobacter species, has been studied for direct EET as a model microorganism. G. sulfurreducens employs electrically conductive pili (e-pili) and c-type cytochromes for the direct EET. The biological function and electronics applications of the e-pili have been reviewed recently, and this review focuses on the cytochromes. Geobacter species have an unusually large number of cytochromes encoded in their genomes. Unlike most other microorganisms, Geobacter species localize multiple cytochromes in each subcellular fraction, outer membrane, periplasm, and inner membrane, as well as in the extracellular space, and differentially utilize these cytochromes for EET with various electron donors and acceptors. Some of the cytochromes are functionally redundant. Thus, the EET in Geobacter is complicated. Geobacter coordinates the cytochromes with other cellular components in the elaborate EET system to flourish in the environment.

Identification of a Diguanylate Cyclase That Facilitates Biofilm Formation on Electrodes by Shewanella oneidensis MR-1

In many bacteria, cyclic diguanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclase (DGC), serves as a second messenger involved in the regulation of biofilm formation. Although studies have suggested that c-di-GMP also regulates the formation of electrochemically active biofilms (EABFs) by Shewanella oneidensis MR-1, DGCs involved in this process remained to be identified. Here, we report that the SO_1646 gene, hereafter named dgcS, is upregulated under medium flow conditions in electrochemical flow cells (EFCs), and its product (DgcS) functions as a major DGC in MR-1. In vitro assays demonstrated that purified DgcS catalyzed the synthesis of c-di-GMP from GTP. Comparisons of intracellular c-di-GMP levels in the wild-type strain and a dgcS deletion mutant (ΔdgcS mutant) showed that production of c-di-GMP was markedly reduced in the ΔdgcS mutant when cells were grown in batch cultures and on electrodes in EFCs. Cultivation of the ΔdgcS mutant in EFCs also revealed that the loss of DgcS resulted in impaired biofilm formation and decreased current generation. These findings demonstrate that MR-1 uses DgcS to synthesize c-di-GMP under medium flow conditions, thereby activating biofilm formation on electrodes.IMPORTANCE Bioelectrochemical systems (BESs) have attracted wide attention owing to their utility in sustainable biotechnology processes, such as microbial fuel cells and electrofermentation systems. In BESs, electrochemically active bacteria (EAB) form biofilms on electrode surfaces, thereby serving as effective catalysts for the interconversion between chemical and electric energy. It is therefore important to understand mechanisms for the formation of biofilm by EAB grown on electrodes. Here, we show that a model EAB, S. oneidensis MR-1, expresses DgcS as a major DGC, thereby activating the formation of biofilms on electrodes via c-di-GMP-dependent signal transduction cascades. The findings presented herein provide the molecular basis for improving electrochemical interactions between EAB and electrodes in BESs. The results also offer molecular insights into how Shewanella regulates biofilm formation on solid surfaces in the natural environment.

Operation mechanism of constructed wetland-microbial fuel cells for wastewater treatment and electricity generation: A review

Constructed wetland-microbial fuel cells (CWL-MFCs) are eco-friendly and sustainable technology, simultaneously implementing contaminant removal and electricity production. According to intensive research over the last five years, this review on the operation mechanism was conducted for in-depth understanding and application guidance of CWL-MFCs. The electrochemical mechanism based on anodic oxidation and cathodic reduction is the core for improved treatment in CWL-MFCs compared to CWLs. As the dominant bacterial community, the abundance and gene-expression patterns of electro-active bacteria responds to electrode potentials and contaminant loadings, further affecting operational efficiency of CWL-MFCs. Plants benefit COD and N removal by supplying oxygen for aerobic degradation and rhizosphere secretions for microorganisms. Multi-electrode configuration, carbon-based electrodes and rich porous substrates affect transfer resistance and bacterial communities. The possibilities of CWL-MFCs targeting at recalcitrant contaminants like flame retardants and interchain interactions among effect components need systematic research.

Redox Electrochemistry to Interrogate and Control Biomolecular Communication

Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.

A redox-based electrogenetic CRISPR system to connect with and control biological information networks

Electronic information can be transmitted to cells directly from microelectronics via electrode-activated redox mediators. These transmissions are decoded by redox-responsive promoters which enable user-specified control over biological function. Here, we build on this redox communication modality by establishing an electronic eCRISPR conduit of information exchange. This system acts as a biological signal processor, amplifying signal reception and filtering biological noise. We electronically amplify bacterial quorum sensing (QS) signaling by activating LasI, the autoinducer-1 synthase. Similarly, we filter out unintended noise by inhibiting the native SoxRS-mediated oxidative stress response regulon. We then construct an eCRISPR based redox conduit in both E. coli and Salmonella enterica. Finally, we display eCRISPR based information processing that allows transmission of spatiotemporal redox commands which are then decoded by gelatin-encapsulated E. coli. We anticipate that redox communication channels will enable biohybrid microelectronic devices that could transform our abilities to electronically interpret and control biological function.

CRISPR/Cas9-mediated genome editing of Shewanella oneidensis MR-1 using a broad host-range pBBR1-based plasmid

Here, we developed an all-in-one, broad host-range CRISPR/Cas9 vector system widely applicable to genome editing of proteobacteria. Plasmid pBBR1-Cas9 was constructed by cloning the cas9 gene from Streptococcus pyogenes into the broad host-range plasmid pBBR1MCS-2. We evaluated its applicability for frameshift mutagenesis of Shewanella oneidensis MR-1. Significant cell death was observed when MR-1 cells were transformed with a pBBR1-Cas9 derivative that expressed a single-guide RNA targeting the crp gene. However, cell death was partially prevented when a donor DNA fragment containing a modified crp sequence with a frameshift mutation was introduced using the same vector. All transformants (9 colonies) contained the expected frameshift mutation in their chromosomal crp genes. These results indicate that this vector system efficiently introduced CRISPR/Cas9-mediated double-strand DNA breaks and subsequent homology-directed repair. This work provides a simple and powerful genome-editing tool for proteobacteria that can harbor pBBR1-based plasmids.

Biofouling effects on the performance of microbial fuel cells and recent advances in biotechnological and chemical strategies for mitigation

The occurrence of biofouling in MFC can cause severe problems such as hindering proton transfer and increasing the ohmic and charge transfer resistance of cathodes, which results in a rapid decline in performance of MFC. This is one of the main reasons why scaling-up of MFCs has not yet been successfully accomplished. The present review article is a wide-ranging attempt to provide insights to the biofouling mechanisms on surfaces of MFC, mainly on proton exchange membranes and cathodes, and their effects on performance of MFC based on theoretical and practical evidence. Various biofouling mitigation techniques for membranes are discussed, including preparation of antifouling composite membranes, modification of the physical and chemical properties of existing membranes, and coating with antifouling agents. For cathodes of MFC, use of Ag nanoparticles, Ag-based composite nanoparticles, and antifouling chemicals is outlined in considerable detail. Finally, prospective techniques for mitigation of biofouling are discussed, which have not been given much previous attention in the field of MFC research. This article will help to enhance understanding of the severity of biofouling issues in MFCs and provides up-to-date solutions. It will be beneficial for scientific communities for further strengthening MFC research and will also help in progressing this cutting-edge technology to scale-up, using the most efficient methods as described here.

Overexpression of the adenylate cyclase gene cyaC facilitates current generation by Shewanella oneidensis in bioelectrochemical systems

Electrochemically active bacteria (EAB) are capable of electrochemical interactions with electrodes via extracellular electron transfer (EET) pathways and serve as essential components in bioelectrochemical systems. Previous studies have suggested that EAB, such as Shewanella oneidensis MR-1, use cyclic AMP (cAMP) receptor proteins to coordinately regulate the expression of catabolic and EET-related genes, prompting us to hypothesize that the intracellular cAMP concentration is an important factor determining the electrochemical activities of EAB. The present study constructed an MR-1 mutant, cyaC-OE, that overexpressed cyaC, a gene encoding a membrane-bound class III adenylate cyclase, and examined its electrochemical and transcriptomic characteristics. We show that the intracellular cAMP concentration in cyaC-OE is more than five times that in wild-type MR-1, and that cya-OE generates approximately two-fold higher current in BES than the wild-type strain. In addition, the expression of genes involved in EET and anaerobic carbon catabolism is up-regulated in cya-OE compared to that in the wild-type strain. These results suggest that increasing the intracellular cAMP level is a promising approach for constructing EAB with high catabolic and electrochemical activities.