Geobacter Protein Nanowires

Electron transfer in multicentre redox proteins: from fundamentals to extracellular electron transfer

Multicentre redox proteins participate in diverse metabolic processes, such as redox shuttling, multielectron catalysis, or long-distance electron conduction. The detail in which these processes can be analysed depends on the capacity of experimental methods to discriminate the multiple microstates that can be populated while the protein changes from the fully reduced to the fully oxidized state. The population of each state depends on the redox potential of the individual centres and on the magnitude of the interactions between the individual redox centres and their neighbours. It also depends on the interactions with binding sites for other ligands, such as protons, giving origin to the redox-Bohr effect. Modelling strategies that match the capacity of experimental methods to discriminate the contributions of individual centres are presented. These models provide thermodynamic and kinetic characterization of multicentre redox proteins. The current state of the art in the characterization of multicentre redox proteins is illustrated using the case of multiheme cytochromes involved in the process of extracellular electron transfer. In this new frontier of biological electron transfer, which can extend over distances that exceed the size of the individual multicentre redox proteins by orders of magnitude, current experimental data are still unable, in most cases, to provide discrimination between incoherent conduction by heme orbitals and coherent band conduction.

Magnetic, conductive nanoparticles as building blocks for steerable micropillar-structured anodic biofilms

In bioelectrochemical systems (BES), biofilm formation and architecture are of crucial importance, especially for flow-through applications. The interface between electroactive microorganisms and the electrode surface plays an important and often limiting role, as the available surface area influences current generation, especially for poor biofilm forming organisms. To overcome the limitation of the available electrode surface, nanoparticles (NPs) with a magnetic iron core and a conductive, hydrophobic carbon shell were used as building blocks to form conductive, magnetic micropillars on the anode surface. The formation of this dynamic three-dimensional electrode architecture was monitored and quantified in situ using optical coherence tomography (OCT) in conjunction with microfluidic BES systems. By cyclic voltammetry the assembled three-dimensional anode extensions were found to be electrically conductive and increased the available electroactive surface area. The NPs were used as controllable carriers for the electroactive model organisms Shewanella oneidensis and Geobacter sulfurreducens, resulting in a 5-fold increase in steady-state current density for S. oneidensis, which could be increased 22-fold when combined with Poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) aggregates. In the case of G. sulfurreducens, the steady-state current density was not increased, but was achieved four times faster. The study presents a controllable, scalable and easy-to-use method to increase the electrode surface area in existing BES by applying a magnetic field and adding conductive magnetic NPs. These findings can most likely also be transferred to other electroactive microorganisms.

Biogeochemical cycles of iron: Processes, mechanisms, and environmental implications

The iron (Fe) biogeochemical cycle is critical for abiotic and biological environmental processes that overlap spatially and may compete with each other. The development of modern molecular biology technologies promoted the understanding of the electron transport mechanisms of Fe-cycling-related microorganisms. Recent studies have revealed a novel pathway for microaerophilic ferrous iron (Fe(II))-oxidizers in extracellular Fe(II) oxidation. In addition, OmcS, OmcZ, and OmcE nanowires on the cell surface have been shown to promote electron transfer between microorganisms and their environment. These processes affect the fate of pollutants in directly or indirectly ways, such as greenhouse gas emissions. In this review, these advances and the environmental implications of the Fe cycle process were discussed, with a particular focus on the mechanisms of intracellular or extracellular electron transport in microorganisms.

Comparative analysis of the influence of BpfA and BpfG on biofilm development and current density in Shewanella oneidensis under oxic, fumarate- and anode-respiring conditions

Biofilm formation by Shewanella oneidensis has been extensively studied under oxic conditions; however, relatively little is known about biofilm formation under anoxic conditions and how biofilm architecture and composition can positively influence current generation in bioelectrochemical systems. In this study, we utilized a recently developed microfluidic biofilm analysis setup with automated 3D imaging to investigate the effects of extracellular electron acceptors and synthetic modifications to the extracellular polymeric matrix on biofilm formation. Our results with the wild type strain demonstrate robust biofilm formation even under anoxic conditions when fumarate is used as the electron acceptor. However, this pattern shifts when a graphite electrode is employed as the electron acceptor, resulting in biofilm formation falling below the detection limit of the optical coherence tomography imaging system. To manipulate biofilm formation, we aimed to express BpfG with a single amino acid substitution in the catalytic center (C116S) and to overexpress bpfA. Our analyses indicate that, under oxic conditions, overarching mechanisms predominantly influence biofilm development, rather than the specific mutations we investigated. Under anoxic conditions, the bpfG mutation led to a quantitative increase in biofilm formation, but both strains exhibited significant qualitative changes in biofilm architecture compared to the controls. When an anode was used as the sole electron acceptor, both the bpfA and bpfG mutations positively impacted mean current density, yielding a 1.8-fold increase for each mutation.

Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective

The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques. We specifically focused on extracellular electron transfer (EET) function and stress resistance, which affect the performance and stability of MECs. Community profiling revealed that the family Geobacteraceae was the key EAM taxon in all biofilms, with Geobacter as the dominant genus. The c-type cytochrome gene imcH showed universal importance for Geobacteraceae EET and was utilized as a marker gene to evaluate the EET potential of EAMs. Additionally, stress response functional genes were used to assess the stress resistance potential of Geobacter species. Comparative analysis of imcH gene abundance revealed that EAMs with comparable overall EET potential could be enriched from artificial and natural inocula (P > 0.05). However, quantification of stress response gene copy numbers in the genomes demonstrated that EAMs originating from natural inocula possessed superior stress resistance potential (196 vs. 163). Overall, this study provides novel perspectives on the inoculum effect in bioreactors and offers theoretical guidance for selecting inoculum in environmental engineering applications.

Magnetite particles accelerate methanogenic degradation of highly concentrated acetic acid in anaerobic digestion process

The anaerobic digestion (AD) process has become significant for its capability to convert organic wastewater into biogas, a valuable energy source. Excessive acetic acid accumulation in the anaerobic digester can inhibit methanogens, ultimately leading to the deterioration of process performance. Herein, the effect of magnetite particles (MP) as an enhancer on the methanogenic degradation of highly-concentrated acetate (6 g COD/L) was examined through long-term sequential AD batch tests. Bioreactors with (AM) and without (AO) MP were compared. AO experienced inhibition and its methane production rate (qm) converged to 0.45 L CH4/g VSS/d after 10 sequential batches (AO10, the 10th batch in a series of the sequential batch tests conducted using bioreactors without MP addition). In contrast, AM achieved 3-425% higher qm through the sequential batches, indicating that MP could counteract the inhibition caused by the highly-concentrated acetate. MP addition to inhibited bioreactors (AO10) successfully restored them, achieving qm of 1.53 L CH4/g VSS/d, 3.4 times increase from AO10 after 8 days lag time, validating its potential as a recovery strategy for inhibited digesters with acetate accumulation. AM exhibited higher microbial populations (1.8-3.8 times) and intracellular activity (9.3 times) compared to AO. MP enriched Methanosaeta, Peptoclostridium, Paraclostridium, OPB41, and genes related to direct interspecies electron transfer and acetate oxidation, potentially driving the improvement of qm through MP-mediated methanogenesis. These findings demonstrated the potential of MP supplementation as an effective strategy to accelerate acetate-utilizing methanogenesis and restore an inhibited anaerobic digester with high acetate accumulation.

Effects of marine eutrophication environment on microbial corrosion: A review

Metal materials undergo severe corrosion in eutrophic environments. The effect of DO decay stimulated by high concentrations of nitrogen and phosphorus pollutants on microorganisms leads to the coupling of electrochemical and microbial corrosion processes. However, there are few studies on microbial corrosion mechanisms in eutrophic environments. This article discusses the corrosive factors of marine eutrophication, summarizes the impact of marine eutrophication on microbial corrosion and the potential mechanisms, including aerobic biofilm corrosion, aerobic & anaerobic mixed biofilm corrosion, and anaerobic microbial electron transfer corrosion, and expounds on the research methods for microbial corrosion of materials serving in estuarine areas prone to pollution. Microbial prevention and control, such as nutrient restriction and microbial interspecies competition, are of research value in the field of green protection. Microbial corrosion mechanisms studies in marine eutrophication environments are significant for environment monitor development, water intake and algae control technologies, and corrosion protection in polluted environments.

Elucidating the development of cooperative anode-biofilm-structures

Microbial electrochemical systems are a highly versatile platform technology with a particular focus on the interplay of chemical and electrical energy conversion and offer immense potential for a sustainable bioeconomy. The industrial realization of this potential requires a critical focus on biofilm optimization if performance is to be controlled over a long period of time. Moreover, the aspect and influence of cooperativity has to be addressed as many applied anodic bioelectrochemical systems will most likely be operated with a diversity of interacting microbial species. Hence, the aim of this study was to analyze how interspecies dependence and cooperativity of a model community influence the development of anodic biofilms. To investigate biofilm activity in a spatially resolved manner, a microfluidic bioelectrochemical flow cell was developed that can be equipped with user-defined electrode materials and operates under laminar flow conditions. With this infrastructure, the development of single and co-culture biofilms of the two model organisms Shewanella oneidensis and Geobacter sulfurreducens on graphite electrodes was monitored by optical coherence tomography analysis. The interdependence in the co-culture biofilm was achieved by feeding the community with lactate, which is converted by S. oneidensis into acetate, which in turn serves as substrate for G. sulfurreducens. The results show that co-cultivation resulted in the formation of denser biofilms than in single culture. Moreover, we hypothesize that S. oneidensis in return utilizes the conductive biofilm matrix build by G. sulfurreducens for direct interspecies electron transfer (DIET) to the anode. FISH analysis revealed that the biofilms consisted of approximately two-thirds G. sulfurreducens cells, which most likely formed a conductive 3D network throughout the biofilm matrix, in which evenly distributed tubular S. oneidensis colonies were embedded without direct contact to the anode surface. Live/dead staining shows that the outermost biofilm contained almost exclusively dead cells (98 %), layers near the anode contained 45-56 % and the entire biofilm contained 82 % live cells. Our results exemplify how the architecture of the exoelectrogenic biofilm dynamically adapts to the respective process conditions.

Enriching electroactive microorganisms from ferruginous lake waters - Mind the sulfate reducers!

Electroactive microorganisms are pivotal players in mineral transformation within redox interfaces characterized by pronounced oxygen and dissolved metal gradients. Yet, their systematic cultivation from such environments remains elusive. Here, we conducted an anodic enrichment using anoxic ferruginous waters from a post-mining lake as inoculum. Weak electrogenicity (j = ∼5 µA cm-2) depended on electroactive planktonic cells rather than anodic biofilms, with a preference for formate as electron donor. Addition of yeast extract decreased the lag phase but did not increase current densities. The enriched bacterial community varied depending on the substrate composition but mainly comprised of sulfate- and nitrate-reducing bacteria (e.g., Desulfatomaculum spp. and Stenotrophomonas spp.). A secondary enrichment strategy resulted in different bacterial communities composed of iron-reducing (e.g., Klebsiella spp.) and fermentative bacteria (e.g., Paeniclostridium spp.). Secondary electron microscopy and energy-dispersive X-ray spectroscopy results indicate the precipitation of sulfur- and iron-rich organomineral aggregates at the anode surface, presumably impeding current production. Our findings indicate that (i) anoxic waters containing geogenically derived metals can be used to enrich weak electricigens, and (ii) it is necessary to specifically inhibit sulfate reducers. Otherwise, sulfate reducers tend to dominate over EAM during cultivation, which can lead to anode passivation due to biomineralization.

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.

Enhancing CH4 production in microbial electrolysis cells: Optimizing electric field via carbon cathode resistivity

Microbial electrolysis cells (MECs) are increasingly recognized as a promising technology for converting CO2 to CH4, offering the dual benefits of energy recovery from organic wastewater and CO2 emission reduction. A critical aspect of this technology is the enhancement of the electron-accepting capacity of the methanogenic biocathode to improve CH4 production efficiency. This study demonstrates that adjusting the cathode resistivity is an effective way to control the electric field intensity, thereby enhancing the electron accepting capacity and CH4 production. By maintaining the electric field intensity within approximately 8.50-10.83 mV·cm-1, the CH4 yield was observed to increase by up to two-fold. The improvement in CH4 production under optimized electric field conditions was attributed to the enhancement of the direct accepting capacity of the biocathode. This enhancement was primarily due to an increase in the relative abundance of Methanosaeta by approximately 10 % and an up to 83.78 % rise in the electron-accepting capacity of the extracellular polymeric substance. These insights offer a new perspective on the operation of methanogenic biocathodes and propose a novel biocathode construction methodology based on these findings, thus contributing to the enhancement of MEC efficiency.

To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'

Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.

Biopolymers for Hygroscopic Material Development

The effective management of atmospheric water will create huge value for mankind. Diversified and sustainable biopolymers that are derived from organisms provide rich building blocks for various hygroscopic materials. Here, a comprehensive review of recent advances in developing biopolymers for hygroscopic materials is provided. It is begun with a brief introduction of species diversity and the processes of obtaining various biopolymer materials from organisms. The fabrication of hygroscopic materials is then illustrated, with a specific focus on the use of biopolymer-derived materials as substrates to produce composites and the use of biopolymers as building blocks to fabricate composite gels. Next, the representative applications of biopolymer-derived hygroscopic materials for dehumidification, atmospheric water harvesting, and power generation are systematically presented. An outlook on future challenges and key issues worthy of attention are finally provided.

Regulation of extracellular polymers based on quorum sensing in wastewater biological treatment from mechanisms to applications: A critical review

Extracellular polymeric substances (EPS) regulated by quorum sensing (QS) could directly mediate adhesion between microorganisms and form tight microbial aggregates. Besides, EPS have redox properties, which can facilitate electron transfer for promoting electroactive bacteria. Currently, the applications research on improving wastewater biological treatment performance based on QS regulated EPS have been widely reported, but reviews on the level of QS regulated EPS to enhance EPS function in microbial systems are still lacking. This work proposes the potential mechanisms of EPS synthesis by QS regulation from the viewpoint of material metabolism and energy metabolism, and summarizes the effects of QS on EPS synthesis. By synthesizing the role of QS in EPS regulation, we further point out the applications of QS-regulated EPS in wastewater biological treatment, which involve a series of aspects such as strengthening microbial colonization, mitigating membrane biofouling, improving the shock resistance of microbial metabolic systems, and strengthening the electron transfer capacity of microbial metabolic systems. According to this comprehensive review, future research on QS-regulated EPS should focus on the exploration of the micro-mechanisms, and economic regulation strategies for QS-regulated EPS should be developed, while the stability of QS-regulated EPS in long-term production experimental research should be further demonstrated.

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al. J. Am. Chem. Soc. 142, 10459-10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. We here explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck-Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

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

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

Cable Bacteria Skeletons as Catalytically Active Electrodes

Cable bacteria are multicellular, filamentous bacteria that use internal conductive fibers to transfer electrons over centimeter distances from donors within anoxic sediment layers to oxygen at the surface. We extracted the fibers and used them as free-standing bio-based electrodes to investigate their electrocatalytic behavior. The fibers catalyzed the reversible interconversion of oxygen and water, and an electric current was running through the fibers even when the potential difference was generated solely by a gradient of oxygen concentration. Oxygen reduction as well as oxygen evolution were confirmed by optical measurements. Within living cable bacteria, oxygen reduction by direct electrocatalysis on the fibers and not by membrane-bound proteins readily explains exceptionally high cell-specific oxygen consumption rates observed in the oxic zone, while electrocatalytic water oxidation may provide oxygen to cells in the anoxic zone.

Recent Developments and Applications of Microbial Electrochemical Biosensors

This chapter provides a comprehensive overview of microbial electrochemical biosensors, which are a unique class of biosensors that utilize the metabolic activity of microorganisms to convert chemical signals into electrical signals. The principles and mechanisms of these biosensors are discussed, including the different types of microorganisms that can be used. The various applications of microbial electrochemical biosensors in fields such as environmental monitoring, medical diagnostics, and food safety are also explored. The chapter concludes with a discussion of future research directions and potential advancements in the field of microbial electrochemical biosensors.

Biochar establishing syntrophic partnership between exoelectrogens to facilitate extracellular electron transfer

Biochar was regarded as a promising accelerator for extracellular electron transfer (EET), while the mechanism of biochar facilitating electricity harvest in bioelectrochemical system (BES) was in debates. In this study, sawdust-based biochar with low conductivity but strong redox-based electron exchange capacity was added into BES with two forms, including a suspended form (S-BC) added in anode chamber and a fixed form closely wrapping up the anode (F-BC). Compared with the control group, S-BC and F-BC addition dramatically increased accumulated electricity output by 2.0 and 5.1 times. However, electrochemical analysis characterized the lowest electrochemical property on anode surface in F-BC modified group. A 2nd period conducted by separating F-BC modified group with "aged F-BC + new anode" group and "single aged anode" group demonstrated that F-BC contributed >95 % to the current generation of F-BC modified group, while the anode almost acted as a conductor to transfer the generated electrons to cathode. Microbial community analysis revealed that both heterotrophic and autotrophic exoelectrogens contributed to current generation. The presence of biochar upregulated functional genes encoding cytochrome-c and type IV pilus, thereby boosting electricity harvest efficiency. Interestingly, the heterotrophic exoelectrogens of Geobacter/Desulfovibrio tended to attach on fixed surfaces of both biochar and anode, and the autotrophic exelectrogen of Hydrogenophaga was selectively enriched on biochar surfaces whatever fixed or suspended form. Consequently, a syntrophic partnership between Geobacter/Desulfovibrio and Hydrogenophaga was potentially establishment on F-BC surface for highly-efficient electricity harvest. In this syntrophic EET model, biochar potentially acted as the redox-active mediator, which temporarily accepted electron released by Geobacter/Desulfovibrio via acetate oxidation, and then donated them to Hydrogenophaga attached on biochar surfaces for autotrophic EET. This was distinct from a regular EET conducted by heterotrophic exoelectrogens. These findings provided new insights to understand the mechanisms of biochar facilitating EET by syntrophic metabolism pathway.

Responses of syntrophic microbial communities and their interactions with polystyrene nanoplastics in a microbial electrolysis cell

Microbial electrochemical technologies are promising for simultaneous energy recovery and wastewater treatment. Although the inhibitory effects of emerging pollutants, particularly micro/nanoplastics (MPs/NPs), on conventional wastewater systems have been extensively studied, the current understanding of their impact on microbial electrochemical systems is still quite limited. Microplastics are plastic particles ranging from 1 μm to 5 mm. However, nanoplastics are smaller plastic particles ranging from 1 to 100 nm. Due to their smaller size and greater surface area, they can penetrate deeper into biofilm structures and cell membranes, potentially disrupting their integrity and leading to changes in biofilm composition and function. This study first reports the impact of polystyrene nanoplastics (PsNPs) on syntrophic anode microbial communities in a microbial electrolysis cell. Low concentrations of PsNPs (50 and 250 μg/L) had a minimal impact on current density and hydrogen production. However, 500 μg/L of PsNPs decreased the maximum current density and specific hydrogen production rate by ∼43 % and ∼48 %, respectively. Exposure to PsNPs increased extracellular polymeric substance (EPS) levels, with a higher ratio of carbohydrates to proteins, suggesting a potential defense mechanism through EPS secretion. The downregulation of genes associated with extracellular electron transfer was observed at 500 μg/L of PsNPs. Furthermore, the detrimental impact of 500 μg/L PsNPs on the microbiome was evident from the decrease in 16S rRNA gene copies, microbial diversity, richness, and relative abundances of key electroactive and fermentative bacteria. For the first time, this study presents the inhibitory threshold of any NPs on syntrophic electroactive biofilms within a microbial electrochemical system.

Electron Transfer Beyond the Outer Membrane: Putting Electrons to Rest

Extracellular electron transfer (EET) is the physiological process that enables the reduction or oxidation of molecules and minerals beyond the surface of a microbial cell. The first bacteria characterized with this capability were Shewanella and Geobacter, both reported to couple their growth to the reduction of iron or manganese oxide minerals located extracellularly. A key difference between EET and nearly every other respiratory activity on Earth is the need to transfer electrons beyond the cell membrane. The past decade has resolved how well-conserved strategies conduct electrons from the inner membrane to the outer surface. However, recent data suggest a much wider and less well understood collection of mechanisms enabling electron transfer to distant acceptors. This review reflects the current state of knowledge from Shewanella and Geobacter, specifically focusing on transfer across the outer membrane and beyond-an activity that enables reduction of highly variable minerals, electrodes, and even other organisms.

Electron Tunneling in Biology: When Does it Matter?

Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport. In addition, universal charge-transport properties are assigned to all proteins, making protein identity, flexibility, and dynamics insignificant. This paradigm is challenged by dynamical models of electron transfer, showing that the electron hopping rate is constant within the crossover distance R* ≃ 12 Å, followed with an exponential falloff at longer distances. If this hypothesis is fully confirmed, natural and man-made energy chains for electron transport should be best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover distance. Changes in protein flexibility between forward and backward transitions contribute to vectorial charge transport. For biological energy chains, charge transport through proteins is not defined by universal parameters, and protein identity matters.

Random walks on modular chains: Detecting structure through statistics

We study kinetic transport through one-dimensional modular networks consisting of alternating domains using both analytical and numerical methods. We demonstrate that the mean velocity is insensitive to the local structure of the network, and it depends only on global, structural-averaged properties. However, by examining high-order cumulants characterizing the kinetics, we reveal information on the degree of inhomogeneity of blocks and the size of repeating units in the network. Specifically, in unbiased diffusion, the kurtosis is the first transport coefficient that exposes structural information, whereas in biased chains, the diffusion coefficient already reveals structural motifs. Nevertheless, this latter dependence is weak, and it disappears at both low and high biasing. Our study demonstrates that high-order moments of the population distribution over sites provide information about the network structure that is not captured by the first moment (mean velocity) alone. These results are useful towards deciphering mechanisms and determining architectures underlying long-range charge transport in biomolecules and biological and chemical reaction networks.

Manganese-mediated ammonium removal by a bacterial consortium from wastewater: Experimental proof and biochemical mechanisms

Manganese-redox-mediated nitrogen transformation is promising for ammonium wastewater treatment. However, due to the limited contact between insoluble Mn and the microbe, extracellular electron transfer (EET) inefficiencies become a technical bottleneck in the technical practical application. To overcome this obstacle, humic acid (HA) was introduced to synthesize manganese-humic acid complex (Mn-HA) to increase Mn solubility. The TIN (Total Inorganic Nitrogen) removal rate constant k was 3.18, 1.08, 3.56, 1.13 and 1.05 times higher than CK (Control group) at 10, 15, 20, 40 and 60 mg/L influent nitrate in the MH group, respectively. Mn-HA was inferred to stimulated the nitrogen removal by providing more reaction active sites, bridging Mn-O bonds to transfer electrons and playing a redox role in the respiratory chain. A Mnammox-NDMO (manganese oxide reduction-coupled ammonium oxidation - nitrate/nitrite- dependent manganese oxidation) bacteria consortium was enriched in MH group, containing Mnammox bacteria Geothrix, Geobacter and NDMO bacteria Pseudomonas and Bacillus.

Fe(III) oxide microparticles modulate extracellular electron transfer in anodic biofilms dominated by bacteria of the Pelobacter genus

Exo-electrogenic microorganisms have been extensively studied for their ability to transfer electrons with solid surfaces using a large variety of metabolic pathways. Most of the studies on these microorganisms consist in the replacement of solid electron acceptors such as Fe(III) oxides found in nature by electrodes with the objective of generating harvestable current in devices such as microbial fuel cells. In this study we show how the presence of solid ferric oxide (Fe₂O₃) particles in the inoculum during bio-anode development influences extracellular electron transfer to the electrode. Amplification and sequencing of the 16S rRNA (V4-V5 region) show bacteria and archaea communities with a large predominance of the Pelobacter genus, which is known to be phylogenetically close to the Geobacter genus, regardless of the presence or absence of ferric oxide in the inoculum. Data indicate that the bacteria at the bio-anode surface can preferentially utilize solid ferric oxide as terminal electron acceptors instead of the anode, though extracellular electron transfer to the anode can be restored by removing the particles. Mixed inoculum commonly used to develop bioanodes may produce similar bacterial communities with divergent electrochemical responses due to the presence of alternate electron acceptors, with direct implications for microbial fuel cell performance.

Engineering nanowires in bacteria to elucidate electron transport structural-functional relationships

Bacterial pilin nanowires are protein complexes, suggested to possess electroactive capabilities forming part of the cells' bioenergetic programming. Their role is thought to be linked to facilitating electron transfer between cells and the external environment to permit metabolism and cell-to-cell communication. There is a significant debate, with varying hypotheses as to the nature of the proteins currently lying between type-IV pilin-based nanowires and polymerised cytochrome-based filaments. Importantly, to date, there is a very limited structure-function analysis of these structures within whole bacteria. In this work, we engineered Cupriavidus necator H16, a model autotrophic organism to express differing aromatic modifications of type-IV pilus proteins to establish structure-function relationships on conductivity and the effects this has on pili structure. This was achieved via a combination of high-resolution PeakForce tunnelling atomic force microscopy (PeakForce TUNA™) technology, alongside conventional electrochemical approaches enabling the elucidation of conductive nanowires emanating from whole bacterial cells. This work is the first example of functional type-IV pili protein nanowires produced under aerobic conditions using a Cupriavidus necator chassis. This work has far-reaching consequences in understanding the basis of bio-electrical communication between cells and with their external environment.

Classification of bacterial nanowire proteins using Machine Learning and Feature Engineering model

Nanowires (NW) have been extensively studied for Shewanella spp. and Geobacter spp. and are mostly produced by Type IV pili or multiheme c-type cytochrome. Electron transfer via NW is the most studied mechanism in microbially induced corrosion, with recent interest in application in bioelectronics and biosensor. In this study, a machine learning (ML) based tool was developed to classify NW proteins. A manually curated 999 protein collection was developed as an NW protein dataset. Gene ontology analysis of the dataset revealed microbial NW is part of membranal proteins with metal ion binding motifs and plays a central role in electron transfer activity. Random Forest (RF), support vector machine (SVM), and extreme gradient boost (XGBoost) models were implemented in the prediction model and were observed to identify target proteins based on functional, structural, and physicochemical properties with 89.33%, 95.6%, and 99.99% accuracy. Dipetide amino acid composition, transition, and distribution protein features of NW are key important features aiding in the model's high performance.

In Situ Enhanced Yields of Microbial Nanowires: The Key Role of Environmental Stress

The conductive microbial nanowires of Geobacter sulfurreducens serve as a model for long-range extracellular electron transfer (EET), which is considered a revolutionary "green" nanomaterial in the fields of bioelectronics, renewable energy, and bioremediation. However, there is no efficient pathway to induce microorganisms to express a large amount of microbial nanowires. Here, several strategies have been used to successfully induce the expression of microbial nanowires. Microbial nanowire expression was closely related to the concentration of electron acceptors. The microbial nanowire was around 17.02 μm in length, more than 3 times compared to its own length. The graphite electrode was used as an alternative electron acceptor by G. sulfurreducens, which obtained a fast start-up time of 44 h in microbial fuel cells (MFCs). Meanwhile, Fe(III) citrate-coated sugarcane carbon and biochar were prepared to test the applicability of these strategies in the actual microbial community. The unsatisfied EET efficiency between c-type cytochrome and extracellular insoluble electron receptors promoted the expression of microbial nanowires. Hence, microbial nanowires were proposed to be an effective survival strategy for G. sulfurreducens to cope with various environmental stresses. Based on this top-down strategy of artificially constructed microbial environmental stress, this study is of great significance for exploring more efficient methods to induce microbial nanowires expression.

Advances in mechanisms and engineering of electroactive biofilms

Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.

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.

Conjugative plasmids inhibit extracellular electron transfer in Geobacter sulfurreducens

Geobacter sulfurreducens is part of a specialized group of microbes with the unique ability to exchange electrons with insoluble materials, such as iron oxides and electrodes. Therefore, G. sulfurreducens plays an essential role in the biogeochemical iron cycle and microbial electrochemical systems. In G. sulfurreducens this ability is primarily dependent on electrically conductive nanowires that link internal electron flow from metabolism to solid electron acceptors in the extracellular environment. Here we show that when carrying conjugative plasmids, which are self-transmissible plasmids that are ubiquitous in environmental bacteria, G. sulfurreducens reduces insoluble iron oxides at much slower rates. This was the case for all three conjugative plasmids tested (pKJK5, RP4 and pB10). Growth with electron acceptors that do not require expression of nanowires was, on the other hand, unaffected. Furthermore, iron oxide reduction was also inhibited in Geobacter chapellei, but not in Shewanella oneidensis where electron export is nanowire-independent. As determined by transcriptomics, presence of pKJK5 reduces transcription of several genes that have been shown to be implicated in extracellular electron transfer in G. sulfurreducens, including pilA and omcE. These results suggest that conjugative plasmids can in fact be very disadvantageous for the bacterial host by imposing specific phenotypic changes, and that these plasmids may contribute to shaping the microbial composition in electrode-respiring biofilms in microbial electrochemical reactors.

Reorganization energy of electron transfer

The theory of electron transfer reactions establishes the conceptual foundation for redox solution chemistry, electrochemistry, and bioenergetics. Electron and proton transfer across the cellular membrane provide all energy of life gained through natural photosynthesis and mitochondrial respiration. Rates of biological charge transfer set kinetic bottlenecks for biological energy storage. The main system-specific parameter determining the activation barrier for a single electron-transfer hop is the reorganization energy of the medium. Both harvesting of light energy in natural and artificial photosynthesis and efficient electron transport in biological energy chains require reduction of the reorganization energy to allow fast transitions. This review article discusses mechanisms by which small values of the reorganization energy are achieved in protein electron transfer and how similar mechanisms can operate in other media, such as nonpolar and ionic liquids. One of the major mechanisms of reorganization energy reduction is through non-Gibbsian (nonergodic) sampling of the medium configurations on the reaction time. A number of alternative mechanisms, such as electrowetting of active sites of proteins, give rise to non-parabolic free energy surfaces of electron transfer. These mechanisms, and nonequilibrium population of donor-acceptor vibrations, lead to a universal phenomenology of separation between the Stokes shift and variance reorganization energies of electron transfer.

Screening of natural phenazine producers for electroactivity in bioelectrochemical systems

Mediated extracellular electron transfer (EET) might be a great vehicle to connect microbial bioprocesses with electrochemical control in stirred-tank bioreactors. However, mediated electron transfer to date is not only much less efficient but also much less studied than microbial direct electron transfer to an anode. For example, despite the widespread capacity of pseudomonads to produce phenazine natural products, only Pseudomonas aeruginosa has been studied for its use of phenazines in bioelectrochemical applications. To provide a deeper understanding of the ecological potential for the bioelectrochemical exploitation of phenazines, we here investigated the potential electroactivity of over 100 putative diverse native phenazine producers and the performance within bioelectrochemical systems. Five species from the genera Pseudomonas, Streptomyces, Nocardiopsis, Brevibacterium and Burkholderia were identified as new electroactive bacteria. Electron discharge to the anode and electric current production correlated with the phenazine synthesis of Pseudomonas chlororaphis subsp. aurantiaca. Phenazine-1-carboxylic acid was the dominant molecule with a concentration of 86.1 μg/ml mediating an anodic current of 15.1 μA/cm² . On the other hand, Nocardiopsis chromatogenes used a wider range of phenazines at low concentrations and likely yet-unknown redox compounds to mediate EET, achieving an anodic current of 9.5 μA/cm² . Elucidating the energetic and metabolic usage of phenazines in these and other species might contribute to improving electron discharge and respiration. In the long run, this may enhance oxygen-limited bioproduction of value-added compounds based on mediated EET mechanisms.

Enhancing electrical outputs of the fuel cells with Geobacter sulferreducens by overexpressing nanowire proteins

Protein nanowires are critical electroactive components for electron transfer of Geobacter sulfurreducens biofilm. To determine the applicability of the nanowire proteins in improving bioelectricity production, their genes including pilA, omcZ, omcS and omcT were overexpressed in G. sulfurreducens. The voltage outputs of the constructed strains were higher than that of the control strain with the empty vector (0.470-0.578 vs. 0.355 V) in microbial fuel cells (MFCs). As a result, the power density of the constructed strains (i.e. 1.39-1.58 W m^-2 ) also increased by 2.62- to 2.97-fold as compared to that of the control strain. Overexpression of nanowire proteins also improved biofilm formation on electrodes with increased protein amount and thickness of biofilms. The normalized power outputs of the constructed strains were 0.18-0.20 W g^-1 that increased by 74% to 93% from that of the control strain. Bioelectrochemical analyses further revealed that the biofilms and MFCs with the constructed strains had stronger electroactivity and smaller internal resistance, respectively. Collectively, these results demonstrate for the first time that overexpression of nanowire proteins increases the biomass and electroactivity of anode-attached microbial biofilms. Moreover, this study provides a new way for enhancing the electrical outputs of MFCs.

Elongated Riboflavin-Producing Shewanella oneidensis in a Hybrid Biofilm Boosts Extracellular Electron Transfer

Shewanella oneidensis is able to carry out extracellular electron transfer (EET), although its EET efficiency is largely limited by low flavin concentrations, poor biofilm forming-ability, and weak biofilm conductivity. After identifying an important role for riboflavin (RF) in EET via in vitro experiments, the synthesis of RF is directed to 837.74 ± 11.42 µm in S. oneidensis. Molecular dynamics simulation reveals RF as a cofactor that binds strongly to the outer membrane cytochrome MtrC, which is correspondingly further overexpressed to enhance EET. Then the cell division inhibitor sulA, which dramatically enhanced the thickness and biomass of biofilm increased by 155% and 77%, respectively, is overexpressed. To reduce reaction overpotential due to biofilm thickness, a spider-web-like hybrid biofilm comprising RF, multiwalled carbon nanotubes (MWCNTs), and graphene oxide (GO) with adsorption-optimized elongated S. oneidensis, achieve a 77.83-fold increase in power (3736 mW m^-2 ) relative to MR-1 and dramatically reduce the charge-transfer resistance and boosted biofilm electroactivity. This work provides an elegant paradigm to boost EET based on a synthetic biology strategy and materials science strategy, opens up further opportunities for other electrogenic bacteria.

Performance of anaerobic digestion of phenol using exogenous hydrogen and granular activated carbon and analysis of microbial community

Anaerobic conversion rate of phenol to methane was low due to its biological toxicity. In this study, the coupling of granular activated carbon (GAC) and exogenous hydrogen (EH) could enhance greatly methane production of phenol anaerobic digestion, and the metagenomic was firstly used to analyze its potential mechanism. The results indicated that a mass of syntrophic acetate-oxidizing bacteria and hydrogen-utilizing methanogens were enriched on the GAC surface, and SAO-HM pathway has become the dominant pathway. The energy transfer analysis implied that the abundance of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NADH) oxidase increased. Furthermore, direct interspecies electron transfer (DIET) was formed by promoting type IV e-pili between Methanobacterium and Syntrophus, thereby improving the interspecies electron transfer efficiency. The dominant SAO-HM pathway was induced and DIET was formed, which was the internal mechanism of the coupling of GAC and EH to enhance anaerobic biotransformation of phenol.

Integrated analysis of transcriptomic and protein-protein interaction data reveals cadmium stress response in Geobacter sulfurreducens

Bacteria have evolved several mechanisms to resist Cd toxicity, which are crucial for Cd detoxication and have the potential to be used for bioremediation of Cd. Geobacter species are widely found in anaerobic environments and play important roles in natural biogeochemical cycles. However, the transcriptomic response of Geobacter sulfurreducens under Cd stress have not been fully elucidated. Through integrated analysis of transcriptomic and protein-protein interaction (PPI) data, we uncovered a global view of mRNA changes in Cd-induced cellular processes in this study. We identified 182 differentially expressed genes (|log₂(fold change)| > 1, adjusted P < 0.05) in G. sulfurreducens exposed to 0.1 mM CdCl₂ using RNA sequencing (RNA-seq). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that CdCl₂ significantly affected sulfur compound metabolic processes. In addition, through PPI network analysis, hub genes related to molecular chaperones were identified to play important role in Cd stress response. We also identified a Cd-responsive transcriptional regulator ArsR2 (coded by GSU2149) and verified the function of ArsR2-P_arsR2 regulatory circuit in Escherichia coli. This study provides new insight into Cd stress response in G. sulfurreducens, and identified a potential sensor element for Cd detection.

Polyphasic Characterization of Geotalea uranireducens NIT-SL11 Newly Isolated from a Complex of Sewage Sludge and Microbially Reduced Graphene Oxide

Graphene oxide (GO), a chemically oxidized sheet of graphite, has been used as a conductive carbon carrier of microbes to boost various bioelectrochemical reactions. However, the types of microbes that can reduce GO have rarely been investigated. In this study, a strain of GO-reducing bacteria, named NIT-SL11, which was obtained from a hydrogel of microbially reduced GO and anaerobic sludge that converts sewage to electricity, was phylogenically identified as a novel strain of Geotalea uraniireducens. Considering the current lack of information on the electrogenic ability of the bacterium and its physicochemical and chemotaxonomic characteristics, the polyphasic characterization of the Geotalea uraniireducens strain NIT-SL11 was performed. NIT-SL11 utilized various organic acids, such as lactate, benzoate, and formate, as electron donors and exhibited respiration using GO, electrodes, fumarate, and malate. The strain contained C16:1ω7c and C16:0 as the major fatty acids and MK-8 and 9 as the major respiratory quinones. The complete genome of NIT-SL11 was 4.7 Mbp in size with a G+C content of 60.9%, and it encoded 80 putative c-type cytochromes and 23 type IV pili-related proteins. The possible extracellular electron transfer (EET) pathways of the strain were the porin-cytochrome (Pcc) EET pathway and type IV pili-based pathway.

An Effective Sneak-Path Solution Based on a Transient-Relaxation Device

An efficient strategy for addressing individual devices is required to unveil the full potential of memristors for high-density memory and computing applications. Existing strategies using two-terminal selectors that are preferable for compact integration have trade-offs in reduced generality or functional window. A strategy that applies to broad memristors and maintains their full-range functional window is proposed. This strategy uses a type of unipolar switch featuring a transient relaxation or retention as the selector. The unidirectional current flow in the switch suppresses the sneak-path current, whereas the transient-relaxation window is exploited for bidirectional programming. A unipolar volatile memristor with ultralow switching voltage (e.g., <100 mV), constructed from a protein nanowire dielectric harvested from Geobacter sulfurreducens, is specifically employed as the example switch to highlight the advantages and scalability in the strategy for array integration.

Chances and challenges of long-distance electron transfer for cellular redox reactions

Biological redox reactions often use a set-up in which final redox partners are localized in different compartments and electron transfer (ET) among them is mediated by redox-active molecules. In enzymes, these ET processes occur over nm distances, whereas multi-protein filaments bridge μm ranges. Electrons are transported over cm ranges in cable bacteria, which are formed by thousands of cells. In this review, we describe molecular mechanisms that explain how respiration in a compartmentalized set-up ensures redox homeostasis. We highlight mechanistic studies on ET through metal-free peptides and proteins demonstrating that long-distance ET is possible because amino acids Tyr, Trp, Phe, and Met can act as relay stations. This cuts one long ET into several short reaction steps. The chances and challenges of long-distance ET for cellular redox reactions are then discussed.

Genetic Manipulation of Desulfovibrio ferrophilus and Evaluation of Fe(III) Oxide Reduction Mechanisms

The sulfate-reducing microbe Desulfovibrio ferrophilus is of interest due to its relatively rare ability to also grow with Fe(III) oxide as an electron acceptor and its rapid corrosion of metallic iron. Previous studies have suggested multiple agents for D. ferrophilus extracellular electron exchange including a soluble electron shuttle, electrically conductive pili, and outer surface multiheme c-type cytochromes. However, the previous lack of a strategy for genetic manipulation of D. ferrophilus limited mechanistic investigations. We developed an electroporation-mediated transformation method that enabled replacement of D. ferrophilus genes of interest with an antibiotic resistance gene via double-crossover homologous recombination. Genes were identified that are essential for flagellum-based motility and the expression of the two types of D. ferrophilus pili. Disrupting flagellum-based motility or expression of either of the two pili did not inhibit Fe(III) oxide reduction, nor did deleting genes for multiheme c-type cytochromes predicted to be associated with the outer membrane. Although redundancies in cytochrome or pilus function might explain some of these phenotypes, overall, the results are consistent with D. ferrophilus primarily reducing Fe(III) oxide via an electron shuttle. The finding that D. ferrophilus is genetically tractable not only will aid in elucidating further details of its mechanisms for Fe(III) oxide reduction but also provides a new experimental approach for developing a better understanding of some of its other unique features, such as the ability to corrode metallic iron at high rates and accept electrons from negatively poised electrodes. IMPORTANCE Desulfovibrio ferrophilus is an important pure culture model for Fe(III) oxide reduction and the corrosion of iron-containing metals in anaerobic marine environments. This study demonstrates that D. ferrophilus is genetically tractable, an important advance for elucidating the mechanisms by which it interacts with extracellular electron acceptors and donors. The results demonstrate that there is not one specific outer surface multiheme D. ferrophilus c-type cytochrome that is essential for Fe(III) oxide reduction. This finding, coupled with the lack of apparent porin-cytochrome conduits encoded in the D. ferrophilus genome and the finding that deleting genes for pilus and flagellum expression did not inhibit Fe(III) oxide reduction, suggests that D. ferrophilus has adopted strategies for extracellular electron exchange that are different from those of intensively studied electroactive microbes like Shewanella and Geobacter species. Thus, the ability to genetically manipulate D. ferrophilus is likely to lead to new mechanistic concepts in electromicrobiology.

Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content

Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.

Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire

A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨H_mn⟩), reaction free energies (ΔG_mn), reorganization energies (λ_mn), and activation energies (E_a) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔG_mn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.

Biohydrogen production and purification: Focusing on bioelectrochemical systems

Innovative technologies on green hydrogen production become significant as the hydrogen economy has grown globally. Biohydrogen is one of green hydrogen production methods, and microbial electrochemical cells (MECs) can be key to biohydrogen provision. However, MECs are immature for biohydrogen technology due to several limitations including extracellular electron transfer (EET) engineering. Fundamental understanding of EET also needs more works to accelerate MEC commercialization. Interestingly, studies on biohydrogen gas purification are limited although biohydrogen gas mixture requires complex purification for use. To facilitate an MEC-based biohydrogen technology as the green hydrogen supply this review discussed EET kinetics, engineering of EET and direct interspecies electron transfer associated with hydrogen yield and the application of advanced molecular biology for improving EET kinetics. Finally, this article reviewed biohydrogen purification technologies to better understand purification and use appropriate for biohydrogen, focusing on membrane separation.

Long-range charge transport in homogeneous and alternating-rigidity chains

We study the interplay of intrinsic-electronic and environmental factors in long-range charge transport across molecular chains with up to N ∼ 80 monomers. We describe the molecular electronic structure of the chain with a tight-binding Hamiltonian. Thermal effects in the form of electron decoherence and inelastic scattering are incorporated with the Landauer–Büttiker probe method. In short chains of up to ten units, we observe the crossover between coherent (tunneling, ballistic) motion and thermally-assisted conduction, with thermal effects enhancing the current beyond the quantum coherent limit. We further show that unconventional (nonmonotonic with size) transport behavior emerges when monomer-to-monomer electronic coupling is made large. In long chains, we identify a different behavior, with thermal effects suppressing the conductance below the coherent-ballistic limit. With the goal to identify a minimal model for molecular chains displaying unconventional and effective long-range transport, we simulate a modular polymer with alternating regions of high and low rigidity. Simulations show that, surprisingly, while charge correlations are significantly affected by structuring environmental conditions, reflecting charge delocalization, the electrical resistance displays an averaging effect, and it is not sensitive to this patterning. We conclude by arguing that efficient long-range charge transport requires engineering both internal electronic parameters and environmental conditions.

Single-cell metagenomics and metagenomics approaches reveal extracellular electron transfer of psychrophilic electroactive biofilms

Revealing the metabolic functions and the extracellular electron transfer (EET) process of psychrophilic electroactive biofilms (PEB) is important for understanding the functional adaptability of electroactive bacteria (EAB) to low temperatures. In this study, single cell sorting (SCS)-based metagenomics sequencing was used to characterize the composition and function of the PEB. Biofilm microbiome analysis showed that Geobacter, with a relative abundance of 62.64%, dominated the PEB enriched in the bioelectrochemical system (BES) at 4 °C. Both the metagenome (MAG) and single-cell metagenome (SCM) revealed that there were no obvious metabolic differences between the original biofilm and the sorted single cells. The presence of genes associated with type IV pilus, c-type cytochromes, and riboflavin indicated that the EET potential was maintained in the PEB at low temperatures. These results suggested that SCM provides an alternative approach to reconstruct the metabolic functions of uncultured and slow-growing EAB.

Desulfoferrobacter suflitae gen. nov., sp. nov., a novel sulphate-reducing bacterium in the Deltaproteobacteria capable of autotrophic growth with hydrogen or elemental iron

A mesophilic sulphate-reducing micro-organism, able to grow chemolithoautotrophically with H2/CO2 (20 : 80) and with elemental iron as a sole electron donor, was isolated from a consortium capable of degrading long-chain paraffins and designated strain DRH4T. Cells were oval shaped often with bright refractile cores and occurred singly or in pairs. The cells formed pili. Strain DRH4T could grow chemolithoautotrophically with H2/CO2 or elemental iron and chemoorganotrophically utilizing a number of organic substrates, such as fatty acids from formate to octanoate (C1–C8). Sulphate and thiosulphate served as terminal electron acceptors, but sulphite and nitrate did not. Optimal growth was observed from 37 to 40 °C and pH from 6.5 to 7.2. Strain DRH4T did not require NaCl for growth and could proliferate under a broad range of salinities from freshwater (1 g l−1 NaCl) to seawater (27 g l−1 NaCl) conditions. The genomic DNA G+C content was 54.46 mol %. Based on 16S rRNA gene sequence analysis. strain DRH4T was distinct from previously described Deltaproteobacteria species exhibiting the closest affiliation to Desulforhabdus amnigena ASRB1T, Syntrophobacterium sulfatireducens TB8106T and Desulfovirga adipica 12016T with 93.35, 93.42 and 92.85 % similarity, respectively. Strain DRH4T showed significant physiological differences with the aforementioned organisms. Based on physiological differences and phylogenetic comparisons, we propose to classify DRH4T as the type strain (=DSM 113 455T=JCM 39 248T) of a novel species of a new genus with the name Desulfoferrobacter suflitae gen. nov., sp. nov.

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing

Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.