Electrospun carbon nanofibers from polyacrylonitrile blended with activated or graphitized carbonaceous materials for improving anodic bioelectrocatalysis

The electrospun carbon nanofibers obtained from polyacrylonitrile (PAN) and PAN blends with either activated carbon (PAN-AC) or graphite (PAN-GR) were tested as anodes using Shewanella oneidensis MR-1. Extensive physico-chemical and electrochemical characterization confirmed their formation, their fibrous and porous nature, and their suitability as electrodes. N2 adsorption measurements revealed high specific surface area (229.8, 415.8 and 485.2m(2) g(-1)) and porosity (0.142, 0.202 and 0.239cm(3)g(-1)) for PAN, PAN-AC and PAN-GR, respectively. The chronoamperometric measurements showed a considerable decrease in start-up time and more than a 10-fold increase in the generation of current with these electrodes (115, 139 and 155μAcm(-2) for PAN, PAN-AC and PAN-GR, respectively) compared to the graphite electrode (11.5μAcm(-2)). These results indicate that the bioelectrocatalysis benefits from the blending of PAN with activated or graphitized carbonaceous materials, presumably due to the increased specific surface area, total pore volume and modification of the carbon microstructure.

Increase of riboflavin biosynthesis underlies enhancement of extracellular electron transfer of Shewanella in alkaline microbial fuel cells

Electrolyte pH tremendously affects the electricity output of microbial fuel cells. However, its underlying molecular mechanism remains elusive, in particular for Shewanella oneidensis MR-1, one of the most widely adopted electrogenic microorganisms. Herein, we found that MFCs were able to deliver a significant (but different) electricity output in a wide range of pH (from 6 to 10), with the maximum at pH=9 (alkaline), which delivers ∼1.5times' higher power output than that at pH=7 (neutral). Furthermore, cyclic voltammetry analysis showed an enhanced electrochemical activity of riboflavin (responsible for extracellular electron transfer of Shewanella) at alkaline pH. Strikingly, the concentration of riboflavin synthesized by Shewanella in MFCs at different pH showed a good correlation with the electricity output of MFCs. Thus, our results substantiated that the increase of riboflavin biosynthesis by Shewanella at the alkaline condition underlies the improvement of the electricity output in MFCs.

Single-cell imaging and spectroscopic analyses of Cr(VI) reduction on the surface of bacterial cells

We investigate the single-cell reduction of toxic Cr(VI) by the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 (MR-1), an important bioremediation process, using Raman spectroscopy and scanning electron microscopy (SEM) combined with energy-dispersive X-ray spectroscopy (EDX). Our experiments indicate that the toxic, highly soluble Cr(VI) can be efficiently reduced to less toxic, nonsoluble Cr(2)O(3) nanoparticles by MR-1. Cr(2)O(3) is observed to emerge as nanoparticles adsorbed on the cell surface and its chemical nature is identified by EDX imaging and Raman spectroscopy. Co-localization of Cr(2)O(3) and cytochromes by EDX imaging and Raman spectroscopy suggests a terminal reductase role for MR-1 surface-exposed cytochromes MtrC and OmcA. Our experiments revealed that the cooperation of surface proteins OmcA and MtrC makes the reduction reaction most efficient, and the sequence of the reducing reactivity of MR-1 is wild type > single mutant ΔmtrC or mutant ΔomcA > double mutant (ΔomcA-ΔmtrC). Moreover, our results also suggest that direct microbial Cr(VI) reduction and Fe(II) (hematite)-mediated Cr(VI) reduction mechanisms may coexist in the reduction processes.

Microsensors and microscale gradients in biofilms

Understanding the limiting factors and mechanisms of biofilm processes requires the direct measurement of microscale gradients using the appropriate tools. Microscale measurements can provide mechanistic information that cannot be obtained from bulk-scale measurements. Among the most used and trusted tools in microscale biofilm research are microsensors. The goal of this chapter is to introduce microsensor technology along with several examples to illustrate microscale processes in biofilms that are usually absent in bulk. We define a microsensor for biofilm research as a needle-type sensor with tip diameter of a few microns and a length up to several hundred microns. Microsensors can be used noninvasively to monitor in situ biofilm processes. Both optical and electrochemical microsensors can be used for biofilm applications. Because of newly discovered biofilm processes, the design and use of microsensors require customization and carefully designed experiments. In this chapter we present several examples describing the use of microsensors (1) in environmental biofilms, (2) in medical biofilms, and (3) in biofilms for energy and bioproducts. Microsensors can be the most useful if the measured profiles are integrated into the study of overall biofilm processes.

Beam-induced oxidation of monomeric U(IV) species

Uranium L(III)-edge X-ray absorption spectroscopy is often used to probe the oxidation state and coordination of uranium in environmental samples, and micrometre-sized beams can be used to spatially map the distribution of uranium relative to other elements. Here a variety of uranium-containing environmental samples are analyzed at both microbeam and larger beam sizes to determine whether reoxidation of U(IV) occurred. Monomeric U(IV), a recently discovered product of U(VI) reduction by microbes and certain iron-bearing minerals at uranium-contaminated field sites, was found to be reoxidized during microbeam (3 µm × 2 µm) analysis of biomass and sediments containing the species but not at larger beam sizes. Thus, care must be taken when using X-ray microprobes to analyze samples containing monomeric U(IV).

Biological accumulation of tellurium nanorod structures via reduction of tellurite by Shewanella oneidensis MR-1

The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, reduced tellurite (Te(IV), TeO(3)(2-)) to elemental tellurium under anaerobic conditions resulting in the intracellular accumulation of needle shaped crystalline Te(0) nanorods. Fatty acid analyses showed that toxic Te(IV) increased the unsaturated fatty acid composition of the lipid components of the cell membrane, implying a deconstruction of the integrity of the cellular membrane structure. The current results suggest that dissimilatory metal reducing bacteria such as S. oneidensis MR-1 may play an important role in recycling toxic tellurium elements, and may be applied as a novel selective biological filter via the accumulation of industry-applicable rare materials, Te(0) nanorods, in the cell.

Temporal expression-based analysis of metabolism

Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM). We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such “history-dependent” sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.

Understanding the dynamic response of microorganisms to environmental changes is a major challenge in systems biology. In many cases, these responses manifest themselves through changes in gene transcription, which then propagate to adjust flow through metabolism. Here, we implement a Temporal Expression-based Analysis of Metabolism (TEAM) by dynamically integrating a genome-scale model of the metabolism of S. oneidensis with high-throughput measurements of gene expression and growth data. TEAM recapitulates the complex cascade of secretion and re-uptake of intermediary carbon sources that S. oneidensis exhibits in the experimental data. We show that these complicated metabolic behaviors are best captured when TEAM explicitly accounts for each gene's unique transcriptional signature. Furthermore, by way of a newly proposed sensitivity analysis, we reveal and study the inherent difficulty of dynamic metabolic flux modeling: small changes early in a simulation can easily spread and lead to significant changes towards the end of it. We expect that further development of robust dynamic flux balance methods will need to overcome such “history-dependent” sensitivities in order to achieve increased predictive accuracy.

Redox reactions of reduced flavin mononucleotide (FMN), riboflavin (RBF), and anthraquinone-2,6-disulfonate (AQDS) with ferrihydrite and lepidocrocite

Flavins are secreted by the dissimilatory iron-reducing bacterium Shewanella and can function as endogenous electron transfer mediators. To assess the potential importance of flavins in Fe(III) bioreduction, we investigated the redox reaction kinetics of reduced flavin mononucleotide (i.e., FMNH(2)) and reduced riboflavin (i.e., RBFH(2)) with ferrihydrite and lepidocrocite. The organic reductants rapidly reduced and dissolved ferrihydrite and lepidocrocite in the pH range 4-8. The rate constant k for 2-line ferrihydrite reductive dissolution by FMNH(2) was 87.5 ± 3.5 M(-1)·s(-1) at pH 7.0 in batch reactors, and k was similar for RBFH(2). For lepidocrocite, k was 500 ± 61 M(-1)·s(-1) for FMNH(2) and 236 ± 22 M(-1)·s(-1) for RBFH(2). The surface area normalized initial reaction rates (r(a)) were between 0.08 and 77 μmol·m(-2)·s(-1) for various conditions in stopped-flow experiments. Initial rates (r(o)) were first-order with respect to iron(III) oxide concentration, and r(a) increased with decreasing pH. Poorly crystalline 2-line ferrihydrite yielded the highest r(a), followed by more crystalline 6-line ferrihydrite and crystalline lepidocrocite. Compared to a previous whole-cell study with Shewanella oneidensis strain MR-1, our findings suggest that the reduction of electron transfer mediators by the Mtr (i.e., metal-reducing) pathway coupled to lactate oxidation is rate limiting, rather than heterogeneous electron transfer to the iron(III) oxide.

Maximising electricity production by controlling the biofilm specific growth rate in microbial fuel cells

The aim of this work is to study the relationship between growth rate and electricity production in perfusion-electrode microbial fuel cells (MFCs), across a wide range of flow rates by co-measurement of electrical output and changes in population numbers by viable counts and optical density. The experiments hereby presented demonstrate, for the first time to the authors' knowledge, that the anodic biofilm specific growth rate can be determined and controlled in common with other loose matrix perfusion systems. Feeding with nutrient-limiting conditions at a critical flow rate (50.8 mL h(-1)) resulted in the first experimental determination of maximum specific growth rate μ(max) (19.8 day(-1)) for Shewanella spp. MFC biofilms, which is considerably higher than those predicted or assumed via mathematical modelling. It is also shown that, under carbon-energy limiting conditions there is a strong direct relationship between growth rate and electrical power output, with μ(max) coinciding with maximum electrical power production.

Is histidine dissociation a critical component of the NO/H-NOX signaling mechanism? Insights from X-ray absorption spectroscopy

The H-NOX (Heme-Nitric oxide/OXygen binding) family of diatomic gas sensing hemoproteins has attracted great interest. Soluble guanylate cyclase (sGC), the well-characterized eukaryotic nitric oxide (NO) sensor is an H-NOX family member. When NO binds sGC at the ferrous histidine-ligated protoporphyrin-IX, the proximal histidine ligand dissociates, resulting in a 5-coordinate (5c) complex; formation of this 5c complex is viewed as necessary for activation of sGC. Characterization of other H-NOX family members has revealed that while most also bind NO in a 5c complex, some bind NO in a 6-coordinate (6c) complex or as a 5c/6c mixture. To gain insight into the heme pocket structural differences between 5c and 6c Fe(ii)-NO H-NOX complexes, we investigated the extended X-ray absorption fine structure (EXAFS) of the Fe(II)-unligated and Fe(II)-NO complexes of H-NOX domains from three species, Thermoanaerobacter tengcongensis, Shewanella woodyi, and Pseudoalteromonas atlantica. Although the Fe(II)-NO complex of TtH-NOX is formally 6c, we found the Fe-N(His) bond is substantially lengthened. Furthermore, although NO binds to SwH-NOX and PaH-NOX as a 5c complex, consistent with histidine dissociation, the EXAFS data do not exclude a very weakly associated histidine. Regardless of coordination number, upon NO-binding, the Fe-N(porphyrin) bond lengths in all three H-NOXs contract by ~0.07 Å. This study reveals that the overall heme structure of 5c and 6c Fe(II)-NO H-NOX complexes are substantially similar, suggesting that formal histidine dissociation may not be required to trigger NO/H-NOX signal transduction. The study has refined our understanding of the molecular mechanisms underlying NO/H-NOX signaling.

The 'porin-cytochrome' model for microbe-to-mineral electron transfer

Many species of bacteria can couple anaerobic growth to the respiratory reduction of insoluble minerals containing Fe(III) or Mn(III/IV). It has been suggested that in Shewanella species electrons cross the outer membrane to extracellular substrates via 'porin-cytochrome' electron transport modules. The molecular structure of an outer-membrane extracellular-facing deca-haem terminus for such a module has recently been resolved. It is debated how, once outside the cells, electrons are transferred from outer-membrane cytochromes to insoluble electron sinks. This may occur directly or by assemblies of cytochromes, perhaps functioning as 'nanowires', or via electron shuttles. Here we review recent work in this field and explore whether it allows for unification of the electron transport mechanisms supporting extracellular mineral respiration in Shewanella that may extend into other genera of Gram-negative bacteria.

Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbe-mineral interface: the application of STXM-XMCD

A combination of scanning transmission X-ray microscopy and X-ray magnetic circular dichroism was used to spatially resolve the distribution of different carbon and iron species associated with Shewanella oneidensis MR-1 cells. S. oneidensis MR-1 couples the reduction of Fe(III)-oxyhydroxides to the oxidation of organic matter in order to conserve energy for growth. Several potential mechanisms may be used by S. oneidensis MR-1 to facilitate Fe(III)-reduction. These include direct contact between the cell and mineral surface, secretion of either exogenous electron shuttles or Fe-chelating agents and the production of conductive 'nanowires'. In this study, the protein/lipid signature of the bacterial cells was associated with areas of magnetite (Fe₃O₄), the product of dissimilatory Fe(III) reduction, which was oversaturated with Fe(II) (compared to stoichiometric magnetite). However, areas of the sample rich in polysaccharides, most likely associated with extracellular polymeric matrix and not in direct contact with the cell surface, were undersaturated with Fe(II), forming maghemite-like (γ-Fe₂O₃) phases compared to stoichiometric magnetite. The reduced form of magnetite will be much more effective in environmental remediation such as the immobilisation of toxic metals. These findings suggest a dominant role for surface contact-mediated electron transfer in this study and also the inhomogeneity of magnetite species on the submicron scale present in microbial reactions. This study also illustrates the applicability of this new synchrotron-based technique for high-resolution characterisation of the microbe-mineral interface, which is pivotal in controlling the chemistry of the Earth's critical zone.

Role of outer membrane c-type cytochromes MtrC and OmcA in Shewanella oneidensis MR-1 cell production, accumulation, and detachment during respiration on hematite

The iron-reducing bacterium Shewanella oneidensis MR-1 has the capacity to contribute to iron cycling over the long term by respiring on crystalline iron oxides such as hematite when poorly crystalline phases are depleted. The ability of outer membrane cytochromes OmcA and MtrC of MR-1 to bind to and transfer electrons to hematite has led to the suggestion that they function as terminal reductases when this mineral is used as a respiratory substrate. Differences in their redox behavior and hematite-binding properties, however, indicate that they play different roles in the electron transfer reaction. Here, we investigated how these differences in cytochrome behavior with respect to hematite affected biofilm development when the mineral served as terminal electron acceptor (TEA). Upon attachment to hematite, cells of the wild-type (WT) strain as well as those of a ΔomcA mutant but not those of a ΔmtrC mutant replicated and accumulated on the mineral surface. The results indicate that MtrC but not OmcA is required for growth when this mineral serves as TEA. While an OmcA deficiency did not impede cell replication and accumulation on hematite prior to achievement of a maximum surface cell density comparable to that established by WT cells, OmcA was required for efficient electron transfer and cell attachment to hematite once maximum surface cell density was achieved. OmcA may therefore play a role in overcoming barriers to electron transfer and cell attachment to hematite imposed by reductive dissolution of the mineral surface from cell respiration associated with achievement of high surface cell densities.

Linking bacterial diversity and geochemistry of uranium-contaminated groundwater

To understand the link between bacterial diversity and geochemistry in uranium-contaminated groundwater, microbial communities were assessed based on clone libraries of 16S rDNA genes from the USDOE Oak Ridge Field Research Centre (FRC) site. Four groundwater wells (GW835, GW836, FW113-47 and FW215-49) with a wide range of pH (3 to 7), nitrate (44 to 23,400 mg L(-1)), uranium (0.73 to 60.36 mg L(-1)) and other metal contamination, were investigated. Results indicated that bacterial diversity correlated with the geochemistry of the groundwater. Microbial diversity decreased in relation to the contamination levels of the wells. The highly contaminated well (FW113-47) had lower gene diversity than less contaminated wells (FW215-49, GW835 and GW836). The high concentrations of contaminants present in well FW113-47 stimulated the growth of organisms capable of reducing uranium (Shewanella and Pseudomonas), nitrate (Pseudomonas, Rhodanobacter and Xanthomonas) and iron (Stenotrophomonas), and which were unique to this well. The clone libraries consisted primarily of sequences closely related to the phylum Proteobacteria, with FW-113-47 almost exclusively containing this phylum. Metal-reducing bacteria were present in all four wells, which may suggest that there is potential for successful bioremediation of the groundwater at the Oak Ridge FRC. The microbial community information gained from this study and previous studies at the site can be used to develop predictive multivariate and geographical information system (GIS) based models for microbial populations at the Oak Ridge FRC. This will allow for a better understanding of what organisms are likely to occur where and when, based on geochemistry, and how these organisms relate to bioremediation processes at the site.

Quantitative separation of monomeric U(IV) from UO2 in products of U(VI) reduction

The reduction of soluble hexavalent uranium to tetravalent uranium can be catalyzed by bacteria and minerals. The end-product of this reduction is often the mineral uraninite, which was long assumed to be the only product of U(VI) reduction. However, recent studies report the formation of other species including an adsorbed U(IV) species, operationally referred to as monomeric U(IV). The discovery of monomeric U(IV) is important because the species is likely to be more labile and more susceptible to reoxidation than uraninite. Because there is a need to distinguish between these two U(IV) species, we propose here a wet chemical method of differentiating monomeric U(IV) from uraninite in environmental samples. To calibrate the method, U(IV) was extracted from known mixtures of uraninite and monomeric U(IV) and tested using X-ray absorption spectroscopy (XAS). Monomeric U(IV) was efficiently removed from biomass and Fe(II)-bearing phases by bicarbonate extraction, without affecting uraninite stability. After confirming that the method effectively separates monomeric U(IV) and uraninite, it is further evaluated for a system containing those reduced U species and adsorbed U(VI). The method provides a rapid complement, and in some cases alternative, to XAS analyses for quantifying monomeric U(IV), uraninite, and adsorbed U(VI) species in environmental samples.

Azo dye decolorization by Shewanella aquimarina under saline conditions

Decolorization of azo dyes under saline conditions was studied with Shewanella aquimarina, which demonstrated good growth at up to 7% NaCl. No inhibition on acid red 27 (AR27) decolorization was caused by 1-3% NaCl. Additionally, 14.5% AR27 (0.2mM) could still be removed in 12h in the presence of 10% NaCl. The relationship between specific decolorization rate and AR27 concentration followed Michaelis-Menten kinetics (K(m)=0.34 mM, V(max)=6.44 μmol mg cell(-1) h(-1)). Lactate and formate were efficient electron donors for AR27 decolorization. The initial decolorization rate was in direct proportion to biomass concentration (0.18-0.72 g l(-1)). Compared to NaCl, slighter inhibitive effects were found with Na(2)SO(4) whereas more severe inhibition was caused by NaNO(3). Lower NaCl concentration stimulated azoreductase, laccase and NADH-DCIP reductase activities of cell extracts. AR27 decolorization products were found to be aromatic amines, which were less phytotoxic than the untreated dye.

Removal of water-insoluble Sudan dyes by Shewanella oneidensis MR-1

Decolorization of water-insoluble Sudan dyes was studied with Shewanella oneidensis MR-1, which removed 66.8%, 43.4%, 56.0% and 33.7% Sudan I-IV in 104 h, respectively and reduced Sudan I to aniline and 1-amino-2-naphthol. Lactate was identified as the most efficient electron donor for Sudan I reduction. Improved reduction performance was obtained in the presence of higher lactate or biomass concentration. The correlation between specific reduction rate and initial Sudan I concentration could be described with Michaelis-Menten kinetics (V(max)=1.8 mg Sudan I mg cell(-1) h(-1) and K(m)=5.3 mg l(-1)). The addition of anthraquinone-2-sulfonate stimulated the reduction significantly whereas the presence of 2-hydroxy-1,4-naphthoquinone had little enhancing effect. The main azoreductase activity was found with membrane-bound proteins of MR-1 and no reduction occurred when Sudan I was incubated with cell extracts. These data indicated for the first time that Shewanella could reduce solid-phase Sudan dye particles.

Flavins secreted by bacterial cells of Shewanella catalyze cathodic oxygen reduction

On Her Majesty's Secrete Service: Oxygen reduction is an important process for microbial fuel cells (MFCs) and microbiologically-influenced corrosion (MIC). We demonstrate that flavins secreted by anode-respiring Shewanella cells can catalyze cathodic oxygen reduction via adsorption on the cathode. The findings will provide new insight for developing methods to improve MFC performance and to prevent MIC.

Doping of biogenic Pd catalysts with Au enables dechlorination of diclofenac at environmental conditions

By using the metal reducing capacities of bacteria, Pd nanoparticles can be produced in a sustainable way ('bio-Pd'). These bio-Pd nanoparticles can be used as a catalyst in, for example, dehalogenation reactions. However, some halogenated compounds are not efficiently degraded using a bio-Pd catalyst. This study shows that the activity of bio-Pd can be improved by doping with Au(0) ('bio-Pd/Au'). In contrast with bio-Pd, bio-Pd/Au could perform the removal of the model pharmaceutical compound diclofenac from an aqueous medium in batch experiments at neutral pH and with H(2) as the hydrogen donor (first order decay constant of 0.078 ± 0.009 h(-1)). Dehalogenation was for both catalysts the only observed reaction. For bio-Pd/Au, a disproportional increase of catalytic activity was observed with increasing Pd-content of the catalyst. In contrast, when varying the Au-content of the catalyst, a Pd/Au mass ratio of 50/1 showed the highest catalytic activity (first order decay value of 0.52 ± 0.02 h(-1)). The removal of 6.40 μg L(-1) diclofenac from a wastewater treatment plant effluent using bio-Pd was not possible even after prolonged reaction time. However, by using the most active bio-Pd/Au catalyst, 43.8 ± 0.5% of the initially present diclofenac could be removed after 24 h. This study shows that doping of bio-Pd nanoparticles with Au(0) can be a promising approach for the reductive treatment of wastewaters containing halogenated contaminants.

Biodecolorization of Naphthol Green B dye by Shewanella oneidensis MR-1 under anaerobic conditions

The anaerobic decolorization of metal-complex dye Naphthol Green B (NGB) by a metal-reducing bacterium, Shewanella oneidensis MR-1, was investigated. S. oneidensis MR-1 showed a high capacity for decolorizing NGB even at a concentration of up to 1000mg/L under anaerobic conditions. Maximum decolorization efficiency was appeared at pH 8.0 and 40°C. Addition of iron oxide caused no inhibition to the NGB decolorization, while the presence of ferric citrate, nitrite, or nitrate almost completely terminated the decolorization. Biosynthesis of nanomaterials was observed coupled with the degradation of NGB when thiosulfate was added. The Mtr respiratory pathway was found to be responsible for the decolorization of NGB by S. oneidensis, in which extracellular electron shuttle also plays a positive role in promoting the decolorization.

Facile fabrication of scalable, hierarchically structured polymer/carbon architectures for bioelectrodes

This research introduces a method for fabrication of conductive electrode materials with hierarchical structure from porous polymer/carbon composite materials. We describe the fabrication of (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) scaffolds doped with carbon materials that provide a conductive three-dimensional architecture that was demonstrated for application in microbial fuel cell (MFC) anodes. Composite electrodes from PHBV were fabricated to defined dimensions by solvent casting and particulate leaching of a size-specific porogen (in this case, sucrose). The cellular biocompatibility of the resulting composite material facilitated effective immobilization of a defined preparation of Shewanella oneidensis DSP-10 as a model microbial catalyst. Bacterial cells were immobilized via chemical vapor deposition (CVD) of silica to create an engineered biofilm that exhibits efficient bioelectrocatalysis of a simple-carbon fuel in a MFC. The functionalized PHBV electrodes demonstrate stable and reproducible anodic open circuit potentials of -320 ± 20 mV (vs Ag/AgCl) with lactate as the electron donor. Maximum power densities achieved by the hierarchically structured electrodes (~5 mW cm(3)) were significantly higher than previously observed for graphite-felt electrodes. The methodology for fabrication of scalable electrode materials may be amenable to other bioelectrochemical applications, such as enzyme fuel cells and biosensors, and could easily be adapted to various design concepts.

Macroporous and monolithic anode based on polyaniline hybridized three-dimensional graphene for high-performance microbial fuel cells

Microbial fuel cell (MFC) is of great interest as a promising green energy source to harvest electricity from various organic matters. However, low bacterial loading capacity and low extracellular electron transfer efficiency between the bacteria and the anode often limit the practical applications of MFC. In this work, a macroporous and monolithic MFC anode based on polyaniline hybridized three-dimensional (3D) graphene is demonstrated. It outperforms the planar carbon electrode because of its abilities to three-dimensionally interface with bacterial biofilm, facilitate electron transfer, and provide multiplexed and highly conductive pathways. This study adds a new dimension to the MFC anode design as well as to the emerging graphene applications.

Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 sequentially utilizes lactate and its waste products (pyruvate and acetate) during batch culture. To decipher MR-1 metabolism, we integrated genome-scale flux balance analysis (FBA) into a multiple-substrate Monod model to perform the dynamic flux balance analysis (dFBA). The dFBA employed a static optimization approach (SOA) by dividing the batch time into small intervals (i.e., ∼400 mini-FBAs), then the Monod model provided time-dependent inflow/outflow fluxes to constrain the mini-FBAs to profile the pseudo-steady-state fluxes in each time interval. The mini-FBAs used a dual-objective function (a weighted combination of "maximizing growth rate" and "minimizing overall flux") to capture trade-offs between optimal growth and minimal enzyme usage. By fitting the experimental data, a bi-level optimization of dFBA revealed that the optimal weight in the dual-objective function was time-dependent: the objective function was constant in the early growth stage, while the functional weight of minimal enzyme usage increased significantly when lactate became scarce. The dFBA profiled biologically meaningful dynamic MR-1 metabolisms: 1. the oxidative TCA cycle fluxes increased initially and then decreased in the late growth stage; 2. fluxes in the pentose phosphate pathway and gluconeogenesis were stable in the exponential growth period; and 3. the glyoxylate shunt was up-regulated when acetate became the main carbon source for MR-1 growth.

Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor

Shewanella oneidensis is a target of extensive research in the fields of bioelectrochemical systems and bioremediation because of its versatile metabolic capabilities, especially with regard to respiration with extracellular electron acceptors. The physiological activity of S. oneidensis to respire at electrodes is of great interest, but the growth conditions in thin-layer biofilms make physiological analyses experimentally challenging. Here, we took a global approach to evaluate physiological activity with an electrode as terminal electron acceptor for the generation of electric current. We performed expression analysis with DNA microarrays to compare the overall gene expression with an electrode to that with soluble iron(III) or oxygen as the electron acceptor and applied new hierarchical model-based statistics for the differential expression analysis. We confirmed the differential expression of many genes that have previously been reported to be involved in electrode respiration, such as the entire mtr operon. We also formulate hypotheses on other possible gene involvements in electrode respiration, for example, a role of ScyA in inter-protein electron transfer and a regulatory role of the cbb3-type cytochrome c oxidase under anaerobic conditions. Further, we hypothesize that electrode respiration imposes a significant stress on S. oneidensis, resulting in higher energetic costs for electrode respiration than for soluble iron(III) respiration, which fosters a higher metabolic turnover to cover energy needs. Our hypotheses now require experimental verification, but this expression analysis provides a fundamental platform for further studies into the molecular mechanisms of S. oneidensis electron transfer and the physiologically special situation of growth on a poised-potential surface.