High-affinity binding and direct electron transfer to solid metals by the Shewanella oneidensis MR-1 outer membrane c-type cytochrome OmcA

Understanding Nanoscale Interactions between Minerals and Microbes: Opportunities for Green Remediation of Contaminated Sites

In situ contaminant degradation and detoxification mediated by microbes and minerals is an important element of green remediation. Improved understanding of microbe-mineral interactions on the nanoscale offers promising opportunities to further minimize the environmental and energy footprints of site remediation. In this Perspective, we describe new methodologies that take advantage of an array of multidisciplinary tools─including multiomics-based analysis, bioinformatics, machine learning, gene editing, real-time spectroscopic and microscopic analysis, and computational simulations─to identify the key microbial drivers in the real environments, and to characterize in situ the dynamic interplay between minerals and microbes with high spatiotemporal resolutions. We then reflect on how the knowledge gained can be exploited to modulate the binding, electron transfer, and metabolic activities at the microbe-mineral interfaces, to develop new in situ contaminant degradation and detoxication technologies with combined merits of high efficacy, material longevity, and low environmental impacts. Two main strategies are proposed to maximize the synergy between minerals and microbes, including using mineral nanoparticles to enhance the versatility of microorganisms (e.g., tolerance to environmental stresses, growth and metabolism, directed migration, selectivity, and electron transfer), and using microbes to synthesize and regenerate highly dispersed nanostructures with desired structural/surface properties and reactivity.

Electron Transfer Mechanism at the Interface of Multi-Heme Cytochromes and Metal Oxide

Electroactive microbial cells have evolved unique extracellular electron transfer to conduct the reactions via redox outer-membrane (OM) proteins. However, the electron transfer mechanism at the interface of OM proteins and nanomaterial remains unclear. In this study, the mechanism for the electron transfer at biological/inorganic interface is investigated by integrating molecular modeling with electrochemical and spectroscopic measurements. For this purpose, a model system composed of OmcA, a typical OM protein, and the hexagonal tungsten trioxide (h-WO3 ) with good biocompatibility is selected. The interfacial electron transfer is dependent mainly on the special molecular configuration of OmcA and the microenvironment of the solvent exposed active center. Also, the apparent electron transfer rate can be tuned by site-directed mutagenesis at the axial ligand of the active center. Furthermore, the equilibrium state of the OmcA/h-WO3 systems suggests that their attachment is attributed to the limited number of residues. The electrochemical analysis of OmcA and its variants reveals that the wild type exhibits the fastest electron transfer rate, and the transient absorption spectroscopy further shows that the axial histidine plays an important role in the interfacial electron transfer process. This study provides a useful approach to promote the site-directed mutagenesis and nanomaterial design for bioelectrocatalytic applications.

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.

The material-microorganism interface in microbial hybrid electrocatalysis systems

This review presents a comprehensive summary of the material-microorganism interface in microbial hybrid electrocatalysis systems. Microbial hybrid electrocatalysis has been developed to combine the advantages of inorganic electrocatalysis and microbial catalysis. However, electron transfer at the interfaces between microorganisms and materials is a very critical issue that affects the efficiency of the system. Therefore, this review focuses on the electron transfer at the material-microorganism interface and the strategies for building efficient microorganism and material interfaces. We begin with a brief introduction of the electron transfer mechanism in both the bioanode and biocathode of bioelectrochemical systems to understand the material-microorganism interface. Next, we summarise the strategies for constructing efficient material-microorganism interfaces including material design and modification and bacterial engineering. We also discuss emerging studies on the bio-inorganic hybrid electrocatalysis system. Understanding the interface between electrode/active materials and the microorganisms, especially the electron transfer processes, could help to drive the evolution of material-microorganism hybrid electrocatalysis systems towards maturity.

Effects of Different Nanoparticles on Microbes

Nanoparticles widely exist in nature and may be formed through inorganic or organic pathways, exhibiting unique physical and chemical properties different from those of bulk materials. However, little is known about the potential consequences of nanomaterials on microbes in natural environments. Herein, we investigated the interactions between microbes and nanoparticles by performing experiments on the inhibition effects of gold, ludox and laponite nanoparticles on Escherichia coli in liquid Luria-Bertani (LB) medium at different nanoparticle concentrations. These nanoparticles were shown to be effective bactericides. Scanning electron microscopy (SEM) images revealed the distinct aggregation of cells and nanoparticles. Transmission electron microscopy (TEM) images showed considerable cell membrane disruption due to nanoparticle accumulation on the cell surfaces, resulting in cell death. We hypothesized that this nanoparticle accumulation on the cell surfaces not only disrupted the cell membranes but also physically blocked the microbes from accessing nutrients. An iron-reducing bacterium, Shewanella putrefaciens, was tested for its ability to reduce the Fe (III) in solid ferrihydrite (HFO) or aqueous ferric citrate in the presence of laponite nanoparticles. It was found that the laponite nanoparticles inhibited the reduction of the Fe (III) in solid ferrihydrite. Moreover, direct contact between the cells and solid Fe (III) coated with the laponite nanoparticles was physically blocked, as confirmed by SEM images and particle size measurements. However, the laponite particles had an insignificant effect on the extent of aqueous Fe (III) bioreduction but slightly enhanced the rate of bioreduction of the Fe (III) in aqueous ferric citrate. The slightly increased rate of bioreduction by laponite nanoparticles may be due to the removal of inhibitory Fe (II) from the cell surface by its sorption onto the laponite nanoparticle surface. This result indicates that the scavenging of toxic heavy metals, such as Fe (II), by nanoparticles may be beneficial for microbes in the environment. On the other hand, microbial cells are also capable of detoxifying nanoparticles by coagulating nanoparticles with extracellular polymeric substances or by changing nanoparticle morphologies. Hence, the interactions between microbes and nanoparticles in natural environments should receive more attention.

Multiple roles of released c-type cytochromes in tuning electron transport and physiological status of Geobacter sulfurreducens

Dissimilatory metal-reducing bacteria (DMRB) can transfer electrons to extracellular insoluble electron acceptors and play important roles in geochemical cycling, biocorrosion, environmental remediation, and bioenergy generation. c-type cytochromes (c-Cyts) are synthesized by DMRB and usually transported to the cell surface to form modularized electron transport conduits through protein assembly, while some of them are released as extracellularly free-moving electron carriers in growth to promote electron transport. However, the type of these released c-Cyts, the timing of their release, and the functions they perform have not been unrevealed yet. In this work, after characterizing the types of c-Cyts released by Geobacter sulfurreducens under a variety of cultivation conditions, we found that these c-Cyts accumulated up to micromolar concentrations in the surrounding medium and conserved their chemical activities. Further studies demonstrated that the presence of c-Cyts accelerated the process of microbial extracellular electron transfer and mediated long-distance electron transfer. In particular, the presence of c-Cyts promoted the microbial respiration and affected the physiological state of the microbial community. In addition, c-Cyts were observed to be adsorbed on the surface of insoluble electron acceptors and modify electron acceptors. These results reveal the overlooked multiple roles of the released c-Cyts in acting as public goods, delivering electrons, modifying electron acceptors, and even regulating bacterial community structure in natural and artificial environments.

Microbes team with nanoscale zero-valent iron: A robust route for degradation of recalcitrant pollutants

Integrating nanoscale zero-valent iron (nZVI) with biological treatment processes holds the promise of inheriting significant advantages from both environmental nano- and bio-technologies. nZVI and microbes can perform in coalition in direct contact and act simultaneously, or be maintained in separate reactors and operated sequentially. Both modes can generate enhanced performance for wastewater treatment and environmental remediation. nZVI scavenges and eliminates toxic metals, and enhances biodegradability of some recalcitrant contaminants while bioprocesses serve to mineralize organic compounds and further remove impurities from wastewater. This has been demonstrated in a number of recent works that nZVI can substantially augment the performance of conventional biological treatment for wastewaters from textile and nonferrous metal industries. Our recent laboratory and field tests show that COD of the industrial effluents can be reduced to a record-low of 50 ppm. Recent literature on the theory and applications of the nZVI-bio system is highlighted in this mini review.

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.

Extracellular electron transfer influences the transport and retention of ferrihydrite nanoparticles in quartz sand coated with Shewanella oneidensis biofilm

Microbial biofilm has been found to impact the mobility of nanoparticles in saturated porous media by altering physicochemical properties of collector surface. However, little is known about the influence of biofilm's biological activity on nanoparticle transport and retention. Here, the transport of ferrihydrite nanoparticles (FhNPs) was studied in quartz sands coated with biofilm of Shewanella oneidensis MR-1 that is capable of reducing Fe(III) through extracellular electron transfer (EET). It was found that MR-1 biofilm coating enhanced FhNPs' deposition under different pH/ionic strength conditions and humic acid concentrations. More importantly, when the influent electron donor (glucose) concentration was increased to promote biofilm's EET activity, the breakthrough of FhNPs in biofilm-coated sands was inhibited. A lack of continuous and stable supply of electron donor, on the contrary, led to remobilization and release of the originally retained FhNPs. Column experiments with biofilm of EET-deficient MR-1 mutants (ΔomcA/ΔmtrC and ΔcymA) further indicated that the impairment of EET activity decreased the retention of FhNPs. It is proposed that the effective surface binding and adhesion of FhNPs that is required by direct EET cannot be neglected when evaluating the transport of FhNPs in sands coated with electroactive biofilm.

The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation

Iron (Fe) is the fourth most abundant element in the Earth's crust where ferrous Fe [Fe(II)] and ferric Fe [Fe(III)] can be used by archaea for energy conservation. In these archaea-Fe interactions, Fe(III) serves as terminal electron acceptor for anaerobic respiration by a variety of archaea, while Fe(II) serves as electron donor and/or energy sources for archaeal growth. As no Fe is incorporated into the archaeal cells, these redox reactions are referred to as dissimilatory Fe(III) reduction and Fe(II) oxidation, respectively. Dissimilatory Fe(III)-reducing archaea (FeRA) and Fe(II)-oxidizing archaea (FeOA) are widespread on Earth where they play crucial roles in biogeochemical cycling of not only Fe, but also carbon and sulfur. To reduce extracellular Fe(III) (oxyhydr)oxides, some FeRA transfer electrons directly to the Fe(III) (oxyhydr)oxides most likely via multiheme c-type cytochromes (c-Cyts). These multiheme c-Cyts may form the pathways similar to those found in bacteria for transferring electrons from the quinone/quinol pool in the cytoplasmic membrane to the Fe(III) (oxyhydr)oxides external to the archaeal cells. Use of multiheme c-Cyts for extracellular Fe(III) reduction by both Domains of Archaea and Bacteria emphasizes an ancient mechanism of extracellular electron transfer, which is well conserved. Other FeRA, however, reduce Fe(III) (oxyhydr)oxides indirectly via electron shuttles. Similarly, it is proposed that FeOA use pathways to oxidize Fe(II) on the surface of the cytoplasmic membrane and then to transfer the released electrons across the cytoplasmic membrane inward to the O2 and NAD+ in the cytoplasm. In this review, we focus on the latest understandings of the molecular mechanisms used by FeRA and FeOA for Fe(III) reduction and Fe(II) oxidation, respectively.

Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media

The fate and transport of bacteria in porous media are essential for bioremediation and water quality control. However, the influence of biological activities like extracellular electron transfer (EET) and swimming motility toward granular media on cell transport remains unknown. Here, electroactive bacteria with higher Fe(III) reduction abilities were found to demonstrate greater retention in ferrihydrite-coated sand. Increasing the concentrations of the electron donor (1-10 mM lactate), shuttle (0-50 μM anthraquinone-2,6-disulfonate), and acceptor (ferrihydrite, MnO₂, or biochar) under flow conditions significantly reduced Shewanella oneidensis MR-1's mobility through redox-active porous media. The deficiency of EET ability or flagellar motion and inhibition of intracellular proton motive force, all of which are essential for energy taxis, enhanced MR-1's transport. It was proposed that EET could facilitate MR-1 to sense, tactically move toward, and attach on redox-active media surface, eventually improving its retention. Positive linear correlations were established among parameters describing MR-1's energy taxis ability (relative taxis index), cell transport behavior (dispersion coefficient and relative change of effluent percentage), and redox activity of media surface (reduction potential or electron-accepting rate), providing novel insights into the critical impacts of bacterial microscale motility on macroscale cell transport through porous media.

Boosting the anode performance of microbial fuel cells with a bacteria-derived biological iron oxide/carbon nanocomposite catalyst

Modifying the electrodes of microbial fuel cells (MFCs) with iron oxides can improve the bacterial attachment performances and electrocatalytic activities for energy conversion, which is of significance in the fabrication of MFCs. However, the conventional modification methods usually result in the aggregation of iron sites, producing the electrodes of poor qualities. Herein, we report a novel method for the modification of electrochemical electrodes to boost the anode performance of MFC. The Shewanella precursor adhered on carbon felt electrode was directly carbonized to form a bacteria-derived biological iron oxide/carbon (Bio-FeOx/C) nanocomposite catalyst. The large spatial separation between the bacteria, as well as those between the iron containing proteins in the bacteria, deliver a highly dispersed Bio-FeOx/C nanocomposite with good electrocatalytic activities. The excellent microbial attachment performance and electron transfer rate of the Bio-FeOx/C modified electrode significantly promote the transfer of produced electrons between bacteria and electrode. Accordingly, the MFC with the Bio-FeOx/C electrode exhibits the maximum power density of 797.0 mW m^-2, much higher than that obtained with the conventional carbon felt anode (226.1 mW m^-2). Our works have paved a new avenue to the conversion of the natural bacterial precursors into active iron oxide nanoparticles as the anode catalyst of MFCs. The high catalytic activity of the prepared Bio-FeOx endows it great application potentials in the construction of high-performance electrodes.

Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium

Biogenic transformation of Fe minerals, associated with extracellular electron transfer (EET), allows microorganisms to exploit high-potential refractory electron acceptors for energy generation. EET-capable thermophiles are dominated by hyperthermophilic archaea and Gram-positive bacteria. Information on their EET pathways is sparse. Here, we describe EET channels in the thermophilic Gram-positive bacterium Carboxydothermus ferrireducens that drive exoelectrogenesis and rapid conversion of amorphous mineral ferrihydrite to large magnetite crystals. Microscopic studies indicated biocontrolled formation of unusual formicary-like ultrastructure of the magnetite crystals and revealed active colonization of anodes in bioelectrochemical systems (BESs) by C. ferrireducens. The internal structure of micron-scale biogenic magnetite crystals is reported for the first time. Genome analysis and expression profiling revealed three constitutive c-type multiheme cytochromes involved in electron exchange with ferrihydrite or an anode, sharing insignificant homology with previously described EET-related cytochromes thus representing novel determinants of EET. Our studies identify these cytochromes as extracellular and reveal potentially novel mechanisms of cell-to-mineral interactions in thermal environments.

Outer Membrane c-Type Cytochromes OmcA and MtrC Play Distinct Roles in Enhancing the Attachment of Shewanella oneidensis MR-1 Cells to Goethite

The outer membrane c-type cytochromes (c-Cyts) OmcA and MtrC in Shewanella are key terminal reductases that bind and transfer electrons directly to iron (hydr)oxides. Although the amounts of OmcA and MtrC at the cell surface and their molecular structures are largely comparable, MtrC is known to play a more important role in dissimilatory iron reduction. To explore the roles of these outer membrane c-Cyts in the interaction of Shewanella oneidensis MR-1 with iron oxides, the processes of attachment of S. oneidensis MR-1 wild type and c-type cytochrome-deficient mutants (the ΔomcA, ΔmtrC, and ΔomcA ΔmtrC mutants) to goethite are compared via quartz crystal microbalance with dissipation monitoring (QCM-D). Strains with OmcA exhibit a rapid initial attachment. The quantitative model for QCM-D responses reveals that MtrC enhances the contact area and contact elasticity of cells with goethite by more than one and two times, respectively. In situ attenuated total reflectance Fourier transform infrared two-dimensional correlation spectroscopic (ATR-FTIR 2D-CoS) analysis shows that MtrC promotes the initial interfacial reaction via an inner-sphere coordination. Atomic force microscopy (AFM) analysis demonstrates that OmcA enhances the attractive force between cells and goethite by about 60%. As a result, OmcA contributes to a higher attractive force with goethite and induces a rapid short-term attachment, while MtrC is more important in the longer-term interaction through an enhanced contact area, which promotes interfacial reactions. These results reveal that c-Cyts OmcA and MtrC adopt different mechanisms for enhancing the attachment of S. oneidensis MR-1 cells to goethite. It improves our understanding of the function of outer membrane c-Cyts and the influence of cell surface macromolecules in cell-mineral interactions.IMPORTANCE Shewanella species are one group of versatile and widespread dissimilatory iron-reducing bacteria, which are capable of respiring insoluble iron minerals via six multiheme c-type cytochromes. Outer membrane c-type cytochromes (c-Cyts) OmcA and MtrC are the terminal reductases in this pathway and have comparable protein structures. In this study, we elucidate the different roles of OmcA and MtrC in the interaction of S. oneidensis MR-1 with goethite at the whole-cell level. OmcA confers enhanced affinity toward goethite and results in rapid attachment. Meanwhile, MtrC significantly increases the contact area of bacterial cells with goethite and promotes the interfacial reaction, which may explain its central role in extracellular electron transfer. This study provides novel insights into the role of bacterial surface macromolecules in the interfacial interaction of bacteria with minerals, which is critical to the development of a comprehensive understanding of cell-mineral interactions.

Virgin (Fe0) and microbially regenerated (Fe2+) iron turning waste for treating chlorinated pesticides in water

This work investigated the applicability of iron turning waste as filtration media for treating mixture of organochlorine pesticides (OCPs) in water and the ability of non-pathogenic bacterium Shewanella oneidensis to regenerate the exhausted iron turning waste for reuse. In batch experiments, 1.5 × 10⁴ mg/L of iron turning waste efficiently removed (≥85%) five out of six pesticides in 200 mL of water (20 μg/L for each pesticide) in 10 min. Increasing the iron dose from 2.5 × 10³ to 1.5 × 10⁴ mg/L enhanced the removal of heptachlor, endosulfan, dieldrin, and endrin by 5.7, 13.2, 23.3, and 39.4%, respectively, whereas lindane and dichlorodiphenyltrichloroethane removal was comparable when using 2.5 × 10³ and 1.5 × 10⁴ mg/L of iron. Better pesticide removal (except lindane) was achieved when the initial concentration of each pesticide was higher (20 μg/L versus 1 μg/L) in the solution. Acidic pH favored OCPs (except endosulfan) removal. S. oneidensis efficiently reduced 80 ± 5% of dissolved ferric iron (Fe³⁺) to ferrous iron (Fe²⁺) in 72 h. Microbially regenerated Fe²⁺ iron removed all six OCPs in water efficiently (52-91%) and at similar levels as provided by virgin iron turning (38-100%). Lindane, endosulfan, and dieldrin removal increased 4-fold using S. oneidensis regenerated iron compared to exhausted iron.

Probing extracellular reduction mechanisms of Bacillus subtilis and Escherichia coli with nitroaromatic compounds

Redox transformations of organic contaminants by bacterial extracellular polymeric substances (EPS) and the associated electron transfer mechanisms are rarely reported. Here we show that a nitroaromatic compound (1,3-dinitrobenzene) can be readily reduced to 3-hydroxylaminonitrobenzene and 3-nitroaniline in aqueous suspension of common bacteria (E. coli or B. subtilis) or in aqueous dissolved EPS extracted from the bacteria. The loss ratio of 1,3-dinitrobenzene by E. coli was unaffected after knocking out the nfsA gene encoding nitroreductase, but was suppressed by removing EPS attached to cells. In contrast, the loss ratio was enhanced by adding aqueous dissolved EPS to E. coli or B. subtilis suspension. The residual 1,3-dinitrobenzene and products formed after reduction were only presented outside the bacterial cells. Thus, bacterial reduction of 1,3-dinitrobenzene was mediated by nonenzymatic extracellular reduction. This was further corroborated by the observation that the stoichiometric demand of electrons in 1,3-dinitrobenzene reduction was nearly equal to the quantity of electrons donated by bacterial cells in the electrochemical cell experiment. Inhibition on the reduction of 1,3-dinitrobenzene by chemical probes combined with fluorescence detection demonstrated that reducing sugars in EPS might act as electron donors, while cytochromes and some low-molecular weight molecules (flavins and quinones) were involved as electron transfer mediators. Linear relationships were observed between the reduction kinetics and the one-electron reduction potentials for a series of substituted dinitrobenzenes in the presence of bacterial cells or dissolved EPS. Their close linear regression slope values suggest that the extracellular matrix and the exfoliated EPS utilized the same reducing agents (likely hydroquinones and reduced flavins) as terminal electron donors to reduce NACs. These results reveal a previously unrecognized mechanism for nonenzymatic extracellular reduction of NACs by common bacteria. CAPSULE: The extracellular matrix of E. coli or B. subtilis supplies both electron donors and electron transfer mediators to efficiently reduce nitroaromatic compounds.

Coating iron oxide nanoparticles with mesoporous silica reduces their interaction and impact on S. oneidensis MR-1

Here, we investigate the impact of iron oxide nanoparticles (IONPs) and mesoporous silica-coated iron oxide nanoparticles (msIONPs) on Shewanella oneidensis in an aerobic environment, which is likely the main environment where such nanoparticles will end up after use in consumer products or biomedical applications. Monitoring the viability of S. oneidensis, a model environmental organism, after exposure to the nanoparticles reveals that IONPs promote bacterial survival, while msIONPs do not impact survival. These apparent impacts are correlated with association of the nanoparticles with the bacterial membrane, as revealed by TEM and ICP-MS studies, and upregulation of membrane-associated genes. However, similar survival in bacteria was observed when exposed to equivalent concentrations of released ions from each nanomaterial, indicating that aqueous nanoparticle transformations are responsible for the observed changes in bacterial viability. Therefore, this work demonstrates that a simple mesoporous silica coating can control the dissolution of the IONP core by greatly reducing the amount of released iron ions, making msIONPs a more sustainable option to reduce perturbations to the ecosystem upon release of nanoparticles into the environment.

Goethite Hinders Azo Dye Bioreduction by Blocking Terminal Reductive Sites on the Outer Membrane of Shewanella decolorationis S12

Iron (hydr)oxides are the most ubiquitous Fe(III)-containing minerals in the near-surface environments and can regulate organic pollutant biotransformation by participating in bacterial extracellular electron transfer under anaerobic conditions. Mechanisms described so far are based on their redox properties in bacterial extracellular respiration. Here, we find that goethite, a typical iron (hydr)oxide, inhibits the bioreduction of different polar azo dyes by Shewanella decolorationis S12 not through electron competition, but by the contact of its surface Fe(III) with the bacterial outer surface. Through the combined results of attenuated total reflectance (ATR) Fourier transform infrared spectroscopy, two-dimensional correlation spectroscopy, and confocal laser scanning microscope, we found that the outer membrane proteins MtrC and OmcA of strain S12 are key binding sites for goethite surface. Meanwhile, they were identified as the important reductive terminals for azo dyes. These results suggest that goethite may block the terminal reductive sites of azo dyes on the bacterial outer membrane to inhibit their bioreduction. This discovered role of goethite in bioreduction provides new insight into the microbial transformation processes of organic pollutants in iron (hydr)oxide-containing environments.

Geometrical Changes in the Hemes of Bacterial Surface c-Type Cytochromes Reveal Flexibility in Their Binding Affinity with Minerals

Microbial extracellular electron transport occurs via the physical and electrical association of outer-membrane c-type cytochromes (OM c-Cyts) with extracellular solid surfaces. However, studies investigating the characteristics of cytochrome binding with solid materials have been limited to the use of purified units of OM c-Cyts dissolved in solution, rather than OM c-Cyts in intact cells, because of the lack of a methodology that specifically allows for the monitoring of OM c-Cyts in whole-cells. Here, we utilized circular dichroism (CD) spectroscopy to examine the molecular mechanisms and binding characteristics of the interaction between MtrC, a unit of OM c-Cyts, in whole Shewanella oneidensis MR-1 cells and hematite nanoparticles. The addition of hematite nanoparticles significantly decreased the intensity of the Soret CD peaks, indicating geometrical changes in the hemes in MtrC associated with their physical contact with hematite. The binding affinity of MtrC estimated using CD spectra changed predominantly depending upon the redox state of MtrC and the concentration of the hematite nanoparticles. In contrast, purified MtrC demonstrated a constant binding affinity following a Langmuir isotherm, with a standard Gibbs free energy of -43 kJ mol^-1, suggesting that the flexibility in the binding affinity of MtrC with hematite was specific in membrane-bound protein complex conditions. Overall, these findings suggest that the binding affinity as well as the heme geometry of OM c-Cyts are flexibly modulated in the membrane complex associated with microbe-mineral interactions.

Structural Changes in Adsorbed Cytochrome c upon Applied Potential Characterized by Neutron Reflectometry

The structural behavior of an electron-transfer protein, cytochrome c, at the 316L stainless steel electrode/aqueous interface was investigated over a range of applied potentials using neutron reflectometry supported by solution depletion isotherms, X-ray reflectometry, and quartz crystal microbalance measurements. A custom-made electrochemical cell allowed in situ observation of the adsorbed protein across a range of applied potentials; models fitted to the NR data showed a compact inner protein layer at the metal/electrolyte interface and a further thicker but highly diffuse layer that could be removed by rinsing. The overall amount adsorbed was found to be strongly dependent on the applied potential and buffer pH. Subtle but significant changes in the structure of the adsorbed protein layer were seen as the potential was swept between ±0.40 V, reflecting changing attractive/repulsive interactions between the protein's charged side groups and the surface. At greater applied potentials, irreversible changes in the stainless steel film structure were also observed and attributed to deuterium absorption into the metal.

Whole-cell circular dichroism difference spectroscopy reveals an in vivo-specific deca-heme conformation in bacterial surface cytochromes

Our novel analytical framework to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell revealed that the heme alignment in reduced MtrC is distinct from that in purified system.

We established whole-cell circular dichroism difference spectroscopy to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell. Our data showed that the heme alignment of reduced MtrC in whole cell is distinct from that in purified one, suggesting the in vivo specific electron transport kinetics.

Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals

The genus Carboxydocella forms a deeply branching family in the class Clostridia and is currently represented by three physiologically diverse species of thermophilic prokaryotes. The type strain of the type species, Carboxydocella thermautotrophica 41T, is an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO oxidation. Another strain, isolated from a hot spring at Uzon caldera, Kamchatka in the course of this work, is capable of coupling carboxydotrophy and dissimilatory reduction of Fe(III) from oxic and phyllosilicate minerals. The processes of carboxydotrophy and Fe(III) reduction appeared to be interdependent in this strain. The genomes of both isolates were sequenced, assembled into single chromosome sequences (for strain 41T a plasmid sequence was also assembled) and analyzed. Genome analysis revealed that each of the two strains possessed six genes encoding diverse Ni,Fe-containing CO dehydrogenases (maximum reported in complete prokaryotic genomes), indicating crucial role of carbon monoxide in C. thermautotrophica metabolism. Both strains possessed a set of 30 multiheme c-type cytochromes, but only the newly isolated Fe-reducing strain 019 had one extra gene of a 17-heme cytochrome, which is proposed to represent a novel determinant of dissimilatory iron reduction in prokaryotes. Mössbauer studies revealed that strain 019 induced reductive transformation of the abundant ferric/ferrous-mica mineral glauconite to siderite during carboxydotrophic growth. Reconstruction of the C. thermautotrophica strains energy metabolism is the first comprehensive genome analysis of a representative of the deep phylogenetic branch Clostridia Incertae Sedis, family V. Our data provide insights into energy metabolism of C. thermautotrophica with an emphasis on its ecological implications.

Tapping into cyanobacteria electron transfer for higher exoelectrogenic activity by imposing iron limited growth

The exoelectrogenic capacity of the cyanobacterium Synechococcus elongatus PCC7942 was studied in iron limited growth in order to establish conditions favouring extracellular electron transfer in cyanobacteria for photo-bioelectricity generation. Investigation into extracellular reduction of ferricyanide by Synechococcus elongatus PCC7942 demonstrated enhanced capability for the iron limited conditions in comparison to the iron sufficient conditions. Furtheremore, the significance of pH showed that higher rates of ferricyanide reduction occurred at pH 7, with a 2.7-fold increase with respect to pH 9.5 for iron sufficient cultures and 24-fold increase for iron limited cultures. The strategy presented induced exoelectrogenesis driven mainly by photosynthesis and an estimated redirection of the 28% of electrons from photosynthetic activity was achieved by the iron limited conditions. In addition, ferricyanide reduction in the dark by iron limited cultures also presented a significant improvement, with a 6-fold increase in comparison to iron sufficient cultures. Synechococcus elongatus PCC7942 ferricyanide reduction rates are unprecedented for cyanobacteria and they are comparable to those of microalgae. The redox activity of biofilms directly on ITO-coated glass, in the absence of any artificial mediator, was also enhanced under the iron limited conditions, implying that iron limitation increased exoelectrogenesis at the outer membrane level. Cyclic voltammetry of Synechococcus elongatus PCC7942 biofilms on ITO-coated glass showed a midpoint potential around 0.22 V vs. Ag/AgCl and iron limited biofilms had the capability to sustain currents in a saturated-like fashion. The present work proposes an iron related exoelectrogenic capacity of Synechococcus elongatus PCC7942 and sets a starting point for the study of this strain in order to improve photo-bioelectricity and dark-bioelectricity generation by cyanobacteria, including more sustainable mediatorless systems.

Biosynthesis and Characterization of Copper Nanoparticles Using Shewanella oneidensis: Application for Click Chemistry

Copper nanoparticles (Cu-NPs) have a wide range of applications as heterogeneous catalysts. In this study, a novel green biosynthesis route for producing Cu-NPs using the metal-reducing bacterium, Shewanella oneidensis is demonstrated. Thin section transmission electron microscopy shows that the Cu-NPs are predominantly intracellular and present in a typical size range of 20-40 nm. Serial block-face scanning electron microscopy demonstrates the Cu-NPs are well-dispersed across the 3D structure of the cells. X-ray absorption near-edge spectroscopy and extended X-ray absorption fine-structure spectroscopy analysis show the nanoparticles are Cu(0), however, atomic resolution images and electron energy loss spectroscopy suggest partial oxidation of the surface layer to Cu2 O upon exposure to air. The catalytic activity of the Cu-NPs is demonstrated in an archetypal "click chemistry" reaction, generating good yields during azide-alkyne cycloadditions, most likely catalyzed by the Cu(I) surface layer of the nanoparticles. Furthermore, cytochrome deletion mutants suggest a novel metal reduction system is involved in enzymatic Cu(II) reduction and Cu-NP synthesis, which is not dependent on the Mtr pathway commonly used to reduce other high oxidation state metals in this bacterium. This work demonstrates a novel, simple, green biosynthesis method for producing efficient copper nanoparticle catalysts.

Humic acids facilitated microbial reduction of polymeric Pu(IV) under anaerobic conditions

Flavins and humic substances have been extensively studied with emphasis on their ability to transfer extracellular electrons to insoluble metal oxides. Nevertheless, whether the low-solubility Pu(IV) polymers are microbially reduced to aqueous Pu(III) remains uncertain. Experiments were conducted under anaerobic and slightly alkaline conditions to study the difference between humic acids and flavins to transport extracellular electrons to Pu(IV) polymers. Our study demonstrates that Shewanella putrefaciens was unable to directly reduce polymeric Pu(IV) with a notably low reduction rate (3.4×10^-12mol/L Pu(III)_aq within 144h). The relatively high redox potential of flavins reveals the thermodynamically unfavorable reduction: E_h(PuO₂(am)/Pu³⁺)<E_h^o'(FMN/FMNH₂)≈E_h^o'(RBF/RBFH₂)≈-220mV at pH7.2. The microbially reduced humic acids facilitated the extracellular electron transfer to the polymers and reduced polymeric Pu(IV) (2.1×10^-10mol/L Pu(III)_aq) 62 times more rapidly than the flavins. The driving force for electron transfer explains the observed reduction: E_h(HA_ox/HA_red)<E_h(PuO₂(am)/Pu³⁺) when S. putrefaciens oxidized lactate and respired on the humic acids. In contrast, flavins were able to substantially reduce aqueous Pu(IV)-EDTA (1.9×10^-9mol/L Pu(III)_aq) because of the available driving force for electron transfer: Δ_rG_m=-F[E_h(PuL₂^4-/PuL₂^5-)-E_h^o'(FMN/FMNH₂)]=-33.5kJ/mol is a result of E_h(PuL₂^4-/PuL₂^5-)≫E_h(PuO₂(am)/Pu³⁺), where L is the EDTA ligand. In the presence of humic acids, the reduction of Pu(IV)-EDTA exhibited the most rapid rate (2.2×10^-9mol/L Pu(III)_aq). This result further demonstrates that humic acids facilitated the extracellular electron transfer to polymeric and aqueous Pu(IV). Reductive solubilization of the polymers may enhance Pu mobility in the geosphere and hence increases risks to human health.

Electron Transfer Strategies Regulate Carbonate Mineral and Micropore Formation

Some microbial carbonates are robust biosignatures due to their distinct morphologies and compositions. However, whether carbonates induced by microbial iron reduction have such features is unknown. Iron-reducing bacteria use various strategies to transfer electrons to iron oxide minerals (e.g., membrane-bound enzymes, soluble electron shuttles, nanowires, as well as different mechanisms for moving over or attaching to mineral surfaces). This diversity has the potential to create mineral biosignatures through manipulating the microenvironments in which carbonate precipitation occurs. We used Shewanella oneidensis MR-1, Geothrix fermentans, and Geobacter metallireducens GS-15, representing three different strategies, to reduce solid ferric hydroxide in order to evaluate their influence on carbonate and micropore formation (micro-size porosity in mineral rocks). Our results indicate that electron transfer strategies determined the morphology (rhombohedral, spherical, or long-chained) of precipitated calcium-rich siderite by controlling the level of carbonate saturation and the location of carbonate formation. Remarkably, electron transfer strategies also produced distinctive cell-shaped micropores in both carbonate and hydroxide minerals, thus producing suites of features that could potentially serve as biosignatures recording information about the sizes, shapes, and physiologies of iron-reducing organisms. Key Words: Microbial iron reduction-Micropore-Electron transfer strategies-Microbial carbonate. Astrobiology 18, 28-36.

Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands

Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal-ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r _{M ⁿ⁺} ), Gibbs free energy of formation (ΔG°_{f,M ⁿ⁺} ), and solvation energy (ΔG°_{s,M ⁿ⁺} )] by 2.303RT log K _ML = (α*_MLΔG°_{f,M ⁿ⁺} - β*_ML r _{M ⁿ⁺} + γ*_MLΔG°_{s,M ⁿ⁺} - δ*_ML), where the coefficients (α*_ML, β*_ML, γ*_ML, and intercept δ*_ML) are determined by fitting the equation to the existing experimental data. Coefficients β*_ML and γ*_ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG°_{f,M ⁿ⁺} ) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α*_ML is an index for the softness or hardness of a complexing ligand. Proton (H⁺) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid-base interactions is determined by the term α*_MLΔG°_{f,M ⁿ⁺} ; a positive product of α*_ML and ΔG°_{f,M ⁿ⁺} indicates that the acid-base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β*_ML r _{M ⁿ⁺} and γ*_MLΔG°_{s,M ⁿ⁺} , which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. The new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.

Adsorption Behavior and Mechanism of SCA-1 on a Calcite Surface: A Molecular Dynamics Study

The crystallization mechanism for natural mineral, especially the role of biological molecules in biomineralization, is still under debate. Protein adsorption on material surfaces plays a key role in biomineralization. In this article, molecular dynamics (MD) simulations were performed to systematically investigate the adsorption behavior of struthio camelus eggshell protein struthiocalcin-1 (SCA-1) on the calcite (104) surface with several different starting orientations in an explicit water environment. For each binding configuration, detailed adsorption behaviors and a mechanism were presented with the analysis of interaction energy, binding residues, hydrogen bonding, and structures (such as DSSP, dipole moment, and the electrostatic potential calculation). The results indicate that the positively charged and polar residues are the dominant residues for protein adsorption on the calcite (104) surface, and the strong electrostatic interaction drives the binding of model protein to the surface. The hydrogen bond bridge was found to play an important role in surface interactions as well. These results also demonstrate that SCA-1 is relatively rigid in spite of strong adsorption with few structural changes in α-helix and β-sheet contents. The results of the orientation calculation suggest that the dipole moment of the protein tends to remain parallel to calcite in most stable cases, which was confirmed by electrostatic potential isosurfaces analysis.

Proton Transport in the Outer-Membrane Flavocytochrome Complex Limits the Rate of Extracellular Electron Transport

The microbial transfer of electrons to extracellularly located solid compounds, termed extracellular electron transport (EET), is critical for microbial electrode catalysis. Although the components of the EET pathway in the outer membrane (OM) have been identified, the role of electron/cation coupling in EET kinetics is poorly understood. We studied the dynamics of proton transport associated with EET in an OM flavocytochrome complex in Shewanella oneidensis MR‐1. Using a whole‐cell electrochemical assay, a significant kinetic isotope effect (KIE) was observed following the addition of deuterated water (D₂O). The removal of a flavin cofactor or key components of the OM flavocytochrome complex significantly increased the KIE in the presence of D₂O to values that were significantly larger than those reported for proton channels and ATP synthase, thus indicating that proton transport by OM flavocytochrome complexes limits the rate of EET.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

Probing electron transfer between hemin and riboflavin using a combination of analytical approaches and theoretical calculations

Proton-coupled electron transfer mechanisms of riboflavin bound hemin in aqueous solution are elucidated by spectroelectrochemical analysis, the electron paramagnetic resonance method and theoretical calculations.

Microbial fuel cells using Cellulomonas spp. with cellulose as fuel

Cellulomonas fimi, Cellulomonas biazotea, and Cellulomonas flavigena are cellulose-degrading microorganisms chosen to compare the degradation of cellulose. C. fimi degraded 2.5 g/L of cellulose within 4 days, which was the highest quantity among the three microorganisms. The electric current generation by the microbial fuel cell (MFC) using the cellulose-containing medium with C. fimi was measured over 7 days. The medium in the MFC was sampled every 24 h to quantify the degradation of cellulose, and the results showed that the electric current increased with the degradation of cellulose. The maximum electric power generated by the MFC was 38.7 mW/m², and this numeric value was 63% of the electric power generated by an MFC with Shewanella oneidensis MR-1, a well-known current-generating microorganism. Our results showed that C. fimi was an excellent candidate to produce the electric current from cellulose via MFCs.

Aggregation Kinetics of Hematite Particles in the Presence of Outer Membrane Cytochrome OmcA of Shewanella oneidenesis MR-1

The aggregation behavior of 9, 36, and 112 nm hematite particles was studied in the presence of OmcA, a bacterial extracellular protein, in aqueous dispersions at pH 5.7 through time-resolved dynamic light scattering, electrophoretic mobility, and circular dichroism spectra, respectively. At low salt concentration, the attachment efficiencies of hematite particles in all sizes first increased, then decreased, and finally remained stable with the increase of OmcA concentration, indicating the dominant interparticle interaction changed along with the increase in the protein-to-particle ratio. Nevertheless, at high salt concentration, the attachment efficiencies of all hematite samples gradually decreased with increasing OmcA concentration, which can be attributed to increasing steric force. Additionally, the aggregation behavior of OmcA-hematite conjugates was more correlated to total particle-surface area than primary particle size. It was further established that OmcA could stabilize hematite nanoparticles more efficiently than bovine serum albumin (BSA), a model plasma protein, due to the higher affinity of OmcA to hematite surface. This study highlighted the effects of particle properties, solution conditions, and protein properties on the complicated aggregation behavior of protein-nanoparticle conjugates in aqueous environments.

Bacteria-Affinity 3D Macroporous Graphene/MWCNTs/Fe3O4 Foams for High-Performance Microbial Fuel Cells

Promoting the performance of microbial fuel cells (MFCs) relies heavily on the structure design and composition tailoring of electrode materials. In this work, three-dimensional (3D) macroporous graphene foams incorporated with intercalated spacer of multiwalled carbon nanotubes (MWCNTs) and bacterial anchor of Fe3O4 nanospheres (named as G/MWCNTs/Fe3O4 foams) were first synthesized and used as anodes for Shewanella-inoculated microbial fuel cells (MFCs). Thanks to the macroporous structure of 3D graphene foams, the expanded electrode surface by MWCNTs spacing, as well as the high affinity of Fe3O4 nanospheres toward Shewanella oneidensis MR-1, the anode exhibited high bacterial loading capability. In addition to spacing graphene nanosheets for accommodating bacterial cells, MWCNTs paved a smoother way for electron transport in the electrode substrate of MFCs. Meanwhile, the embedded bioaffinity Fe3O4 nanospheres capable of preserving the bacterial metabolic activity provided guarantee for the long-term durability of the MFCs. With these merits, the constructed MFC possessed significantly higher power output and stronger stability than that with conventional graphite rod anode.

Bioinspired Nanosucker Array for Enhancing Bioelectricity Generation in Microbial Fuel Cells

A bioinspired active anode with a suction effect is demonstrated for microbial fuel cells by constructing polypyrrole (PPy) nanotubular arrays on carbon textiles. The oxygen in the inner space of the nanosucker can be depleted by micro-organisms with the capability of facul-tative respiration, forming a vacuum, which then activates the electrode to draw the microorganism by suction and thus improve the bioelectricity generation.

Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities

Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.