Evaluation of electron-shuttling compounds in microbial ferric iron reduction

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.

Effects of Fe(III) Oxide Mineralogy and Phosphate on Fe(II) Secondary Mineral Formation during Microbial Iron Reduction

The bioreduction of Fe(III) oxides by dissimilatory iron-reducing bacteria may result in the formation of a suite of Fe(II)-bearing secondary minerals, including magnetite (a mixed Fe(II)/Fe(III) oxide), siderite (Fe(II) carbonate), vivianite (Fe(II) phosphate), chukanovite (ferrous hydroxy carbonate), and green rusts (mixed Fe(II)/Fe(III) hydroxides). In an effort to better understand the factors controlling the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of Fe(III) oxide mineralogy, phosphate concentration, and the availability of an electron shuttle (9,10-anthraquinone-2,6-disulfonate, AQDS) on the bioreduction of a series of Fe(III) oxides (akaganeite, feroxyhyte, ferric green rust, ferrihydrite, goethite, hematite, and lepidocrocite) by Shewanella putrefaciens CN32, and the resulting formation of secondary minerals, as determined by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. The overall extent of Fe(II) production was highly dependent on the type of Fe(III) oxide provided. With the exception of hematite, AQDS enhanced the rate of Fe(II) production; however, the presence of AQDS did not always lead to an increase in the overall extent of Fe(II) production and did not affect the types of Fe(II)-bearing secondary minerals that formed. The effects of the presence of phosphate on the rate and extent of Fe(II) production were variable among the Fe(III) oxides, but in general, the highest loadings of phosphate resulted in decreased rates of Fe(II) production, but ultimately higher levels of Fe(II) than in the absence of phosphate. In addition, phosphate concentration had a pronounced effect on the types of secondary minerals that formed; magnetite and chukanovite formed at phosphate concentrations of ≤1 mM (ferrihydrite), <~100 µM (lepidocrocite), 500 µM (feroxyhyte and ferric green rust), while green rust, or green rust and vivianite, formed at phosphate concentrations of 10 mM (ferrihydrite), ≥100 µM (lepidocrocite), and 5 mM (feroxyhyte and ferric green rust). These results further demonstrate that the bioreduction of Fe(III) oxides, and accompanying Fe(II)-bearing secondary mineral formation, is controlled by a complex interplay of mineralogical, geochemical, and microbiological factors.

NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction

Microbial iron(III) reduction can have a profound effect on the fate of contaminants in natural and engineered environments. Different mechanisms of extracellular electron transport are used by Geobacter and Shewanella spp. to reduce insoluble Fe(III) minerals. Here we prepared a thin film of iron(III)-(oxyhydr)oxide doped with arsenic, and allowed the mineral coating to be colonised by Geobacter sulfurreducens or Shewanella ANA3 labelled with ¹³C from organic electron donors. This preserved the spatial relationship between metabolically active Fe(III)-reducing bacteria and the iron(III)-(oxyhydr)oxide that they were respiring. NanoSIMS imaging showed cells of G. sulfurreducens were co-located with the iron(III)-(oxyhydr)oxide surface and were significantly more ¹³C-enriched compared to cells located away from the mineral, consistent with Geobacter species requiring direct contact with an extracellular electron acceptor to support growth. There was no such intimate relationship between ¹³C-enriched S. ANA3 and the iron(III)-(oxyhydr)oxide surface, consistent with Shewanella species being able to reduce Fe(III) indirectly using a secreted endogenous mediator. Some differences were observed in the amount of As relative to Fe in the local environment of G. sulfurreducens compared to the bulk mineral, highlighting the usefulness of this type of analysis for probing interactions between microbial cells and Fe-trace metal distributions in biogeochemical experiments.

Electricity from methane by reversing methanogenesis

Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current. Notably, this methane microbial fuel cell operates at high Coulombic efficiency.

Microbial fuel cells generate electricity from a variety of sources, however from methane only negligible electrical power has been reported so far. Here the authors convert methane into electricity using a synthetic consortium consisting of an engineered archaeal strain, microorganisms from methane-acclimated sludge, and Geobacter sulfurreducens.

Iron reactivity in anoxic sediments in the Ría de Vigo (NW Spain)

The high sedimentation rates and high organic matter contents in the sediments of the Ría de Vigo (NW Spain) promote the development of anoxic conditions, determining the dynamics of elements like Fe and conditioning his speciation and reactivity. Four gravity cores were retrieved in anoxic sediments of the Ría de Vigo in November 2012. In order to understand the behavior of Fe in these complex environments different fractions of reactive iron were analyzed. The decrease in highly reactive iron and sulfide contents with depth showed the relationship between the iron and sulfur cycle in the middle and outer zones of the ría. In the inner zone, the apparition of shallow methane gas may cause the slower decrease of the highly reactive iron contents. In zones without methane, sediment layers enriched in iron -with a reactivity higher than in other sediment samples- were observed. An increase was observed in the dithionite and total reactive iron contents from the inner to the outer zone of the ría, according to the gas depth. Furthermore, a decrease in Fe (III)-bearing minerals contents with depth was observed in the outer and middle zones, but not in the innermost area where the gas is shallow. The high organic matter and sulfide contents, mainly in the inner zone of the ría, indicate that the most of the Fe (II) is FeS. Moreover, the high contents of total reactive iron and pH values (6.86-7.98) could contribute the formation of stable minerals like pyrite along the Ría de Vigo.

Extracellular Electron Transfer and Biosensors

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

Nano-graphene induced positive effects on methanogenesis in anaerobic digestion

The effects of nano-graphene on methanogenesis in anaerobic digestion was investigated. Short-term results showed that graphene (30 and 120mg/L) had significantly positive effects on methane production rate, which increased by 17.0% and 51.4%. Further investigation indicated that acetate-consuming methanogenesis was enhanced. The failure of quinones to replicate graphene stimulation effects on methanogenesis suggested that graphene did not function as electron shuttles. After 55 day's operation at room temperature (from 20 to 10°C, the methane production rate with 30mg/L graphene was 14.3% higher than that of the control, while 120mg/L graphene showed a slight inhibition on methane yield. Illumina sequencing data showed that the archaeal community structure remained fairly constant as the incubated sludge with graphene at low temperature, in which Methanoregula, Methanosaeta and Methanospirillum were the dominant species. Besides, Geobacter enrichment was observed with graphene, suggesting that the direct interspecies electron transfer might be promoted.

Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park

Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was investigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sustained DIR driven by oxidation of acetate, lactate, and H2 . Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abiotic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides. Pyrosequencing of 16S rRNA genes from enrichment cultures showed dominant sequences closely affiliated with Geobacter metallireducens, a mesophilic Fe(III) oxide reducer. Shotgun metagenomic analysis of enrichment cultures confirmed the presence of a dominant G. metallireducens-like population and other less dominant populations from the phylum Ignavibacteriae, which appear to be capable of DIR. Gene (protein) searches revealed the presence of heat-shock proteins that may be involved in increased thermotolerance in the organisms present in the enrichments as well as porin-cytochrome complexes previously shown to be involved in extracellular electron transport. This analysis offers the first detailed insight into how DIR may impact the Fe geochemistry and isotope composition of a Fe-rich, circumneutral pH geothermal environment.

Methanogens rapidly transition from methane production to iron reduction

Methanogenesis, the microbial methane (CH4 ) production, is traditionally thought to anchor the mineralization of organic matter as the ultimate respiratory process in deep sediments, despite the presence of oxidized mineral phases, such as iron oxides. This process is carried out by archaea that have also been shown to be capable of reducing iron in high levels of electron donors such as hydrogen. The current pure culture study demonstrates that methanogenic archaea (Methanosarcina barkeri) rapidly switch from methanogenesis to iron-oxide reduction close to natural conditions, with nitrogen atmosphere, even when faced with substrate limitations. Intensive, biotic iron reduction was observed following the addition of poorly crystalline ferrihydrite and complex organic matter and was accompanied by inhibition of methane production. The reaction rate of this process was of the first order and was dependent only on the initial iron concentrations. Ferrous iron production did not accelerate significantly with the addition of 9,10-anthraquinone-2,6-disulfonate (AQDS) but increased by 11-28% with the addition of phenazine-1-carboxylate (PCA), suggesting the possible role of methanophenazines in the electron transport. The coupling between ferrous iron and methane production has important global implications. The rapid transition from methanogenesis to reduction of iron-oxides close to the natural conditions in sediments may help to explain the globally-distributed phenomena of increasing ferrous concentrations below the traditional iron reduction zone in the deep 'methanogenic' sediment horizon, with implications for metabolic networking in these subsurface ecosystems and in past geological settings.

Going wireless: Fe(III) oxide reduction without pili by Geobacter sulfurreducens strain JS-1

Previous studies have suggested that the conductive pili of Geobacter sulfurreducens are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of G. sulfurreducens reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the c-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through G. sulfurreducens biofilms is more effective via pili.

Model-driven elucidation of the inherent capacity of Geobacter sulfurreducens for electricity generation

Background

G. sulfurreducens is one of the commonest microbes used in microbial fuel cells (MFCs) for organic-to-electricity biotransformation. In MFCs based on this microorganism, electrons can be conveyed to the anode via three ways: 1) direct electron transfer (DET) mode, in which electrons of reduced c-type cytochromes in the microbial outer membrane are directly oxidized by the anode; 2) mediated electron transfer (MET) mode, in which the reducing potential available from cell metabolism in the form of NADH is targeted as an electron source for electricity generation with the aid of exogenous mediators; and 3) a putative mixed operation mode involving both electron transfer mechanisms described above (DET and MET). However, the potential of G. sulfurreducens for current output in these three operation modes and the metabolic mechanisms underlying the extraction of the reducing equivalents are still unknown.

Results

In this study, we performed flux balance analysis (FBA) of the genome-scale metabolic network to compute the fundamental metabolic potential of G. sulfurreducens for current output that is compatible with reaction stoichiometry, given a realistic nutrient uptake rate. We also developed a method, flux variability analysis with target flux minimization (FATMIN) to eliminate futile NADH cycles. Our study elucidates the possible metabolic strategies to sustain the NADH for current production under the MET and Mixed modes. The results showed that G. sulfurreducens had a potential to output current at up to 3.710 A/gDW for DET mode, 2.711 A/gDW for MET mode and 3.272 A/gDW for a putative mixed MET and DET mode. Compared with DET, which relies on only one contributing reaction, MET and Mixed mode were more resilient with ten and four reactions respectively for high current production.

Conclusions

The DET mode can achieve a higher maximum limit of the current output than the MET mode, but the MET has an advantage of higher power output and more flexible metabolic choices to sustain the electric current. The MET and DET modes compete with each other for the metabolic resource for the electricity generation.

Transcriptomic and genetic analysis of direct interspecies electron transfer

The possibility that metatranscriptomic analysis could distinguish between direct interspecies electron transfer (DIET) and H2 interspecies transfer (HIT) in anaerobic communities was investigated by comparing gene transcript abundance in cocultures in which Geobacter sulfurreducens was the electron-accepting partner for either Geobacter metallireducens, which performs DIET, or Pelobacter carbinolicus, which relies on HIT. Transcript abundance for G. sulfurreducens uptake hydrogenase genes was 7-fold lower in cocultures with G. metallireducens than in cocultures with P. carbinolicus, consistent with DIET and HIT, respectively, in the two cocultures. Transcript abundance for the pilus-associated cytochrome OmcS, which is essential for DIET but not for HIT, was 240-fold higher in the cocultures with G. metallireducens than in cocultures with P. carbinolicus. The pilin gene pilA was moderately expressed despite a mutation that might be expected to repress pilA expression. Lower transcript abundance for G. sulfurreducens genes associated with acetate metabolism in the cocultures with P. carbinolicus was consistent with the repression of these genes by H2 during HIT. Genes for the biogenesis of pili and flagella and several c-type cytochrome genes were among the most highly expressed in G. metallireducens. Mutant strains that lacked the ability to produce pili, flagella, or the outer surface c-type cytochrome encoded by Gmet_2896 were not able to form cocultures with G. sulfurreducens. These results demonstrate that there are unique gene expression patterns that distinguish DIET from HIT and suggest that metatranscriptomics may be a promising route to investigate interspecies electron transfer pathways in more-complex environments.

Mitigating ammonia inhibition of thermophilic anaerobic treatment of digested piggery wastewater: use of pH reduction, zeolite, biomass and humic acid

High free ammonia released during anaerobic digestion of livestock wastes is widely known to inhibit methanogenic microorganisms and result in low methane production. This was encountered during our earlier thermophilic semi-continuously fed continuously-stirred tank reactor (CSTR) treatment of piggery wastewater. This study explored chemical and biological means to mitigate ammonia inhibition on thermophilic anaerobic treatment of piggery wastewater with the aim to increase organic volatile carbon reduction and methane production. A series of thermophilic anaerobic batch experiments were conducted on the digested piggery effluent to investigate the effects of pH reduction (pH 8.3 to 7.5, 7.0 and 6.5) and additions of biomass (10% v/v and 19% v/v anaerobic digested piggery biomass and aerobic-anaerobic digested municipal biomass), natural zeolite (10, 15 and 20 g/L) and humic acid (1, 5 and 10 g/L) on methane production at 55 °C for 9-11 days. Reduction of the wastewater pH from its initial pH of 8.3 to 6.5 produced the greatest stimulation of methane production (3.4 fold) coupled with reductions in free ammonia (38 fold) and total volatile fatty acids (58% TVFA), particularly acetate and propionate. Addition of 10-20 g/L zeolite to piggery wastewater with and without pH reduction to 6.5 further enhanced total VFA reduction and methane production over their respective controls, with 20 g/L zeolite producing the highest enhancement effect despite the ammonia-nitrogen concentrations of the treated wastewaters remaining high. Without pH reduction, zeolite concentration up to 20 g/L was required to achieve comparable methane enhancement as the pH-reduced wastewater at pH 6.5. Although biomass (10% v/v piggery and municipal wastes) and low humic acid (1 and 5 g/L) additions enhanced total VFA reduction and methane production, they elevated the residual effluent total COD concentrations over the control wastewaters (pH-unadjusted and pH-reduced) unlike zeolite treatment. The outcomes from these batch experiments support the use of pH reduction to 6.5 and zeolite treatment (10-20 g/L) as effective strategies to mitigate ammonia inhibition of the thermophilic anaerobic treatment of piggery wastewater.

Glutathione reductase/glutathione is responsible for cytotoxic elemental sulfur tolerance via polysulfide shuttle in fungi

Fungi that can reduce elemental sulfur to sulfide are widely distributed, but the mechanism and physiological significance of the reaction have been poorly characterized. Here, we purified elemental sulfur-reductase (SR) and cloned its gene from the elemental sulfur-reducing fungus Fusarium oxysporum. We found that NADPH-glutathione reductase (GR) reduces elemental sulfur via glutathione as an intermediate. A loss-of-function mutant of the SR/GR gene generated less sulfide from elemental sulfur than the wild-type strain. Its growth was hypersensitive to elemental sulfur, and it accumulated higher levels of oxidized glutathione, indicating that the GR/glutathione system confers tolerance to cytotoxic elemental sulfur by reducing it to less harmful sulfide. The SR/GR reduced polysulfide as efficiently as elemental sulfur, which implies that soluble polysulfide shuttles reducing equivalents to exocellular insoluble elemental sulfur and generates sulfide. The ubiquitous distribution of the GR/glutathione system together with our findings that GR-deficient mutants derived from Saccharomyces cerevisiae and Aspergillus nidulans reduced less sulfur and that their growth was hypersensitive to elemental sulfur indicated a wide distribution of the system among fungi. These results indicate a novel biological function of the GR/glutathione system in elemental sulfur reduction, which is distinguishable from bacterial and archaeal mechanisms of glutathione- independent sulfur reduction.

Impact of alternative electron acceptors on selenium(IV) reduction by Anaeromyxobacter dehalogenans

The capability of Anaeromyxobacter dehalogenans to reduce Se(IV) to Se(0) as a detoxification mechanism suggests a potential role of these ecologically important microorganisms in the biogeochemical cycling of selenium and the control of selenium contamination. However, the reduction of Se(IV) by the energetically versatile A. dehalogenans could be hindered by its ability to use alternative electron acceptors, particularly Fe(III) and humic substances which are ubiquitous in the environment. Indeed, the presence of Fe(III) partially inhibited Se(IV)-reducing activity. Nonetheless, reduction of both Se(IV) and Fe(III) proceeded simultaneously, a characteristic desirable for bioremediation efforts in many environments abundant with Fe(III). The enhancement of Se(IV) reduction by anthraquinone-2,6-disulfonate, a humic substance analog, is advantageous for microbial selenium biotransformation given the broad distribution of humic substances in natural environments, which could be exploited for the design of improved control strategies for selenium pollution.

Geobacter: the microbe electric's physiology, ecology, and practical applications

Geobacter species specialize in making electrical contacts with extracellular electron acceptors and other organisms. This permits Geobacter species to fill important niches in a diversity of anaerobic environments. Geobacter species appear to be the primary agents for coupling the oxidation of organic compounds to the reduction of insoluble Fe(III) and Mn(IV) oxides in many soils and sediments, a process of global biogeochemical significance. Some Geobacter species can anaerobically oxidize aromatic hydrocarbons and play an important role in aromatic hydrocarbon removal from contaminated aquifers. The ability of Geobacter species to reductively precipitate uranium and related contaminants has led to the development of bioremediation strategies for contaminated environments. Geobacter species produce higher current densities than any other known organism in microbial fuel cells and are common colonizers of electrodes harvesting electricity from organic wastes and aquatic sediments. Direct interspecies electron exchange between Geobacter species and syntrophic partners appears to be an important process in anaerobic wastewater digesters. Functional and comparative genomic studies have begun to reveal important aspects of Geobacter physiology and regulation, but much remains unexplored. Quantifying key gene transcripts and proteins of subsurface Geobacter communities has proven to be a powerful approach to diagnose the in situ physiological status of Geobacter species during groundwater bioremediation. The growth and activity of Geobacter species in the subsurface and their biogeochemical impact under different environmental conditions can be predicted with a systems biology approach in which genome-scale metabolic models are coupled with appropriate physical/chemical models. The proficiency of Geobacter species in transferring electrons to insoluble minerals, electrodes, and possibly other microorganisms can be attributed to their unique "microbial nanowires," pili that conduct electrons along their length with metallic-like conductivity. Surprisingly, the abundant c-type cytochromes of Geobacter species do not contribute to this long-range electron transport, but cytochromes are important for making the terminal electrical connections with Fe(III) oxides and electrodes and also function as capacitors, storing charge to permit continued respiration when extracellular electron acceptors are temporarily unavailable. The high conductivity of Geobacter pili and biofilms and the ability of biofilms to function as supercapacitors are novel properties that might contribute to the field of bioelectronics. The study of Geobacter species has revealed a remarkable number of microbial physiological properties that had not previously been described in any microorganism. Further investigation of these environmentally relevant and physiologically unique organisms is warranted.

Oxidation-reduction transformations of chromium in aerobic soils and the role of electron-shuttling quinones

Oxidation of Cr(III) and reduction of Cr(VI) can occur simultaneously in aerobic soils, but the mechanisms involved are not well-understood, especially how electron shuttling by redox-active organic acids is involved. A and B soil horizons from three topohydrosequences from the Coastal Plain and Piedmont physiographic provinces of Maryland were chosen to investigate oxidation-reduction transformations of Cr under field moist conditions. Reduction of added Cr(VI) to Cr(III) was observed in all 18 samples, and 11 demonstrated enhanced reduction with added anthraquinone-2,6-disulfonate (AQDS) acting as an electron shuttle in 24 h quick tests under aerobic conditions. Oxidation of Cr(III) to Cr(VI) was observed in 12 samples, with 7 demonstrating diminished oxidation with AQDS added. Cr(VI) was undetectable after 11 d of incubation when lactic acid was added as a reductant for Cr(VI) to the Watchung soil A horizon. This reduction occurred in the presence of AQDS and a high salt background to suppress microbial growth, suggesting abiotic reduction was the dominant pathway. The results of this study demonstrate that in field-moist, aerobic soils, the electron shuttle, AQDS, enhanced Cr(VI) reduction and inhibited Cr(III) oxidation. This suggests redox-active organic C amendments and electron shuttles can be important in enhancing rates and extent of Cr(VI) reduction, while inhibiting Cr(III) oxidation in the in situ remediation of Cr(VI)-contaminated soils.

Arsenic redox changes by microbially and chemically formed semiquinone radicals and hydroquinones in a humic substance model quinone

Arsenic is a redox-active metalloid whose toxicity and mobility strongly depends on its oxidation state, with arsenite (As(III)) being more toxic and mobile than arsenate (As(V)). Humic substances (HS) are also redox-active and can potentially react with arsenic and change its redox state. In this study we show that semiquinone radicals produced during microbial or chemical reduction of a HS model quinone (AQDS, 9,10-anthraquinone-2,6-disulfonic acid) are strong oxidants. They oxidize arsenite to arsenate, thus decreasing As toxicity and mobility. This reaction depends strongly on pH with more arsenite (up to 67.3%) being oxidized at pH 11 compared to pH 7 (12.6% oxidation) and pH 3 (0.5% oxidation). In addition to As(III) oxidation by semiquinone radicals, hydroquinones that were also produced during quinone reduction reduced As(V) to As(III) at neutral and acidic pH values (less than 12%) but not at alkaline pH. In order to understand redox reactions between arsenite/arsenate and reduced/oxidized HS, we quantified the radical content in reduced quinone solutions and constructed Eh-pH diagrams that explain the observed redox reactions. The results from this study can be used to better predict the fate of arsenic in the environment and potentially explain the occurrence of oxidized As(V) in anoxic environments.

Carbon and hydrogen isotope fractionation during anaerobic toluene oxidation by Geobacter metallireducens with different Fe(III) phases as terminal electron acceptors

Microbial oxidation of BTEX compounds under iron-reducing conditions is an important attenuation process for fuel-contaminated sites. We evaluated the use of compound-specific isotope analysis for the identification and quantification of anaerobic toluene oxidation by Geobacter metallireducens. 13C and 2H enrichment of toluene was measured in laboratory batch systems and varied significantly for a solid vs a dissolved Fe(III) phase provided as terminal electron acceptor. 13C enrichment factors (epsilonC) in suspensions of a solid Fe(III) phase were between -1.0 and -1.3% per hundred, whereas epsilonC-values were significantly higher in solutions of Fe(lll) citrate (-2.9 to -3.6% per hundred. The same trend was observed for 2H fractionation. Solid phase reduction resulted in an epsilonH-value of -34.6 +/- 0.9% per hundred, compared to -98.4 +/- 3.0% per hundred for the reduction of dissolved Fe(lll). The linear correlation of delta(2)H vs. delta(13)C during toluene oxidation resulted in nearly identical slopes for both systems, confirming that the reaction mechanism, that is enzymatic methyl-group oxidation, was the same. We hypothesize that smaller 2H and 13C fractionation in suspensions is due to toluene transport limitations to cells of G. metallireducens at surfaces of solid Fe(III) phases. Enrichment factors determined in Fe(III) mineral suspensions should be more representative for anaerobic toluene degradation owing to the abundance of solid Fe(III) in soils and aquifers.

Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor

The mechanisms for Fe(III) oxide reduction in Geobacter species are of interest because Fe(III) oxides are the most abundant form of Fe(III) in many soils and sediments and Geobacter species are prevalent Fe(III)-reducing microorganisms in many of these environments. Protein abundance in G. sulfurreducens grown on poorly crystalline Fe(III) oxide or on soluble Fe(III) citrate was compared with a global accurate mass and time tag proteomic approach in order to identify proteins that might be specifically associated with Fe(III) oxide reduction. A total of 2991 proteins were detected in G. sulfurreducens grown with acetate as the electron donor and either Fe(III) oxide or soluble Fe(III) citrate as the electron acceptor, resulting in 86% recovery of the genes predicted to encode proteins. Of the total expressed proteins 76% were less abundant in Fe(III) oxide cultures than in Fe(III) citrate cultures, which is consistent with the overall slower rate of metabolism during growth with an insoluble electron acceptor. A total of 269 proteins were more abundant in Fe(III) oxide-grown cells than in cells grown on Fe(III) citrate. Most of these proteins were in the energy metabolism category: primarily electron transport proteins, including 13 c-type cytochromes and PilA, the structural protein for electrically conductive pili. Several of the cytochromes that were more abundant in Fe(III) oxide-grown cells were previously shown with genetic approaches to be essential for optimal Fe(III) oxide reduction. Other proteins that were more abundant during growth on Fe(III) oxide included transport and binding proteins, proteins involved in regulation and signal transduction, cell envelope proteins, and enzymes for amino acid and protein biosynthesis, among others. There were also a substantial number of proteins of unknown function that were more abundant during growth on Fe(III) oxide. These results indicate that electron transport to Fe(III) oxide requires additional and/or different proteins than electron transfer to soluble, chelated Fe(III) and suggest proteins whose functions should be further investigated in order to better understand the mechanisms of electron transfer to Fe(III) oxide in G. sulfurreducens.

Electrochemical characterization of Geobacter sulfurreducens cells immobilized on graphite paper electrodes

Bacteria able to transfer electrons to conductive surfaces are of interest as catalysts in microbial fuel cells, as well as in bioprocessing, bioremediation, and corrosion. New procedures for immobilization of Geobacter sulfurreducens on graphite electrodes are described that allow routine, repeatable electrochemical analysis of cell-electrode interactions. Immediately after immobilizing G. sulfurreducens on electrodes, electrical current was obtained without addition of exogenous electron shuttles or electroactive polymers. Voltammetry and impedance analysis of pectin-immobilized bacteria transferring electrons to electrode surfaces could also be performed. Cyclic voltammetry of immobilized cells revealed voltage-dependent catalytic current similar to what is commonly observed with adsorbed enzymes, with catalytic waves centered at -0.15 V (vs. SHE). Electrodes maintained at +0.25 V (vs. SHE) initially produced 0.52 A/m(2) in the presence of acetate as the electron donor. Electrical Impedance Spectroscopy of coatings was also consistent with a catalytic mechanism, controlled by charge transfer rate. When electrodes were maintained at an oxidizing potential for 24 h, electron transfer to electrodes increased to 1.75 A/m(2). These observations of electron transfer by pectin-entrapped G. sulfurreducens appear to reflect native mechanisms used for respiration. The ability of washed G. sulfurreducens cells to immediately produce electrical current was consistent with the external surface of this bacterium possessing a pathway linking oxidative metabolism to extracellular electron transfer. This electrochemical activity of pectin-immobilized bacteria illustrates a strategy for preparation of catalytic electrodes and study of Geobacter under defined conditions.

Iron and arsenic release from aquifer solids in response to biostimulation

Biostimulation has been used at various contaminated sites to promote the reductive dechlorination of trichloroethylene (TCE), but the addition of carbon and energy donor also stimulates bacteria that use Fe(III) as the terminal electron acceptor (TEA) in potential competition with dechlorination processes. Microcosm studies were conducted to determine the influence of various carbon donors on the extent of reductive dissolution of aquifer solids containing Fe(III) and arsenic. Glucose, a fermentable and respirable carbon donor, led to the production of 1500 mg Fe(II) kg(-1), or 24% of the total Fe in the aquifer sediment being reduced to Fe(II), whereas the same concentration of carbon as acetate resulted in only 300 mg Fe(II) kg(-1) being produced. The biogenic Fe(II) produced with acetate was exclusively associated with the solid phase whereas with fermentable carbon donors as whey and glucose, 22 and 54% of the Fe(II) was in solution. With fermentation, some of the metabolites appear to be electron shuttling chemicals and chelating agents that facilitate the reductive dissolution of even crystalline Fe(III) oxides. Without the presence of electron shuttling chemicals, only surficial Fe in direct contact with the bacteria was bioavailable, as illustrated when acetate was used. Regardless of carbon donor type and concentration, As concentrations in the water exceeded drinking water standards. The As dissolution appears to have been the result of the direct use of As as an electron acceptor by dissimilatory arsenic reducing bacteria. Our findings indicate that selection of the carbon and energy donor for biostimulation for remediation of chlorinated solvent impacted aquifers may greatly influence the extent of the reductive dissolution of iron minerals in direct competition with dechlorination processes. Biostimulation may also result in a significant release of As to the solution phase, contributing to further contamination of the aquifer.

Exocellular electron transfer in anaerobic microbial communities

Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

Shewanella oneidensis MR-1 uses overlapping pathways for iron reduction at a distance and by direct contact under conditions relevant for Biofilms

We developed a new method to measure iron reduction at a distance based on depositing Fe(III) (hydr)oxide within nanoporous glass beads. In this "Fe-bead" system, Shewanella oneidensis reduces at least 86.5% of the iron in the absence of direct contact. Biofilm formation accompanies Fe-bead reduction and is observable both macro- and microscopically. Fe-bead reduction is catalyzed by live cells adapted to anaerobic conditions, and maximal reduction rates require sustained protein synthesis. The amount of reactive ferric iron in the Fe-bead system is available in excess such that the rate of Fe-bead reduction is directly proportional to cell density; i.e., it is diffusion limited. Addition of either lysates prepared from anaerobic cells or exogenous electron shuttles stimulates Fe-bead reduction by S. oneidensis, but iron chelators or additional Fe(II) do not. Neither dissolved Fe(III) nor electron shuttling activity was detected in culture supernatants, implying that the mediator is retained within the biofilm matrix. Strains with mutations in omcB or mtrB show about 50% of the wild-type levels of reduction, while a cymA mutant shows less than 20% of the wild-type levels of reduction and a menF mutant shows insignificant reduction. The Fe-bead reduction defect of the menF mutant can be restored by addition of menaquinone, but menaquinone itself cannot stimulate Fe-bead reduction. Because the menF gene encodes the first committed step of menaquinone biosynthesis, no intermediates of the menaquinone biosynthetic pathway are used as diffusible mediators by this organism to promote iron reduction at a distance. CymA and menaquinone are required for both direct and indirect mineral reduction, whereas MtrB and OmcB contribute to but are not absolutely required for iron reduction at a distance.

Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities

The anaerobic oxidation of methane (AOM) is one of the major sinks for methane on earth and is known to be mediated by at least two phylogenetically different groups of anaerobic methanotrophic Archaea (ANME-I and ANME-II). We present the first comparative in vitro study of the environmental regulation and physiology of these two methane-oxidizing communities, which occur naturally enriched in the anoxic Black Sea (ANME-I) and at Hydrate Ridge (ANME-II). Both types of methanotrophic communities are associated with sulfate-reducing-bacteria (SRB) and oxidize methane anaerobically in a 1:1 ratio to sulfate reduction (SR). They responded sensitively to elevated methane partial pressures with increased substrate turnover. The ANME-II-dominated community showed significantly higher cell-specific AOM rates. Besides sulfate, no other electron acceptor was used for AOM. The processes of AOM and SR could not be uncoupled by feeding the SRB with electron donors such as acetate, formate or molecular hydrogen. AOM was completely inhibited by the addition of bromoethanesulfonate in both communities, indicating the participation of methanogenic enzymes in the process. Temperature influenced the intensity of AOM, with ANME-II being more adapted to cold temperatures than ANME-I. The variation of other environmental parameters, such as sulfate concentration, pH and salinity, did not influence the activity of both communities. In conclusion, the ecological niches of methanotrophic Archaea seem to be mainly defined by the availability of methane and sulfate, but it remains open which additional factors lead to the dominance of ANME-I or -II in the environment.

The mechanism of bacterial indigo reduction

The reduction of water-insoluble indigo by the recently isolated moderate thermophile, Clostridium isatidis, has been studied with the aim of developing a sustainable technology for industrial indigo reduction. The ability to reduce indigo was not shared with C. aurantibutyricum, C. celatum and C. papyrosolvens, but C. papyrosolvens could reduce indigo carmine (5,5'-indigosulfonic acid), a soluble indigo derivative. The supernatant from cultures of C. isatidis, but not from cultures of the other bacteria tested, decreased indigo particle size to one-tenth diameter. Addition of madder powder, anthraquinone-2,6-disulfonic acid, and humic acid all stimulated indigo reduction by C. isatidis. Redox potentials of cultures of C. isatidis were about 100 mV more negative than those of C. aurantibutyricum, C. celatum and C. papyrosolvens, and reached -600 mV versus the SCE in the presence of indigo, but potentials were not consistently affected by the addition of the quinone compounds, which probably act by modifying the surface of the bacteria or indigo particles. It is concluded that C. isatidis can reduce indigo because (1) it produces an extracellular factor that decreases indigo particle size, and (2) it generates a sufficiently reducing potential.

Ferrihydrite-dependent growth of Sulfurospirillum deleyianum through electron transfer via sulfur cycling

Observations in enrichment cultures of ferric iron-reducing bacteria indicated that ferrihydrite was reduced to ferrous iron minerals via sulfur cycling with sulfide as the reductant. Ferric iron reduction via sulfur cycling was investigated in more detail with Sulfurospirillum deleyianum, which can utilize sulfur or thiosulfate as an electron acceptor. In the presence of cysteine (0.5 or 2 mM) as the sole sulfur source, no (microbial) reduction of ferrihydrite or ferric citrate was observed, indicating that S. deleyianum is unable to use ferric iron as an immediate electron acceptor. However, with thiosulfate at a low concentration (0.05 mM), growth with ferrihydrite (6 mM) was possible and sulfur was cycled up to 60 times. Also, spatially distant ferrihydrite in agar cultures was reduced via diffusible sulfur species. Due to the low concentrations of thiosulfate, S. deleyianum produced only small amounts of sulfide. Obviously, sulfide delivered electrons to ferrihydrite with no or only little precipitation of black iron sulfides. Ferrous iron and oxidized sulfur species were produced instead, and the latter served again as the electron acceptor. These oxidized sulfur species have not yet been identified. However, sulfate and sulfite cannot be major products of ferrihydrite-dependent sulfide oxidation, since neither compound can serve as an electron acceptor for S. deleyianum. Instead, sulfur (elemental S or polysulfides) and/or thiosulfate as oxidized products could complete a sulfur cycle-mediated reduction of ferrihydrite.

Shewanella oneidensis MR-1 restores menaquinone synthesis to a menaquinone-negative mutant

The mechanisms underlying the use of insoluble electron acceptors by metal-reducing bacteria, such as Shewanella oneidensis MR-1, are currently under intensive study. Current models for shuttling electrons across the outer membrane (OM) of MR-1 include roles for OM cytochromes and the possible excretion of a redox shuttle. While MR-1 is able to release a substance that restores the ability of a menaquinone (MK)-negative mutant, CMA-1, to reduce the humic acid analog anthraquinone-2,6-disulfonate (AQDS), cross-feeding experiments conducted here showed that the substance released by MR-1 restores the growth of CMA-1 on several soluble electron acceptors. Various strains derived from MR-1 also release this substance; these include mutants lacking the OM cytochromes OmcA and OmcB and the OM protein MtrB. Even though strains lacking OmcB and MtrB cannot reduce Fe(III) or AQDS, they still release a substance that restores the ability of CMA-1 to use MK-dependent electron acceptors, including AQDS and Fe(III). Quinone analysis showed that this released substance restores MK synthesis in CMA-1. This ability to restore MK synthesis in CMA-1 explains the cross-feeding results and challenges the previous hypothesis that this substance represents a redox shuttle that facilitates metal respiration.

Dissimilatory Fe(III) and Mn(IV) reduction

Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.

Combining in situ reverse transcriptase polymerase chain reaction, optical microscopy, and X-ray photoelectron spectroscopy to investigate mineral surface-associated microbial activities

A study was undertaken to investigate expression of a gene encoding a c-type cytochrome in cells of the dissimilatory metal reducing bacterium (DMRB) Geobacter sulfurreducens during association with poorly crystalline and crystalline solid-phase Fe(III)-oxides. The gene encoding OmcC (outer membrane c-type cytochrome) was used as a target for PCR-based molecular detection and visualization of omcC gene expression by individual cells and aggregates of cells of G. sulfurreducens associated with ferrihydrite and hematite mineral particles. Expression of omcC was demonstrated in individual bacterial cells associated with these Fe-oxide surfaces by in situ RT-PCR (IS-RT PCR) and epifluorescence microscopy. Epifluorescence microscopy also permitted visualization of total DAPI-stained cells in the same field of view to assess the fraction of the cell population expressing omcC. By combining reflected differential interference contrast (DIC) microscopy and epifluorescence microscopy, it was possible to determine the spatial relationship between cells expressing omcC and the mineral surface. Introduction of the fluorescently labeled lectin concanavalin A revealed extracellular polymeric substances (EPS) extending between aggregations of bacterial cells and the mineral surface. The results indicate that EPS mediates an association between cells of G. sulfurreducens and ferrihydrite particles, but that direct cell contact with the mineral surface is not required for expression of omcC. XPS analysis revealed forms of reduced Fe associated with areas of the mineral surface where EPS-mediated bacterial associations occurred. The results demonstrate that by combining molecular biology, reflectance microscopy, and XPS, chemical transformations at a mineral surface can be related to the expression of specific genes by individual bacterial cells and cell aggregates associated with the mineral surface. The approach should be useful in establishing involvement of specific gene products in a wide variety of surface chemical processes.

The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments

Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.