Extracellular electron transfer to Fe(III) oxides by the hyperthermophilic archaeon Geoglobus ahangari via a direct contact mechanism

Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments?

Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS₂ in iron-sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS₂ in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe₃ S₄ greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.

Adaptive Synthesis of a Rough Lipopolysaccharide in Geobacter sulfurreducens for Metal Reduction and Detoxification

The ability of some metal-reducing bacteria to produce a rough (no O-antigen) lipopolysaccharide (LPS) could facilitate surface interactions with minerals and metal reduction. Consistent with this, the laboratory model metal reducer Geobacter sulfurreducens PCA produced two rough LPS isoforms (with or without a terminal methyl-quinovosamine sugar) when growing with the soluble electron acceptor fumarate but expressed only the shorter and more hydrophilic variant when reducing iron oxides. We reconstructed from genomic data conserved pathways for the synthesis of the rough LPS and generated heptosyltransferase mutants with partial (ΔrfaQ) or complete (ΔrfaC) truncations in the core oligosaccharide. The stepwise removal of the LPS core sugars reduced the hydrophilicity of the cell and increased outer membrane vesiculation. These changes in surface charge and remodeling did not substantially impact planktonic growth but disrupted the developmental stages and structure of electroactive biofilms. Furthermore, the mutants assembled conductive pili for extracellular mineralization of the toxic uranyl cation but were unable to prevent permeation and mineralization of the radionuclide in the cell envelope. Hence, not only does the rough LPS promote cell-cell and cell-mineral interactions critical to biofilm formation and metal respiration but it also functions as a permeability barrier to toxic metal cations. In doing so, the rough LPS maximizes the extracellular reduction of soluble and insoluble metals and preserves cell envelope functions critical to the environmental survival of Geobacter bacteria in metal-rich environments and their performance in bioremediation and bioenergy applications. IMPORTANCE Some metal-reducing bacteria produce an LPS without the repeating sugars (O-antigen) that decorate the surface of most Gram-negative bacteria, but the biological significance of this adaptive feature was not previously investigated. Using the model representative Geobacter sulfurreducens strain PCA and mutants carrying stepwise truncations in the LPS core sugars, we demonstrate the importance of the rough LPS in the control of cell surface chemistry during the respiration of iron minerals and the formation of electroactive biofilms. Importantly, we describe hitherto overlooked roles for the rough LPS in metal sequestration and outer membrane vesiculation that are critical for the extracellular reduction and detoxification of toxic metals and radionuclides. These results are of interest for the optimization of bioremediation schemes and electricity-harvesting platforms using these bacteria.

Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms

Electroactive microorganisms markedly affect many environments in which they establish outer-surface electrical contacts with other cells and minerals or reduce soluble extracellular redox-active molecules such as flavins and humic substances. A growing body of research emphasizes their broad phylogenetic diversity and shows that these microorganisms have key roles in multiple biogeochemical cycles, as well as the microbiome of the gut, anaerobic waste digesters and metal corrosion. Diverse bacteria and archaea have independently evolved cytochrome-based strategies for electron exchange between the outer cell surface and the cell interior, but cytochrome-free mechanisms are also prevalent. Electrically conductive protein filaments, soluble electron shuttles and non-biological conductive materials can substantially extend the electronic reach of microorganisms beyond the surface of the cell. The growing appreciation of the diversity of electroactive microorganisms and their unique electronic capabilities is leading to a broad range of applications.

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.

Microorganisms from deep-sea hydrothermal vents

With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-020-00086-4.

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.

Microbe-Mineral Interaction and Novel Proteins for Iron Oxide Mineral Reduction in the Hyperthermophilic Crenarchaeon Pyrodictium delaneyi

Understanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a membrane-bound molybdopterin respiratory complex sets iron reduction in this organism apart from previously described iron reduction processes.

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and generally relies on microbe-mineral interactions that transform various iron oxide minerals. In this study, the physiology of dissimilatory iron and nitrate reduction was examined in the hyperthermophilic crenarchaeon type strain Pyrodictium delaneyi Su06. Iron barrier experiments showed that P. delaneyi required direct contact with the Fe(III) oxide mineral ferrihydrite for reduction. The separate addition of an exogenous electron shuttle (anthraquinone-2,6-disulfonate), a metal chelator (nitrilotriacetic acid), and 75% spent cell-free supernatant did not stimulate growth with or without the barrier. Protein electrophoresis showed that the c-type cytochrome and general protein compositions of P. delaneyi changed when grown on ferrihydrite relative to nitrate. Differential proteomic analyses using tandem mass tagged protein fragments and mass spectrometry detected 660 proteins and differential production of 127 proteins. Among these, two putative membrane-bound molybdopterin-dependent oxidoreductase complexes increased in relative abundance 60- to 3,000-fold and 50- to 100-fold in cells grown on iron oxide. A putative 8-heme c-type cytochrome was 60-fold more abundant in iron-grown cells and was unique to the Pyrodictiaceae. There was also a >14,700-fold increase in a membrane transport protein in iron-grown cells. For flagellin proteins and a putative nitrate reductase, there were no changes in abundance, but a membrane nitric oxide reductase was more abundant on nitrate. These data help to elucidate the mechanisms by which hyperthermophilic crenarchaea generate energy and transfer electrons across the membrane to iron oxide minerals.

IMPORTANCE Understanding iron reduction in the hyperthermophilic crenarchaeon Pyrodictium delaneyi provides insight into the diversity of mechanisms used for this process and its potential impact in geothermal environments. The ability of P. delaneyi to reduce Fe(III) oxide minerals through direct contact potentially using a novel cytochrome respiratory complex and a membrane-bound molybdopterin respiratory complex sets iron reduction in this organism apart from previously described iron reduction processes. A model is presented where obligatory H₂ oxidation on the membrane coupled with electron transport and either Fe(III) oxide or nitrate reduction leads to the generation of a proton motive force and energy generation by oxidative phosphorylation. However, P. delaneyi cannot fix CO₂ and relies on organic compounds from its environment for biosynthesis.

Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney

To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m^-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H₂ and indirect production from yeast extract and peptone through the production of H₂ and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.

Electrochemical properties of the interaction between cytochrome c and a hematite nanowire array electrode

We investigate the interaction of horse heart cytochrome c (cyt c) with hematite nanowire array electrodes by cyclic voltammetry to study the electron transfer between redox active proteins and mineral surfaces. Using this model system, we quantify electron transfer rates between cyt c and hematite under varying electric potential and pH conditions. The results are consistent with two cyt c conformations adsorbed at the hematite surface: the native and a partially unfolded form. The partially unfolded protein maintained redox activity, but at a lower redox potential than the native protein. Adsorption of cyt c allowed direct electron transfer between cyt c and hematite, with an interfacial electron transfer rate, k°_ET, of 0.4 s^-1 for the native form and 0.55 s^-1 for the partially unfolded protein at pH 7.07. At pH 4.66, protein adsorption decreased compared to neutral pH and the fraction of partially unfolded protein increased. Additionally, the diffusion controlled electron transfer rate between hematite and the electron shuttling compound anthraquinone-2,6-disulfonate (AQDS) was determined to be k°_ET = 8.0·10^-3 cm·s^-1 at pH 7.07. Modulation of electron transfer rates as a result of conformational changes by redox active proteins has broad implications for describing chemical transformations at biological-mineral interfaces.

Understanding the Impact of Extracellular Polymeric Substances on Lead Release in Drinking Water Systems

Lead release in a lead (Pb, anode)-iron oxide (α-Fe₂O₃, cathode) galvanic system was studied under the influence of synthetic extracellular polymeric substances (sEPS). Sodium alginate, bovine serum albumin (BSA), and cytochrome c represented extracellular polysaccharides, proteins, and electrochemically active components, respectively. Microbiologically influenced corrosion was investigated using sEPS and pelleted and resuspended Pseudomonas aeruginosa cells. Relative to the anaerobic inorganic control, Pb release increased by 156, 202, and 198 μg/L when sEPS was present on the cathode side at 200 mg/L (100 mg/L alginate + 100 mg/L BSA), 400 mg/L (200 mg/L alginate + 200 mg/L BSA), and 200 mg/L with 123.84 mg/L cytochrome c, respectively, under anaerobic conditions. When the cathode was aerated, Pb release increased by 75, 260, and -71 μg/L under the aforementioned conditions, all relative to the aerated inorganic control. When sEPS was instead present on the anode side, sEPS caused localized corrosion on Pb and resulted in higher Pb release than predicted by electric current. P. aeruginosa generally enhanced corrosion; when cells were dosed in the anode side, part of the oxidized Pb was immobilized by cells or organic compounds adhered to the electrodes.

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations

Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.

Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support

While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.

EDDS enhanced Shewanella putrefaciens CN32 and α-FeOOH reductive dechlorination of carbon tetrachloride

S,S-ethylenediamine-N,N-disuccinic acid (EDDS) enhanced reductive dissolution of α-FeOOH by Shewanella putrefaciens CN32 (CN32), resulting in formation of surface-bound Fe(II) species (Fe^IIEDDS) to improve reductive dechlorination of carbon tetrachloride (CT). The pseudo-first-order rate constants for bio-reduction extents of α-FeOOH by CN32 in the presence of 1.36 mM EDDS was 0.023 ± 0.0003 d^-1 which was higher than without EDDS. The enhancement mechanism of bio-reduction was attributed to the strong complexation ability of EDDS to formed Fe^IIIEDDS, which could be better utilized by CN32. The dechlorination kinetic of CT by Fe^IIEDDS (2.016 h^-1) in the presence of 1.36 mM EDDS was 24 times faster than without EDDS. Chloroform were detected as main products for the degradation of CT. The chemical analyses and morphological observation showed that combination between EDDS and Fe²⁺ produced Fe^IIEDDS complex, which had a reductive potential of -0.375 V and significantly enhanced CT dechlorination. The results showed that EDDS played an important role in enhancing the bio-reduction of α-FeOOH to accelerate reductive dechlorination of CT.

Electron transfer process in microbial electrochemical technologies: The role of cell-surface exposed conductive proteins

Electroactive microorganisms have attracted significant interest for the development of novel biotechnological systems of low ecological footprint. These can be used for the sustainable production of energy, bioremediation of metal-contaminated environments and production of added-value products. Currently, almost 100 microorganisms from the Bacterial and Archaeal domains are considered electroactive, given their ability to efficiently interact with electrodes in microbial electrochemical technologies. Cell-surface exposed conductive proteins are key players in the electron transfer between cells and electrodes. Interestingly, it seems that among the electroactive organisms identified so far, these cell-surface proteins fall into one of four groups. In this review, the different types of cell-surface conductive proteins found in electroactive organisms will be overviewed, focusing on their structural and functional properties.

Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari

Few microorganisms have been examined for current generation under thermophilic (40-65°C) or hyperthermophilic temperatures (≥80°C) in microbial electrochemical systems. Two iron-reducing archaea from the family Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A current density (j) of 0.68±0.11A/m² was attained in F. placidus MECs at 85°C, and 0.57±0.10A/m² in G. ahangari MECs at 80°C, with an applied voltage of 0.7V. Cyclic voltammetry (CV) showed that both strains produced a sigmoidal catalytic wave, with a mid-point potential of -0.39V (vs. Ag/AgCl) for F. placidus and -0.37V for G. ahangari. The comparison of CVs using spent medium and turnover CVs, coupled with the detection of peaks at the same potentials in both turnover and non-turnover conditions, suggested that mediators were not used for electron transfer and that both archaea produced current through direct contact with the electrode. These two archaeal species, and other hyperthermophilic exoelectrogens, have the potential to broaden the applications of microbial electrochemical technologies for producing biofuels and other bioelectrochemical products under extreme environmental conditions.

The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction

Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.

Comparative metabolomic studies of Alkanivorax xenomutans showing differential power output in a three chambered microbial fuel cell

Metabolomic study of electrogenic bacteria is a necessity to understand the extent of complex organic matter degradation and to invent new co-culture techniques to achieve complete degradation. In this study, we have subjected Alkanivorax xenomutans (KCTC 23751^T; NBRC 108843^T), a bacterium capable for biodegradation of complex hydrocarbons, to oxic and anoxic conditions in a three chambered microbial fuel cell. In an attempt to understand the molecular mechanisms during the electrogenic processes of A. xenomutans, intra cellular (endo metabolome or the fingerprint) and exo metabolome (extracellular metabolome or the foot print) were analyzed under oxic and anoxic conditions, using FTIR and GC-MS. Interpretation of the data revealed higher number of metabolites in the anoxic fraction as compared to oxic fraction. In addition, expression of putative metabolites that influence electron transfer like flavins, fumarate and quinones were found to be predominant in the organisms when grown in anoxic conditions. Hence, the presence of anoxic conditions governed the electrogenic bacteria to produce enhanced power output by modulating differential metabolomic profiling, compared to the culture grown in oxic conditions.

Simultaneous Decolorization and Biohydrogen Production from Xylose by Klebsiella oxytoca GS-4-08 in the Presence of Azo Dyes with Sulfonate and Carboxyl Groups

Biohydrogen production from the pulp and paper effluent containing rich lignocellulosic material could be achieved by the fermentation process. Xylose, an important hemicellulose hydrolysis product, is used less efficiently as a substrate for biohydrogen production. Moreover, azo dyes are usually added to fabricate anticounterfeiting paper, which further increases the complexity of wastewater. This study reports that xylose could serve as the sole carbon source for a pure culture of Klebsiella oxytoca GS-4-08 to achieve simultaneous decolorization and biohydrogen production. With 2 g liter^-1 of xylose as the substrate, a maximum xylose utilization rate (UR_xyl) and a hydrogen molar yield (HMY) of 93.99% and 0.259 mol of H₂ mol of xylose^-1, respectively, were obtained. Biohydrogen kinetics and electron equivalent (e^- equiv) balance calculations indicated that methyl red (MR) penetrates and intracellularly inhibits both the pentose phosphate pathway and pyruvate fermentation pathway, while methyl orange (MO) acted independently of the glycolysis and biohydrogen pathway. The data demonstrate that biohydrogen pathways in the presence of azo dyes with sulfonate and carboxyl groups were different, but the azo dyes could be completely reduced during the biohydrogen production period in the presence of MO or MR. The feasibility of hydrogen production from industrial pulp and paper effluent by the strain if the xylose is sufficient was also proved and was not affected by toxic substances which usually exist in such wastewater, except for chlorophenol. This study offers a promising energy-recycling strategy for treating pulp and paper wastewaters, especially for those containing azo dyes.IMPORTANCE The pulp and paper industry is a major industry in many developing countries, and the global market of pulp and paper wastewater treatment is expected to increase by 60% between 2012 and 2020. Such wastewater contains large amounts of refractory contaminants, such as lignin, whose reclamation is considered economically crucial and environmentally friendly. Furthermore, azo dyes are usually added in order to fabricate anticounterfeiting paper, which further increases the complexity of the pulp and paper wastewater. This work may offer a better understanding of biohydrogen production from xylose in the presence of azo dyes and provide a promising energy-recycling method for treating pulp and paper wastewater, especially for those containing azo dyes.

The Roles of Biofilm Conductivity and Donor Substrate Kinetics in a Mixed-Culture Biofilm Anode

We experimentally assessed the kinetics and thermodynamics of electron transfer (ET) from the donor substrate (acetate) to the anode for a mixed-culture biofilm anode. We interpreted the results with a modified biofilm-conduction model consisting of three ET steps in series: (1) intracellular ET, (2) non-Ohmic extracellular ET (EET) from an outer membrane protein to an extracellular cofactor (EC), and (3) ET from the EC to the anode by Ohmic-conduction in the biofilm matrix. The steady-state current density was 0.82 ± 0.03 A/m² in a miniature microbial electrochemical cell operated at fixed anode potential of -0.15 V versus the standard hydrogen electrode. Illumina 16S-rDNA and -rRNA sequences showed that the Geobacter genus was less than 30% of the community of the biofilm anode. Biofilm conductivity was high at 2.44 ± 0.42 mS/cm, indicating that the maximum current density could be as high as 270 A/m² if only Ohmic-conduction EET was limiting. Due to the high biofilm conductivity, the maximum energy loss for Ohmic-conduction EET was negligible, 0.085 mV. The energy loss in the second ET step also was small, only 20 mV, and the potential for the EC involved in the second ET was -0.15 V, a value documenting that >99% of the EC was in the oxidized state. Monod kinetics for utilization of acetate were relatively slow, and at least 87% of the energy loss was in the intracellular step. Thus, intracellular ET was the main kinetic and thermodynamic bottleneck to ET from donor substrate to the anode for a highly conductive biofilm.

Genetic Identification of a PilT Motor in Geobacter sulfurreducens Reveals a Role for Pilus Retraction in Extracellular Electron Transfer

The metal-reducing bacterium Geobacter sulfurreducens requires the expression of conductive pili to reduce iron oxides and to wire electroactive biofilms, but the role of pilus retraction in these functions has remained elusive. Here we show that of the four PilT proteins encoded in the genome of G. sulfurreducens, PilT3 powered pilus retraction in planktonic cells of a PilT-deficient strain of P. aeruginosa and restored the dense mutant biofilms to wild-type levels. Furthermore, PilT3 and PilT4 rescued the twitching motility defect of the PilT-deficient mutant. However, PilT4 was the only paralog whose inactivation in G. sulfurreducens lead to phenotypes associated with the hyperpiliation of non-retractile mutants such as enhanced adhesion and biofilm-forming abilities. In addition, PilT4 was required to reduce iron oxides. Taken together, the results indicate that PilT4 is the motor ATPase of G. sulfurreducens pili and reveal a previously unrecognized role for pilus retraction in extracellular electron transfer, a strategy that confers on Geobacter spp. an adaptive advantage for metal reduction in the natural environment.

The complete genome sequence and emendation of the hyperthermophilic, obligate iron-reducing archaeon "Geoglobus ahangari" strain 234(T)

“Geoglobus ahangari” strain 234^T is an obligate Fe(III)-reducing member of the Archaeoglobales, within the archaeal phylum Euryarchaeota, isolated from the Guaymas Basin hydrothermal system. It grows optimally at 88 °C by coupling the reduction of Fe(III) oxides to the oxidation of a wide range of compounds, including long-chain fatty acids, and also grows autotrophically with hydrogen and Fe(III). It is the first archaeon reported to use a direct contact mechanism for Fe(III) oxide reduction, relying on a single archaellum for locomotion, numerous curled extracellular appendages for attachment, and outer-surface heme-containing proteins for electron transfer to the insoluble Fe(III) oxides. Here we describe the annotation of the genome of “G. ahangari” strain 234^T and identify components critical to its versatility in electron donor utilization and obligate Fe(III) respiratory metabolism at high temperatures. The genome comprises a single, circular chromosome of 1,770,093 base pairs containing 2034 protein-coding genes and 52 RNA genes. In addition, emended descriptions of the genus “Geoglobus” and species “G. ahangari” are described.

Mechanisms involved in Fe(III) respiration by the hyperthermophilic archaeon Ferroglobus placidus

The hyperthermophilic archaeon Ferroglobus placidus can utilize a wide variety of electron donors, including hydrocarbons and aromatic compounds, with Fe(III) serving as an electron acceptor. In Fe(III)-reducing bacteria that have been studied to date, this process is mediated by c-type cytochromes and type IV pili. However, there currently is little information available about how this process is accomplished in archaea. In silico analysis of the F. placidus genome revealed the presence of 30 genes coding for putative c-type cytochrome proteins (more than any other archaeon that has been sequenced to date), five of which contained 10 or more heme-binding motifs. When cell extracts were analyzed by SDS-PAGE followed by heme staining, multiple bands corresponding to c-type cytochromes were detected. Different protein expression patterns were observed in F. placidus cells grown on soluble and insoluble iron forms. In order to explore this result further, transcriptomic studies were performed. Eight genes corresponding to multiheme c-type cytochromes were upregulated when F. placidus was grown with insoluble Fe(III) oxide compared to soluble Fe(III) citrate as an electron acceptor. Numerous archaella (archaeal flagella) also were observed on Fe(III)-grown cells, and genes coding for two type IV pilin-like domain proteins were differentially expressed in Fe(III) oxide-grown cells. This study provides insight into the mechanisms for dissimilatory Fe(III) respiration by hyperthermophilic archaea.

The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon

Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genus Geoglobus is their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds, n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multiheme c-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds and n-alkanes, although an ability of G. acetivorans to grow on these substrates was not observed in laboratory experiments. Overall, our results suggest that Geoglobus species could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.

The characteristics and two-step reaction model of p-nitroacetophenone biodegradation mediated by Shewanella decolorationis S12 and electron shuttle in the presence/absence of goethite

The current study mainly focused on the biodegradation process of p-nitroacetophenone (NP) in the presence and absence of goethite mediated by iron-reducing microbe (Shewanella decolorationis S12) and electron shuttle. The results showed that introduction of electron shuttle could obviously lead to an accumulation of biodegradation intermediate, especially in reaction systems containing high content of electron shuttle in the absence of goethite. Goethite could enhance the degree and rate of NP biodegradation. The microbial reductively generated Fe(II) played an active role in the biodegradation process. The relationship between the concentrations of biodegradation end product and the reaction times could be fitted by a consecutive reaction model with correlation coefficients (adjusted R(2)) in the range from 0.9241 to 0.9831 during the biodegradation stage from the beginning to about 250 h of incubation. However, during the subsequent biodegradation stages, in the presence and absence of goethite, transitions from the consecutive reaction model to zero-order reaction model and from the consecutive reaction model to exponential growth reaction model were observed, respectively. The newly proposed two-step reaction model will help understand the mechanism of the biodegradation process of nitroaromatic compounds and related pollutants.