Periplasmic electron transfer via the c-type cytochromes MtrA and FccA of Shewanella oneidensis MR-1

A biocompatible surface display approach in Shewanella promotes current output efficiency

The biology-material hybrid method for chemical-electricity conversion via microbial fuel cells (MFCs) has garnered significant attention in addressing global energy and environmental challenges. However, the efficiency of these systems remains unsatisfactory due to the complex manufacturing process and limited biocompatibility. To overcome these challenges, here, we developed a simple bio-inorganic hybrid system for bioelectricity generation in Shewanella oneidensis (S. oneidensis) MR-1. A biocompatible surface display approach was designed, and silver-binding peptide AgBP2 was expressed on the cell surface. Notably, the engineered Shewanella showed a higher electrochemical sensitivity to Ag+, and a 60 % increase in power density was achieved even at a low concentration of 10 μM Ag+. Further analysis revealed significant upregulations of cell surface negative charge intensity, ATP metabolism, and reducing equivalent (NADH/NAD+) ratio in the engineered S. oneidensis-Ag nanoparticles biohybrid. This work not only provides a novel insight for electrochemical biosensors to detect metal ions, but also offers an alternative biocompatible surface display approach by combining compatible biomaterials with electricity-converting bacteria for advancements in biohybrid MFCs.

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.

Effect of soil organic matter-mediated electron transfer on heavy metal remediation: Current status and perspectives

Soil contamination by heavy metals poses major risks to human health and the environment. Given the current status of heavy metal pollution, many remediation techniques have been tested at laboratory and contaminated sites. The effects of soil organic matter-mediated electron transfer on heavy metal remediation have not been adequately studied, and the key mechanisms underlying this process have not yet been elucidated. In this review, microbial extracellular electron transfer pathways, organic matter electron transfer for heavy metal reduction, and the factors affecting these processes were discussed to enhance our understanding of heavy metal pollution. It was found that microbial extracellular electrons delivered by electron shuttles have the longest distance among the three electron transfer pathways, and the application of exogenous electron shuttles lays the foundation for efficient and persistent remediation of heavy metals. The organic matter-mediated electron transfer process, wherein organic matter acts as an electron shuttle, promotes the conversion of high valence state metal ions, such as Cr(VI), Hg(II), and U(VI), into less toxic and morphologically stable forms, which inhibits their mobility and bioavailability. Soil type, organic matter structural and content, heavy metal concentrations, and environmental factors (e.g., pH, redox potential, oxygen conditions, and temperature) all influence organic matter-mediated electron transfer processes and bioremediation of heavy metals. Organic matter can more effectively mediate electron transfer for heavy metal remediation under anaerobic conditions, as well as when the heavy metal content is low and the redox potential is suitable under fluvo-aquic/paddy soil conditions. Organic matter with high aromaticity, quinone groups, and phenol groups has a stronger electron transfer ability. This review provides new insights into the control and management of soil contamination and heavy metal remediation technologies.

Optimizing the Metal Bioreduction Process in Recombinant Shewanella azerbaijanica Bacteria: A Novel Approach via mtrC Gene Cloning and Nitrate-Reducing Pathway Destruction

Environmental pollution is growing every day in terms of the increase in population, industrialization, and urbanization. Shewanella azerbaijanica is introduced as a highly potent bacterium in metal bioremediation. The mtrC gene was selected as a cloning target to improve electron flux chains in the EET (extracellular electron transfer) pathway. Using the SDM (site-directed mutagenesis) technique, the unique gene assembly featured the mtrC gene sandwiched between two napD/B genes to disrupt the nitrate reduction pathway, which serves as the primary metal reduction competitor. Shew-mtrC gene construction was transferred to expression plasmid pET28a (+) in the expression host bacteria (E. coli BL21 and S. azerbaijanica), in pUC57, cloning plasmid, which was transferred to the cloning host bacteria E. coli Top10 and S. azerbaijanica. All cloning procedures (i.e., synthesis, insertion, transformation, cloning, and protein expression) were verified and confirmed by precise tests. ATR-FTIR analysis, CD, western blotting, affinity chromatography, SDS-PAGE, and other techniques were used to confirm the expression and structure of the MtrC protein. The genome sequence and primers were designed according to the submitted Shewanella oneidensis MR-1 genome, the most similar bacteria to this native species. The performance of recombinant S. azerbaijanica bacterium in metal bioremediation, as sustainable strategy, has to be verified by more research.

Enhanced MFC sensor performances and extracellular electron transport efficiency mediated by biochar and underlying biochemical mechanisms

To explore the application of biosensor in real-time monitoring of composite heavy metal polluted wastewater in view of the low performance of MFC sensor, this study used sodium alginate to immobilize biochar to the anode of MFC biosensor, and conducted a study on the sensor performance and related biological processes. The results showed that under the optimal HRT conditions, the output power of the MFC-sensor (BC-300) was 0.432 W/m³ after biochar modification, which was much higher than the highest power density of CG and BC-0 of 0.117 and 0.088 W/m³. The correlation coefficient was greater than that of the control group at the plating wastewater concentration of 0.1-1.0 M and had a wider detection range, and the time to recover the output voltage was 1/3 of that of the control group. The biochar significantly promoted the sensitivity, interference resistance, recovery and anti-interference performance of the MFC-sensor. The intrinsic mechanism was that the composition and structure of biochar lead to a 1.53 fold increase in the abundance of electrogenic microorganisms and the abundance of functional genes such as cytochrome c (MtrABC, CymA, Cox, etc.) and flavin (riba, Rib B, gdh, ushA, IDH, etc.) increased by about 1.03-3.20 times, which promoted the shift of electrons from intracellular to extracellular receptors and significantly improved the electron transfer and the energy metabolism efficiency. The results of this study can provide a reference for the application of MFCsensor to the detection of complex heavy metal effluents.

Synthetic Biology Toolbox, Including a Single-Plasmid CRISPR-Cas9 System to Biologically Engineer the Electrogenic, Metal-Resistant Bacterium Cupriavidus metallidurans CH34

Cupriavidus metallidurans CH34 exhibits extraordinary metabolic versatility, including chemolithoautotrophic growth; degradation of BTEX (benzene, toluene, ethylbenzene, xylene); high resistance to numerous metals; biomineralization of gold, platinum, silver, and uranium; and accumulation of polyhydroxybutyrate (PHB). These qualities make it a valuable host for biotechnological applications such as bioremediation, bioprocessing, and the generation of bioelectricity in microbial fuel cells (MFCs). However, the lack of genetic tools for strain development and studying its fundamental physiology represents a bottleneck to boosting its commercial applications. In this study, inducible and constitutive promoter libraries were built and characterized, providing the first comprehensive list of biological parts that can be used to regulate protein expression and optimize the CRISPR-Cas9 genome editing tools for this host. A single-plasmid CRISPR-Cas9 system that can be delivered by both conjugation and electroporation was developed, and its efficiency was demonstrated by successfully targeting the pyrE locus. The CRISPR-Cas9 system was next used to target candidate genes encoding type IV pili, hypothesized by us to be involved in extracellular electron transfer (EET) in this organism. Single and double deletion strains (ΔpilA, ΔpilE, and ΔpilAE) were successfully generated. Additionally, the CRISPR-Cas9 tool was validated for constructing genomic insertions (ΔpilAE::gfp and ΔpilAE::λ_Prgfp). Finally, as type IV pili are believed to play an important role in extracellular electron transfer to solid surfaces, C. metallidurans CH34 ΔpilAE was further studied by means of cyclic voltammetry using disposable screen-printed carbon electrodes. Under these conditions, we demonstrated that C. metallidurans CH34 could generate extracellular currents; however, no difference in the intensity of the current peaks was found in the ΔpilAE double deletion strain when compared to the wild type. This finding suggests that the deleted type IV pili candidate genes are not involved in extracellular electron transfer under these conditions. Nevertheless, these experiments revealed the presence of different redox centers likely to be involved in both mediated electron transfer (MET) and direct electron transfer (DET), the first interpretation of extracellular electron transfer mechanisms in C. metallidurans CH34.

A Common Target of Nitrite and Nitric Oxide for Respiration Inhibition in Bacteria

Nitrite and nitric oxide (NO) are well-known bacteriostatic agents with similar biochemical properties. However, many studies have demonstrated that inhibition of bacterial growth by nitrite is independent of NO. Here, with Shewanella oneidensis as the research model because of its unusually high cytochrome (cyt) c content, we identify a common mechanism by which nitrite and NO compromise cyt c biosynthesis in bacteria, and thereby inhibit respiration. This is achieved by eliminating the inference of the cyclic adenosine monophosphate-catabolite repression protein (cAMP-Crp), a primary regulatory system that controls the cyt c content and whose activity is subjected to the repression of nitrite. Both nitrite and NO impair the CcmE of multiple bacteria, an essential heme chaperone of the System I cyt c biosynthesis apparatus. Given that bacterial targets of nitrite and NO differ enormously and vary even in the same genus, these observations underscore the importance of cyt c biosynthesis for the antimicrobial actions of nitrite and NO.

Enhancing Microbial Electron Transfer Through Synthetic Biology and Biohybrid Approaches: Part II : Combining approaches for clean energy

It is imperative to develop novel processes that rely on cheap, sustainable and abundant resources whilst providing carbon circularity. Microbial electrochemical technologies (MET) offer unique opportunities to facilitate the conversion of chemicals to electrical energy or vice versa by harnessing the metabolic processes of bacteria to valorise a range of waste products including greenhouse gases (GHGs). Part I (1) introduced the EET pathways, their limitations and applications. Here in Part II, we outline the strategies researchers have used to modulate microbial electron transfer, through synthetic biology and biohybrid approaches and present the conclusions and future directions.

Autotrophic nitrate reduction to ammonium via reverse electron transfer in Geobacter dominated biofilm

Geobacter dominated electroactive biofilms (EABs) have been demonstrated to perform bidirectional extracellular electron transfer (EET) in bioelectrochemical systems, but it is largely unknown when nitrate is the electron acceptor at the cathode. If reverse EET occurs on biocathode, this EAB has to perform dissimilatory nitrate reduction to ammonia (DNRA) rather than denitrification according to genomes. Here, we have proven the feasibility of reverse bioelectron transfer in EAB, achieving a DNRA efficiency up to 93 ± 3% and high Faraday efficiency of 74 ± 1%. Constant current was found to be more effective than constant potential to maintain Geobacter on the cathode, which highly determines this electrotrophic respiration. The prevalent DNRA at constant current surpassed denitrification, demonstrated by the reverse tendencies of DNRA (nrfA) and denitrification (nirS and nirK) gene transcription. Metatranscriptomics further revealed the possible electron uptake mechanisms by which the outer membrane (OmcZ and OmcB) and periplasmic cytochromes (PpcB and PpcD) may be involved. These findings extend our understanding of the bidirectional electron transfer and advance the applications of EABs.

Direct microbial electron uptake as a mechanism for stainless steel corrosion in aerobic environments

Shewanella oneidensis MR-1 is an attractive model microbe for elucidating the biofilm-metal interactions that contribute to the billions of dollars in corrosion damage to industrial applications each year. Multiple mechanisms for S. oneidensis-enhanced corrosion have been proposed, but none of these mechanisms have previously been rigorously investigated with methods that rule out alternative routes for electron transfer. We found that S. oneidensis grown under aerobic conditions formed thick biofilms (∼50 µm) on stainless steel coupons, accelerating corrosion over sterile controls. H₂ and flavins were ruled out as intermediary electron carriers because stainless steel did not reduce riboflavin and previous studies have demonstrated stainless does not generate H₂. Strain ∆mtrCBA, in which the genes for the most abundant porin-cytochrome conduit in S. oneidensis were deleted, corroded stainless steel substantially less than wild-type in aerobic cultures. Wild-type biofilms readily reduced nitrate with stainless steel as the sole electron donor under anaerobic conditions, but strain ∆mtrCBA did not. These results demonstrate that S. oneidensis can directly consume electrons from iron-containing metals and illustrate how direct metal-to-microbe electron transfer can be an important route for corrosion, even in aerobic environments.

Modular configurations of living biomaterials incorporating nano-based artificial mediators and synthetic biology to improve bioelectrocatalytic performance: A review

Currently, the industrial application of bioelectrochemical systems (BESs) that are incubated with natural electrochemically active microbes (EABs) is limited due to inefficient extracellular electron transfer (EET) by natural EABs. Notably, recent studies have identified several novel living biomaterials comprising highly efficient electron transfer systems allowing unparalleled proficiency of energy conversion. Introduction of these biomaterials into BESs could fundamentally increase their utilization for a wide range of applications. This review provides a comprehensive assessment of recent advancements in the design of living biomaterials that can be exploited to enhance bioelectrocatalytic performance. Further, modular configurations of abiotic and biotic components promise a powerful enhancement through integration of nano-based artificial mediators and synthetic biology. Herein, recent advancements in BESs are synthesized and assessed, including heterojunctions between conductive nanomaterials and EABs, in-situ hybrid self-assembly of EABs and nano-sized semiconductors, cytoprotection in biohybrids, synthetic biological modifications of EABs and electroactive biofilms. Since living biomaterials comprise a broad range of disciplines, such as molecular biology, electrochemistry and material sciences, full integration of technological advances applied in an interdisciplinary framework will greatly enhance/advance the utility and novelty of BESs. Overall, emerging fundamental knowledge concerning living biomaterials provides a powerful opportunity to markedly boost EET efficiency and facilitate the industrial application of BESs to meet global sustainability challenges/goals.

Determinants of Multiheme Cytochrome Extracellular Electron Transfer Uncovered by Systematic Peptide Insertion

The multiheme cytochrome MtrA enables microbial respiration by transferring electrons across the outer membrane to extracellular electron acceptors. While structural studies have identified residues that mediate the binding of MtrA to hemes and to other cytochromes that facilitate extracellular electron transfer (EET), the relative importance of these interactions for EET is not known. To better understand EET, we evaluated how insertion of an octapeptide across all MtrA backbone locations affects Shewanella oneidensis MR-1 respiration on Fe(III). The EET efficiency was found to be inversely correlated with the proximity of the insertion to the heme prosthetic groups. Mutants with decreased EET efficiencies also arose from insertions in a subset of the regions that make residue-residue contacts with the porin MtrB, while all sites contacting the extracellular cytochrome MtrC presented high peptide insertion tolerance. MtrA variants having peptide insertions within the CXXCH motifs that coordinate heme cofactors retained some ability to support respiration on Fe(III), although these variants presented significantly decreased EET efficiencies. Furthermore, the fitness of cells expressing different MtrA variants under Fe(III) respiration conditions correlated with anode reduction. The peptide insertion profile, which represents the first comprehensive sequence-structure-function map for a multiheme cytochrome, implicates MtrA as a strategic protein engineering target for the regulation of EET.

CRISPR/dCas9-RpoD-Mediated Simultaneous Transcriptional Activation and Repression in Shewanella oneidensis MR-1

Extracellular electron transfer (EET) of electroactive microorganisms (EAMs) is the dominating factor for versatile applications of bio-electrochemical systems. Shewanella oneidensis MR-1 is one of the model EAMs for the study of EET, which is associated with a variety of cellular activities. However, due to the lack of a transcriptional activation tool, regulation of multiple genes is labor-intensive and time-consuming, which hampers the advancement of improving the EET efficiency in S. oneidensis. In this study, we developed an easily operated and multifunctional regulatory tool, that is, a simultaneous clustered regularly interspaced short palindromic repeats (CRISPR)-mediated transcriptional activation (CRISPRa) and interference (CRISPRi) system, for application in S. oneidensis. First, a large number of activators were screened, and RpoD (σ⁷⁰) was determined as the optimal activator. Second, the effective activation range was identified to be 190-216 base upstream of the transcriptional start site. Third, up- and downregulation was achieved in concert by two orthogonal single guide RNAs targeting different positions. The activation of the cell division gene (minCDE) and repression of the cytotoxic gene (SO_3166) were concurrently implemented, increasing the power density by 2.5-fold and enhancing the degradation rate of azo dyes by 2.9-fold. The simultaneous CRISPRa and CRISPRi system enables simultaneous multiplex genetic regulation, offering the potential to further advance studies of the EET mechanism and application in S. oneidensis.

Unexpected role of electron-transfer hub in direct degradation of pollutants by exoelectrogenic bacteria

Exoelectrogenic bacteria (EEB) are capable of anaerobic respiration with diverse extracellular electron acceptors including insoluble minerals, electrodes and flavins, but the detailed electron transfer pathways and reaction mechanisms remain elusive. Here, we discover that CymA, which is usually considered to solely serve as an inner-membrane electron transfer hub in Shewanella oneidensis MR-1 (a model EEB), might also function as a reductase for direct reducing diverse nitroaromatic compounds (e.g., 2,4-dichloronitrobenzene) and azo dyes. Such a process can be accelerated by dosing anthraquinone-2,6-disulfonate. The CymA-based reduction pathways in S. oneidensis MR-1 for different contaminants could be functionally reconstructed and strengthened in Escherichia coli. The direct reduction of lowly polar contaminants by quinol oxidases like CymA homologs might be universal in diverse microbes. This work offers new insights into the pollutant reduction mechanisms of EEB and unveils a new function of CymA to act as a terminal reductase. This article is protected by copyright. All rights reserved.

Promoting Extracellular Electron Transfer of Shewanella oneidensis MR-1 by Optimizing the Periplasmic Cytochrome c Network

The low efficiency of extracellular electron transfer (EET) is a major bottleneck for Shewanella oneidensis MR-1 acting as an electroactive biocatalyst in bioelectrochemical systems. Although it is well established that a periplasmic c-type cytochrome (c-Cyt) network plays a critical role in regulating EET efficiency, the understanding of the network in terms of structure and electron transfer activity is obscure and partial. In this work, we attempted to systematically investigate the impacts of the network components on EET in their absence and overproduction individually in microbial fuel cell (MFC). We found that overexpression of c-Cyt CctA leads to accelerated electron transfer between CymA and the Mtr system, which function as the primary quinol oxidase and the outer-membrane (OM) electron hub in EET. In contrast, NapB, FccA, and TsdB in excess severely impaired EET, reducing EET capacity in MFC by more than 50%. Based on the results from both strategies, a series of engineered strains lacking FccA, NapB, and TsdB in combination while overproducing CctA were tested for a maximally optimized c-Cyt network. A strain depleted of all NapB, FccA, and TsdB with CctA overproduction achieved the highest maximum power density in MFCs (436.5 mW/m²), ∼3.62-fold higher than that of wild type (WT). By revealing that optimization of periplasmic c-Cyt composition is a practical strategy for improving EET efficiency, our work underscores the importance in understanding physiological and electrochemical characteristics of c-Cyts involved in EET.

Extracellular riboflavin induces anaerobic biofilm formation in Shewanella oneidensis

BACKGROUND

Some microorganisms can respire with extracellular electron acceptors using an extended electron transport chain to the cell surface. This process can be applied in bioelectrochemical systems in which the organisms produce an electrical current by respiring with an anode as electron acceptor. These organisms apply flavin molecules as cofactors to facilitate one-electron transfer catalyzed by the terminal reductases and in some cases as endogenous electron shuttles.

RESULTS

In the model organism Shewanella oneidensis, riboflavin production and excretion trigger a specific biofilm formation response that is initiated at a specific threshold concentration, similar to canonical quorum-sensing molecules. Riboflavin-mediated messaging is based on the overexpression of the gene encoding the putrescine decarboxylase speC which leads to posttranscriptional overproduction of proteins involved in biofilm formation. Using a model of growth-dependent riboflavin production under batch and biofilm growth conditions, the number of cells necessary to produce the threshold concentration per time was deduced. Furthermore, our results indicate that specific retention of riboflavin in the biofilm matrix leads to localized concentrations, which by far exceed the necessary threshold value.

CONCLUSION

This study describes a new quorum-sensing mechanism in S. oneidensis. Biofilm formation of S. oneidensis is induced by low concentrations of riboflavin resulting in an upregulation of the ornithine-decarboxylase speC. The results can be applied for the development of strains catalyzing increased current densities in bioelectrochemical systems.

Bacterial extracellular electron transfer: a powerful route to the green biosynthesis of inorganic nanomaterials for multifunctional applications

Synthesis of inorganic nanomaterials such as metal nanoparticles (MNPs) using various biological entities as smart nanofactories has emerged as one of the foremost scientific endeavors in recent years. The biosynthesis process is environmentally friendly, cost-effective and easy to be scaled up, and can also bring neat features to products such as high dispersity and biocompatibility. However, the biomanufacturing of inorganic nanomaterials is still at the trial-and-error stage due to the lack of understanding for underlying mechanism. Dissimilatory metal reduction bacteria, especially Shewanella and Geobacter species, possess peculiar extracellular electron transfer (EET) features, through which the bacteria can pump electrons out of their cells to drive extracellular reduction reactions, and have thus exhibited distinct advantages in controllable and tailorable fabrication of inorganic nanomaterials including MNPs and graphene. Our aim is to present a critical review of recent state-of-the-art advances in inorganic biosynthesis methodologies based on bacterial EET using Shewanella and Geobacter species as typical strains. We begin with a brief introduction about bacterial EET mechanism, followed by reviewing key examples from literatures that exemplify the powerful activities of EET-enabled biosynthesis routes towards the production of a series of inorganic nanomaterials and place a special emphasis on rationally tailoring the structures and properties of products through the fine control of EET pathways. The application prospects of biogenic nanomaterials are then highlighted in multiple fields of (bio-) energy conversion, remediation of organic pollutants and toxic metals, and biomedicine. A summary and outlook are given with discussion on challenges of bio-manufacturing with well-defined controllability.

Engineering S. oneidensis for Performance Improvement of Microbial Fuel Cell-a Mini Review

Microbial fuel cell (MFC) is a promising technology that utilizes exoelectrogens cultivated in the form of biofilm to generate power from various types of sources supplied. A metal-reducing pathway is utilized by these organisms to transfer electrons obtained from the metabolism of substrate from anaerobic respiration extracellularly. A widely established model organism that is capable of extracellular electron transfer (EET) is Shewanella oneidensis. This review highlights the strategies used in the transformation of S. oneidensis and the recent development of MFC in terms of intervention through genetic modifications. S. oneidensis was genetically engineered for several aims including the study on the underlying mechanisms of EET, and the enhancement of power generation and wastewater treating potential when used in an MFC. Through engineering S. oneidensis, genes responsible for EET are identified and strategies on enhancing the EET efficiency are studied. Overexpressing genes related to EET to enhance biofilm formation, mediator biosynthesis, and respiration appears as one of the common approaches.

Rediverting Electron Flux with an Engineered CRISPR-ddAsCpf1 System to Enhance the Pollutant Degradation Capacity of Shewanella oneidensis

Pursuing efficient approaches to promote the extracellular electron transfer (EET) of extracellular respiratory bacteria is essential to their application in environmental remediation and waste treatment. Here, we report a new strategy of tuning electron flux by clustered regularly interspaced short palindromic repeat (CRISPR)-ddAsCpf1-based rediverting (namely STAR) to enhance the EET capacity of Shewanella oneidensis MR-1, a model extracellular respiratory bacterium widely present in the environment. The developed CRISPR-ddAsCpf1 system enabled approximately 100% gene repression with the green fluorescent protein (GFP) as a reporter. Using a WO₃ probe, 10 representative genes encoding for putative competitive electron transfer proteins were screened, among which 7 genes were identified as valid targets for EET enhancement. Repressing the valid genes not only increased the transcription level of the l-lactate metabolism genes but also affected the genes involved in direct and indirect EET. Increased riboflavin production was also observed. The feasibility of this strategy to enhance the bioreduction of methyl orange, an organic pollutant, and chromium, a typical heavy metal, was demonstrated. This work implies a great potential of the STAR strategy with the CIRPSR-ddAsCpf1 system for enhancing bacterial EET to favor more efficient environmental remediation applications.

A Novel "Microbial Bait" Technique for Capturing Fe(III)-Reducing Bacteria

Microbial reduction of Fe(III) is a key geochemical process in anoxic environments, controlling the degradation of organics and the mobility of metals and radionuclides. To further understand these processes, it is vital to develop a reliable means of capturing Fe(III)-reducing microorganisms from the field for analysis and lab-based investigations. In this study, a novel method of capturing Fe(III)-reducing bacteria using Fe(III)-coated pumice "microbe-baits" was demonstrated. The methodology involved the coating of pumice (approximately diameter 4 to 6 mm) with a bioavailable Fe(III) mineral (akaganeite), and was verified by deployment into a freshwater spring for 2 months. On retrieval, the coated pumice baits were incubated in a series of lab-based microcosms, amended with and without electron donors (lactate and acetate), and incubated at 20°C for 8 weeks. 16S rRNA gene sequencing using the Illumina MiSeq platform showed that the Fe(III)-coated pumice baits, when incubated in the presence of lactate and acetate, enriched for Deltaproteobacteria (relative abundance of 52% of the sequences detected corresponded to Geobacter species and 24% to Desulfovibrio species). In the absence of added electron donors, Betaproteobacteria were the most abundant class detected, most heavily represented by a close relative to Rhodoferax ferrireducens (15% of species detected), that most likely used organic matter sequestered from the spring waters to support Fe(III) reduction. In addition, TEM-EDS analysis of the Fe(III)-coated pumice slurries amended with electron donors revealed that a biogenic Fe(II) mineral, magnetite, was formed at the end of the incubation period. These results demonstrate that Fe(III)-coated pumice "microbe baits" can potentially help target metal-reducing bacteria for culture-dependent studies, to further our understanding of the nano-scale microbe-mineral interactions in aquifers.

Lack of Periplasmic Non-heme Protein SorA Increases Shewanella decolorationis Current Generation

Bacterial extracellular electron transport (EET) plays an important role in many natural and engineering processes. Some periplasmic non-heme redox proteins usually coexist with c-type cytochromes (CTCs) during the EET process. However, in contrast to CTCs, little is known about the roles of these non-heme redox proteins in EET. In this study, the transcriptome of Shewanella decolorationis S12 showed that the gene encoding a periplasmic sulfite dehydrogenase molybdenum-binding subunit SorA was significantly up-regulated during electrode respiration in microbial fuel cells (MFCs) compared with that during azo-dye reduction. The maximum current density of MFCs catalyzed by a mutant strain lacking SorA (ΔsorA) was 25% higher than that of wild strain S12 (20 vs. 16 μA/cm2). Both biofilm formation and the current generation of the anodic biofilms were increased by the disruption of sorA, which suggests that the existence of SorA in S. decolorationis S12 inhibits electrode respiration. In contrast, disruption of sorA had no effect on respiration by S. decolorationis S12 with oxygen, fumarate, azo dye, or ferric citrate as electron acceptors. This is the first report of the specific effect of a periplasmic non-heme redox protein on EET to electrode and provides novel information for enhancing bacterial current generation.

Secreted Flavin Cofactors for Anaerobic Respiration of Fumarate and Urocanate by Shewanella oneidensis: Cost and Role

Shewanella oneidensis strain MR-1, a facultative anaerobe and model organism for dissimilatory metal reduction, uses a periplasmic flavocytochrome, FccA, both as a terminal fumarate reductase and as a periplasmic electron transfer hub for extracellular respiration of a variety of substrates. It is currently unclear how maturation of FccA and other periplasmic flavoproteins is achieved, specifically in the context of flavin cofactor loading, and the fitness cost of flavin secretion has not been quantified. We demonstrate that deletion of the inner membrane flavin adenine dinucleotide (FAD) exporter Bfe results in a 23% slower growth rate than that of the wild type during fumarate respiration and an 80 to 90% loss in fumarate reductase activity. Exogenous flavin supplementation does not restore FccA activity in a Δbfe mutant unless the gene encoding the periplasmic FAD hydrolase UshA is also deleted. We demonstrate that the small Bfe-independent pool of FccA is sufficient for anaerobic growth with fumarate. Strains lacking Bfe were unable to grow using urocanate as the sole electron acceptor, which relies on the periplasmic flavoprotein UrdA. We show that periplasmic flavoprotein maturation occurs in careful balance with periplasmic FAD hydrolysis, and that the current model for periplasmic flavin cofactor loading must account for a Bfe-independent mechanism for flavin transport. Finally, we determine that the metabolic burden of flavin secretion is not significant during growth with flavin-independent anaerobic electron acceptors. Our work helps frame the physiological motivations that drove evolution of flavin secretion by Shewanella IMPORTANCE Shewanella species are prevalent in marine and aquatic environments, throughout stratified water columns, in mineral-rich sediments, and in association with multicellular marine and aquatic organisms. The diversity of niches shewanellae can occupy are due largely to their respiratory versatility. Shewanella oneidensis is a model organism for dissimilatory metal reduction and can respire a diverse array of organic and inorganic compounds, including dissolved and solid metal oxides. The fumarate reductase FccA is a highly abundant multifunctional periplasmic protein that acts to bridge the periplasm and temporarily store electrons in a variety of respiratory nodes, including metal, nitrate, and dimethyl sulfoxide respiration. However, maturation of this central protein, particularly flavin cofactor acquisition, is poorly understood. Here, we quantify the fitness cost of flavin secretion and describe how free flavins are acquired by FccA and a homologous periplasmic flavoprotein, UrdA.

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.

Microbial Electrosynthesis I: Pure and Defined Mixed Culture Engineering

In the past 6 years, microbial bioelectrochemistry has strongly increased in attraction and audience when expanding from mainly environmental technology applications to biotechnology. In particular, the promise to combine electrosynthesis with microbial catalysis opens attractive approaches for new sustainable redox-cofactor recycling, redox-balancing, or even biosynthesis processes. Much of this promise is still not fulfilled, but it has opened and fueled entirely new research areas in this discipline. Activities in designing, tailoring, and applying specific microbial catalysts as pure or defined co-cultures for defined target bioproductions are greatly accelerating. This chapter gives an overview of the current progress as well as the emerging trends in molecular and ecological engineering of defined microbial biocatalysts to prepare them for evolving microbial electrosynthesis processes. In addition, the multitude of microbial electrosynthetic processes with complex undefined mixed cultures is covered by ter Heijne et al. (Adv Biochem Eng Biotechnol. https://doi.org/10.1007/10_2017_15 , 2017). Graphical Abstract.

Improvement of the electron transfer rate in Shewanella oneidensis MR-1 using a tailored periplasmic protein composition

Periplasmic c-type cytochromes are essential for the electron transport between the cytoplasmic membrane bound menquinol oxidase CymA and the terminal ferric iron reductase MtrABC in the outer membrane of Shewanella oneidensis cells. Either STC or FccA are necessary for periplasmic electron transfer. We followed the hypothesis that the elimination of potential competing reactions in the periplasm and the simultaneous overexpression of STC (cctA) could lead to an accelerated electron transfer to the cell surface. The genes nrfA, ccpA, napB and napA were replaced by cctA. This led to a 1.7-fold increased ferric iron reduction rate and a 23% higher current generation in a bioelectrochemical system. Moreover, the quadruple mutant had a higher periplasmic flavin content. Further deletion of fccA and its replacement by cctA resulted in a strain with ferric iron reduction rates similar to the wild type and a lower concentration of periplasmic flavin compared to the quadruple mutant. A transcriptomic analysis revealed that the quadruple mutant had a 3.7-fold higher cctA expression which could not be further increased by the replacement of fccA. This work indicates that a synthetic adaptation of Shewanella towards extracellular respiration holds potential for increased respiratory rates and consequently higher current densities.

A Synthetic Plasmid Toolkit for Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a platform microorganism for understanding extracellular electron transfer (EET) with a fully sequenced and annotated genome. In comparison to other model microorganisms such as Escherichia coli, the available plasmid parts (such as promoters and replicons) are not sufficient to conveniently and quickly fine-tune the expression of multiple genes in S. oneidensis MR-1. Here, we constructed and characterized a plasmid toolkit that contains a set of expression vectors with a combination of promoters, replicons, antibiotic resistance genes, and an RK2 origin of transfer (oriT) cassette, in which each element can be easily changed by fixed restriction enzyme sites. The expression cassette is also compatible with BioBrick synthetic biology standards. Using green fluorescent protein (GFP) as a reporter, we tested and quantified the strength of promoters. The copy number of different replicons was also measured by real-time quantitative PCR. We further transformed two compatible plasmids with different antibiotic resistance genes into the recombinant S. oneidensis MR-1, enabling control over the expression of two different fluorescent proteins. This plasmid toolkit was further used for overexpression of the MtrCAB porin-c-type cytochrome complex in the S. oneidensis ΔmtrA strain. Tungsten trioxide (WO₃) reduction and microbial fuel cell (MFC) assays revealed that the EET efficiency was improved most significantly when MtrCAB was expressed at a moderate level, thus demonstrating the utility of the plasmid toolkit in the EET regulation in S. oneidensis. The plasmid toolkit developed in this study is useful for rapid and convenient fine-tuning of gene expression and enhances the ability to genetically manipulate S. oneidensis MR-1.

Engineering an electroactive Escherichia coli for the microbial electrosynthesis of succinate from glucose and CO2

BACKGROUND

Electrochemical energy is a key factor of biosynthesis, and is necessary for the reduction or assimilation of substrates such as CO₂. Previous microbial electrosynthesis (MES) research mainly utilized naturally electroactive microbes to generate non-specific products.

RESULTS

In this research, an electroactive succinate-producing cell factory was engineered in E. coli T110(pMtrABC, pFccA-CymA) by expressing mtrABC, fccA and cymA from Shewanella oneidensis MR-1, which can utilize electricity to reduce fumarate. The electroactive T110 strain was further improved by incorporating a carbon concentration mechanism (CCM). This strain was fermented in an MES system with neutral red as the electron carrier and supplemented with HCO₃⁺, which produced a succinate yield of 1.10 mol/mol glucose-a 1.6-fold improvement over the parent strain T110.

CONCLUSIONS

The strain T110(pMtrABC, pFccA-CymA, pBTCA) is to our best knowledge the first electroactive microbial cell factory engineered to directly utilize electricity for the production of a specific product. Due to the versatility of the E. coli platform, this pioneering research opens the possibility of engineering various other cell factories to utilize electricity for bioproduction.

Metal Reduction and Protein Secretion Genes Required for Iodate Reduction by Shewanella oneidensis

The metal-reducing gammaproteobacterium Shewanella oneidensis reduces iodate (IO₃ ^-) as an anaerobic terminal electron acceptor. Microbial IO₃ ^- electron transport pathways are postulated to terminate with nitrate (NO₃ ^-) reductase, which reduces IO₃ ^- as an alternative electron acceptor. Recent studies with S. oneidensis, however, have demonstrated that NO₃ ^- reductase is not involved in IO₃ ^- reduction. The main objective of the present study was to determine the metal reduction and protein secretion genes required for IO₃ ^- reduction by Shewanella oneidensis with lactate, formate, or H₂ as the electron donor. With all electron donors, the type I and type V protein secretion mutants retained wild-type IO₃ ^- reduction activity, while the type II protein secretion mutant lacking the outer membrane secretin GspD was impaired in IO₃ ^- reduction. Deletion mutants lacking the cyclic AMP receptor protein (CRP), cytochrome maturation permease CcmB, and inner membrane-tethered c-type cytochrome CymA were impaired in IO₃ ^- reduction with all electron donors, while deletion mutants lacking c-type cytochrome MtrA and outer membrane β-barrel protein MtrB of the outer membrane MtrAB module were impaired in IO₃ ^- reduction with only lactate as an electron donor. With all electron donors, mutants lacking the c-type cytochromes OmcA and MtrC of the metal-reducing extracellular electron conduit MtrCAB retained wild-type IO₃ ^- reduction activity. These findings indicate that IO₃ ^- reduction by S. oneidensis involves electron donor-dependent metal reduction and protein secretion pathway components, including the outer membrane MtrAB module and type II protein secretion of an unidentified IO₃ ^- reductase to the S. oneidensis outer membrane.IMPORTANCE Microbial iodate (IO₃ ^-) reduction is a major component in the biogeochemical cycling of iodine and the bioremediation of iodine-contaminated environments; however, the molecular mechanism of microbial IO₃ ^- reduction is poorly understood. Results of the present study indicate that outer membrane (type II) protein secretion and metal reduction genes encoding the outer membrane MtrAB module of the extracellular electron conduit MtrCAB are required for IO₃ ^- reduction by S. oneidensis On the other hand, the metal-reducing c-type cytochrome MtrC of the extracellular electron conduit is not required for IO₃ ^- reduction by S. oneidensis These findings indicate that the IO₃ ^- electron transport pathway terminates with an as yet unidentified IO₃ ^- reductase that associates with the outer membrane MtrAB module to deliver electrons extracellularly to IO₃^.

Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili

Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.

Extracellular reduction of solid electron acceptors by Shewanella oneidensis

Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.

Recent developments and key barriers to advanced biofuels: A short review

Biofuels are regarded as one of the most viable options for reduction of CO₂ emissions in the transport sector. However, conventional plant-based biofuels (e.g., biodiesel, bioethanol)'s share of total transportation-fuel consumption in 2016 was very low, about 4%, due to several major limitations including shortage of raw materials, low CO₂ mitigation effect, blending wall, and poor cost competitiveness. Advanced biofuels such as drop-in, microalgal, and electro biofuels, especially from inedible biomass, are considered to be a promising solution to the problem of how to cope with the growing biofuel demand. In this paper, recent developments in oxy-free hydrocarbon conversion via catalytic deoxygenation reactions, the selection of and lipid-content enhancement of oleaginous microalgae, electrochemical biofuel conversion, and the diversification of valuable products from biomass and intermediates are reviewed. The challenges and prospects for future development of eco-friendly and economically advanced biofuel production processes also are outlined herein.

The Small RNA RyhB Is a Regulator of Cytochrome Expression in Shewanella oneidensis

Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.

A portable bioelectronic sensing system (BESSY) for environmental deployment incorporating differential microbial sensing in miniaturized reactors

Current technologies are lacking in the area of deployable, in situ monitoring of complex chemicals in environmental applications. Microorganisms metabolize various chemical compounds and can be engineered to be analyte-specific making them naturally suited for robust chemical sensing. However, current electrochemical microbial biosensors use large and expensive electrochemistry equipment not suitable for on-site, real-time environmental analysis. Here we demonstrate a miniaturized, autonomous bioelectronic sensing system (BESSY) suitable for deployment for instantaneous and continuous sensing applications. We developed a 2x2 cm footprint, low power, two-channel, three-electrode electrochemical potentiostat which wirelessly transmits data for on-site microbial sensing. Furthermore, we designed a new way of fabricating self-contained, submersible, miniaturized reactors (m-reactors) to encapsulate the bacteria, working, and counter electrodes. We have validated the BESSY’s ability to specifically detect a chemical amongst environmental perturbations using differential current measurements. This work paves the way for in situ microbial sensing outside of a controlled laboratory environment.

CRISPRi-sRNA: Transcriptional-Translational Regulation of Extracellular Electron Transfer in Shewanella oneidensis

Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i.e., clustered regularly interspaced short palindromic repeats interference (CRISPRi), in S. oneidensis MR-1 using green fluorescent protein (GFP) as a reporter. We used this CRISPRi technology to repress the expression levels of target genes, individually and in combination, in the EET pathways (e.g., the MtrCAB pathway and genes affecting the formation of electroactive biofilms in S. oneidensis), which in turn enabled the efficient regulation of EET efficiency. We then established a translational regulation technology, i.e., Hfq-dependent small regulatory RNA (sRNA), in S. oneidensis by repressing the GFP reporter and mtrA, which is a critical gene in the EET pathways in S. oneidensis. To achieve coordinated transcriptional and translational regulation at the genomic level, the CRISPRi and Hfq-dependent sRNA systems were incorporated into a single plasmid harbored in a recombinant S. oneidensis strain, which enabled an even higher efficiency of mtrA gene repression in the EET pathways than that achieved by the CRISPRi and Hfq-dependent sRNA system alone, as exhibited by the reduced electricity output. Overall, we developed a combined CRISPRi-sRNA method that enabled the synergistic transcriptional and translational regulation of target genes in S. oneidensis. This technology involving CRISPRi-sRNA transcriptional-translational regulation of gene expression at the genomic level could be applied to other microorganisms.

Vibrio cholerae VciB Mediates Iron Reduction

Vibrio cholerae is the causative agent of the severe diarrheal disease cholera. V. cholerae thrives within the human host, where it replicates to high numbers, but it also persists within the aquatic environments of ocean and brackish water. To survive within these nutritionally diverse environments, V. cholerae must encode the necessary tools to acquire the essential nutrient iron in all forms it may encounter. A prior study of systems involved in iron transport in V. cholerae revealed the existence of vciB, which, while unable to directly transport iron, stimulates the transport of iron through ferrous (Fe²⁺) iron transport systems. We demonstrate here a role for VciB in V. cholerae in which VciB stimulates the reduction of Fe³⁺ to Fe²⁺, which can be subsequently transported into the cell with the ferrous iron transporter Feo. Iron reduction is independent of functional iron transport but is associated with the electron transport chain. Comparative analysis of VciB orthologs suggests a similar role for other proteins in the VciB family. Our data indicate that VciB is a dimer located in the inner membrane with three transmembrane segments and a large periplasmic loop. Directed mutagenesis of the protein reveals two highly conserved histidine residues required for function. Taken together, our results support a model whereby VciB reduces ferric iron using energy from the electron transport chain.IMPORTANCEVibrio cholerae is a prolific human pathogen and environmental organism. The acquisition of essential nutrients such as iron is critical for replication, and V. cholerae encodes a number of mechanisms to use iron from diverse environments. Here, we describe the V. cholerae protein VciB that increases the reduction of oxidized ferric iron (Fe³⁺) to the ferrous form (Fe²⁺), thus promoting iron acquisition through ferrous iron transporters. Analysis of VciB orthologs in Burkholderia and Aeromonas spp. suggest that they have a similar activity, allowing a functional assignment for this previously uncharacterized protein family. This study builds upon our understanding of proteins known to mediate iron reduction in bacteria.

CRP Regulates D-Lactate Oxidation in Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a heterotrophic facultative anaerobe that respires using various organic and inorganic compounds. This organism has served as a model to study bacterial metabolic and regulatory systems that facilitate their survival in redox-stratified environments. The expression of many anaerobic respiratory genes in MR-1, including those for the reduction of fumarate, dimethyl sulfoxide, and metal oxides, is regulated by cyclic AMP receptor protein (CRP). However, relatively little is known about how this organism regulates the expression of catabolic enzymes catalyzing the oxidation of organic compounds, including lactate. Here, we investigated transcriptional mechanisms for the lldP (SO_1522) and dld (SO_1521) genes, which encode putative lactate permease and D-lactate dehydrogenase, respectively, and demonstrate that CRP regulates their expression in MR-1. We found that a crp-deletion mutant of MR-1 (Δcrp) showed impaired growth on D-lactate. Complementary expression of dld in Δcrp restored the ability to grow on D-lactate, indicating that the deficient growth of Δcrp on D-lactate is attributable to decreased expression of dld. In vivo transcription and in vitro electrophoretic mobility shift assays reveal that CRP positively regulates the expression of the lldP and dld genes by directly binding to an upstream region of lldP. Taken together, these results indicate that CRP is a global transcriptional regulator that coordinately regulates the expression of catabolic and respiratory pathways in MR-1, including D-lactate dehydrogenase and anaerobic terminal reductases.

A Synthetic Biology Approach to Engineering Living Photovoltaics

The ability to electronically interface living cells with electron accepting scaffolds is crucial for the development of next-generation biophotovoltaic technologies. Although recent studies have focused on engineering synthetic interfaces that can maximize electronic communication between the cell and scaffold, the efficiency of such devices is limited by the low conductivity of the cell membrane. This review provides a materials science perspective on applying a complementary, synthetic biology approach to engineering membrane-electrode interfaces. It focuses on the technical challenges behind the introduction of foreign extracellular electron transfer pathways in bacterial host cells and the past and future efforts to engineer photosynthetic organisms with artificial electron-export capabilities for biophotovoltaic applications. The article highlights advances in engineering protein-based, electron-exporting conduits in a model host organism, E. coli, before reviewing state-of-the-art biophotovoltaic technologies that use both unmodified and bioengineered photosynthetic bacteria with improved electron transport capabilities. A thermodynamic analysis is used to propose an energetically feasible pathway for extracellular electron transport in engineered cyanobacteria and identify metabolic bottlenecks amenable to protein engineering techniques. Based on this analysis, an engineered photosynthetic organism expressing a foreign, protein-based electron conduit yields a maximum theoretical solar conversion efficiency of 6-10% without accounting for additional bioengineering optimizations for light-harvesting.

A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation

The well-studied nature of the metabolic diversity of Shewanella bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation. The Shewanella phylogeny is diverged into two major branches, referred to as group 1 and group 2. While the genotype-phenotype connections of group 2 species have been extensively studied with metabolic modeling, a genome-scale model has been missing for the group 1 species. The metabolic reconstruction of Shewanella piezotolerans strain WP3 represented the first model for Shewanella group 1 and the first model among piezotolerant and psychrotolerant deep-sea bacteria. The model brought insights into the mechanisms of energy conservation in WP3 under anaerobic conditions and highlighted its metabolic flexibility in using diverse carbon sources. Overall, the model opens up new opportunities for investigating energy conservation and metabolic adaptation, and it provides a prototype for systems-level modeling of other deep-sea microorganisms.

Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 Shewanella species. Metabolic simulations with the WP3 model demonstrated consistency with existing knowledge about the physiology of the organism. A comparison of model simulations with experimental measurements verified the predicted growth profiles under increasing concentrations of carbon sources. The WP3 model was applied to study mechanisms of anaerobic respiration through investigating energy conservation, redox balancing, and the generation of proton motive force. Despite being an obligate respiratory organism, WP3 was predicted to use substrate-level phosphorylation as the primary source of energy conservation under anaerobic conditions, a trait previously identified in other Shewanella species. Further investigation of the ATP synthase activity revealed a positive correlation between the availability of reducing equivalents in the cell and the directionality of the ATP synthase reaction flux. Comparison of the WP3 model with an existing model of a group 2 species, Shewanella oneidensis MR-1, revealed that the WP3 model demonstrated greater flexibility in ATP production under the anaerobic conditions. Such flexibility could be advantageous to WP3 for its adaptation to fluctuating availability of organic carbon sources in the deep sea.

IMPORTANCE The well-studied nature of the metabolic diversity of Shewanella bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation. The Shewanella phylogeny is diverged into two major branches, referred to as group 1 and group 2. While the genotype-phenotype connections of group 2 species have been extensively studied with metabolic modeling, a genome-scale model has been missing for the group 1 species. The metabolic reconstruction of Shewanella piezotolerans strain WP3 represented the first model for Shewanella group 1 and the first model among piezotolerant and psychrotolerant deep-sea bacteria. The model brought insights into the mechanisms of energy conservation in WP3 under anaerobic conditions and highlighted its metabolic flexibility in using diverse carbon sources. Overall, the model opens up new opportunities for investigating energy conservation and metabolic adaptation, and it provides a prototype for systems-level modeling of other deep-sea microorganisms.

Electrode-assisted acetoin production in a metabolically engineered Escherichia coli strain

BACKGROUND

This paper describes the metabolic engineering of Escherichia coli for the anaerobic fermentation of glucose to acetoin. Acetoin has well-established applications in industrial food production and was suggested to be a platform chemical for a bio-based economy. However, the biotechnological production is often hampered by the simultaneous formation of several end products in the absence of an electron acceptor. Moreover, typical production strains are often potentially pathogenic. The goal of this study was to overcome these limitations by establishing an electrode-assisted fermentation process in E. coli. Here, the surplus of electrons released in the production process is transferred to an electrode as anoxic and non-depletable electron acceptor.

RESULTS

In a first step, the central metabolism was steered towards the production of pyruvate from glucose by deletion of genes encoding for enzymes of central reactions of the anaerobic carbon metabolism (ΔfrdA-D ΔadhE ΔldhA Δpta-ack). Thereafter, the genes for the acetolactate synthase (alsS) and the acetolactate decarboxylase (alsD) were expressed in this strain from a plasmid. Addition of nitrate as electron acceptor led to an anaerobic acetoin production with a yield of up to 0.9 mol acetoin per mol of glucose consumed (90% of the theoretical maximum). In a second step, the electron acceptor nitrate was replaced by a carbon electrode. This interaction necessitated the further expression of c-type cytochromes from Shewanella oneidensis and the addition of the soluble redox shuttle methylene blue. The interaction with the non-depletable electron acceptor led to an acetoin formation with a yield of 79% of the theoretical maximum (0.79 mol acetoin per mol glucose).

CONCLUSION

Electrode-assisted fermentations are a new strategy to produce substances of biotechnological value that are more oxidized than the substrates. Here, we show for the first time a process in which the commonly used chassis strain E. coli was tailored for an electrode-assisted fermentation approach branching off from the central metabolite pyruvate. At this early stage, we see promising results regarding carbon and electron recovery and will use further strain development to increase the anaerobic metabolic turnover rate.

Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures

The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl₄^2- and PtCl₆^2-, the amine-complex Pt(NH₃)₄Cl₂ and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl₄^2- and PtCl₆^2- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%), all in the presence of H₂ as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7), whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM) revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment.

Extracellular Electron Transfer and Biosensors

This chapter summarizes in the beginning our current understanding of extracellular electron transport processes in organisms belonging to the genera Shewanella and Geobacter. Organisms belonging to these genera developed strategies to transport respiratory electrons to the cell surface that are defined by modules of which some seem to be rather unique for one or the other genus while others are similar. We use this overview regarding our current knowledge of extracellular electron transfer to explain the physiological interaction of microorganisms in direct interspecies electron transfer, a process in which one organism basically comprises the electron acceptor for another microbe and that depends also on extended electron transport chains. This analysis of mechanisms for the transport of respiratory electrons to insoluble electron acceptors ends with an overview of questions that remain so far unanswered. Moreover, we use the description of the biochemistry of extracellular electron transport to explain the fundamentals of biosensors based on this process and give an overview regarding their status of development and applicability. Graphical Abstract.

Manganese in Marine Microbiology

The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn²⁺), a potent oxidant (Mn³⁺) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.

CymA and Exogenous Flavins Improve Extracellular Electron Transfer and Couple It to Cell Growth in Mtr-Expressing Escherichia coli

Introducing extracellular electron transfer pathways into heterologous organisms offers the opportunity to explore fundamental biogeochemical processes and to biologically alter redox states of exogenous metals for various applications. While expression of the MtrCAB electron nanoconduit from Shewanella oneidensis MR-1 permits extracellular electron transfer in Escherichia coli, the low electron flux and absence of growth in these cells limits their practicality for such applications. Here we investigate how the rate of electron transfer to extracellular Fe(III) and cell survival in engineered E. coli are affected by mimicking different features of the S. oneidensis pathway: the number of electron nanoconduits, the link between the quinol pool and MtrA, and the presence of flavin-dependent electron transfer. While increasing the number of pathways does not significantly improve the extracellular electron transfer rate or cell survival, using the native inner membrane component, CymA, significantly improves the reduction rate of extracellular acceptors and increases cell viability. Strikingly, introducing both CymA and riboflavin to Mtr-expressing E. coli also allowed these cells to couple metal reduction to growth, which is the first time an increase in biomass of an engineered E. coli has been observed under Fe2O3 (s) reducing conditions. Overall, this work provides engineered E. coli strains for modulating extracellular metal reduction and elucidates critical factors for engineering extracellular electron transfer in heterologous organisms.

Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1

Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.