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Sample records for geobacter metallireducens gs15

  1. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15.

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    Shuang-yong Xu

    Full Text Available The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²⁺-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.

  2. Decolorization of azo dyes by Geobacter metallireducens.

    Science.gov (United States)

    Liu, Guangfei; Zhou, Jiti; Chen, Congcong; Wang, Jing; Jin, Ruofei; Lv, Hong

    2013-09-01

    Geobacter metallireducens was found to be capable of decolorizing several azo dyes with different structures to various extents. Pyruvate, ethanol, acetate, propionate, and benzoate could support 66.3 ± 2.6-93.7 ± 2.1 % decolorization of 0.1 mM acid red 27 (AR27) in 40 h. The dependence of the specific decolorization rate on AR27 concentration (25 to 800 μM) followed Michaelis-Menten kinetics (K m = 186.9 ± 1.4 μΜ, V max = 0.65 ± 0.02 μmol mg protein(-1) h(-1)). Enhanced AR27 decolorization was observed with the increase of cell concentrations ranging from 7.5 to 45 mgL(-1). AR27 decolorization by G. metallireducens was retarded by the presence of goethite, which competed electrons with AR27 and was reduced to Fe(II). The addition of low concentrations of humic acid (1-100 mgL(-1)) or 2-hydroxy-1,4-naphthoquinone (0.5-50 μM) could improve the decolorization performance of G. metallireducens. High-performance liquid chromatography analysis suggested reductive pathway to be responsible for decolorization. This was the first study on azo dye decolorization by Geobacter strain and might improve our understanding of natural attenuation and bioremediation of environments polluted by azo dyes.

  3. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

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    Feist, Adam M; Nagarajan, Harish; Rotaru, Amelia-Elena; Tremblay, Pier-Luc; Zhang, Tian; Nevin, Kelly P; Lovley, Derek R; Zengler, Karsten

    2014-04-01

    Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.

  4. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

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    Adam M Feist

    2014-04-01

    Full Text Available Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III, nitrate, and fumarate by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.

  5. Genome-scale constraint-based modeling of Geobacter metallireducens

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    Famili Iman

    2009-01-01

    Full Text Available Abstract Background Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens. Results The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens' specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome

  6. Anaerobic benzene oxidation via phenol in Geobacter metallireducens.

    Science.gov (United States)

    Zhang, Tian; Tremblay, Pier-Luc; Chaurasia, Akhilesh Kumar; Smith, Jessica A; Bain, Timothy S; Lovley, Derek R

    2013-12-01

    Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated in Geobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (Geobacter metallireducens anaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures of Geobacter sulfurreducens, a Geobacter species that cannot metabolize benzene. The phenol produced in G. metallireducens cultures was labeled with (18)O during growth in H2(18)O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in which Geobacter species are considered to play an important role in anaerobic benzene degradation.

  7. Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

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    Feist, AM; Nagarajan, H; Rotaru, AE; Tremblay, PL; Zhang, T; Nevin, KP; Lovley, DR; Zengler, K

    2014-04-24

    Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species. Author Summary The ability of microorganisms to exchange electrons directly with their environment has large implications for our knowledge of industrial and environmental processes. For decades, it has been known that microbes can use electrodes as electron acceptors in microbial fuel cell settings. Geobacter metallireducens has been one of the model organisms for characterizing microbe-electrode interactions as well as environmental processes such as bioremediation. Here, we significantly expand the knowledge of metabolism and energetics of this model organism by employing constraint-based metabolic modeling. Through this analysis, we build the metabolic pathways necessary for carbon fixation, a desirable property for industrial chemical production. We

  8. Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Liu, Fanghua

    2014-01-01

    Direct interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability of Methanosarcina barkeri, to participate in DIET was evaluated in co-culture with Geobacter...... metallireducens. Co-cultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of ethanol to methane. Co-cultures could not be initiated with a pilin-deficient G. metallireducens, suggesting that long-range electron transfer along pili was important for DIET. Amendments...... physical contact was not necessary for interspecies H2 transfer. M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. Furthermore, M. barkeri is genetically tractable, making...

  9. Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri.

    Science.gov (United States)

    Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Liu, Fanghua; Markovaite, Beatrice; Chen, Shanshan; Nevin, Kelly P; Lovley, Derek R

    2014-08-01

    Direct interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability of Methanosarcina barkeri to participate in DIET was evaluated in coculture with Geobacter metallireducens. Cocultures formed aggregates that shared electrons via DIET during the stoichiometric conversion of ethanol to methane. Cocultures could not be initiated with a pilin-deficient G. metallireducens strain, suggesting that long-range electron transfer along pili was important for DIET. Amendments of granular activated carbon permitted the pilin-deficient G. metallireducens isolates to share electrons with M. barkeri, demonstrating that this conductive material could substitute for pili in promoting DIET. When M. barkeri was grown in coculture with the H2-producing Pelobacter carbinolicus, incapable of DIET, M. barkeri utilized H2 as an electron donor but metabolized little of the acetate that P.carbinolicus produced. This suggested that H2, but not electrons derived from DIET, inhibited acetate metabolism. P. carbinolicus-M. barkeri cocultures did not aggregate, demonstrating that, unlike DIET, close physical contact was not necessary for interspecies H2 transfer. M. barkeri is the second methanogen found to accept electrons via DIET and the first methanogen known to be capable of using either H2 or electrons derived from DIET for CO2 reduction. Furthermore, M. barkeri is genetically tractable,making it a model organism for elucidating mechanisms by which methanogens make biological electrical connections with other cells.

  10. A Whole Genome Pairwise Comparative and Functional Analysis of Geobacter sulfurreducens PCA

    OpenAIRE

    2013-01-01

    Geobacter species are involved in electricity production, bioremediations, and various environmental friendly activities. Whole genome comparative analyses of Geobacter sulfurreducens PCA, Geobacter bemidjiensis Bem, Geobacter sp. FRC-32, Geobacter lovleyi SZ, Geobacter sp. M21, Geobacter metallireducens GS-15, Geobacter uraniireducens Rf4 have been made to find out similarities and dissimilarities among them. For whole genome comparison of Geobacter species, an in-house tool, Geobacter Compa...

  11. Expressing the Geobacter metallireducens PilA in Geobacter sulfurreducens Yields Pili with Exceptional Conductivity

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    Tan, Yang; Adhikari, Ramesh Y.; Malvankar, Nikhil S.; Ward, Joy E.; Woodard, Trevor L.; Nevin, Kelly P.

    2017-01-01

    ABSTRACT The electrically conductive pili (e-pili) of Geobacter sulfurreducens serve as a model for a novel strategy for long-range extracellular electron transfer. e-pili are also a new class of bioelectronic materials. However, the only other Geobacter pili previously studied, which were from G. uraniireducens, were poorly conductive. In order to obtain more information on the range of pili conductivities in Geobacter species, the pili of G. metallireducens were investigated. Heterologously expressing the PilA gene of G. metallireducens in G. sulfurreducens yielded a G. sulfurreducens strain, designated strain MP, that produced abundant pili. Strain MP exhibited phenotypes consistent with the presence of e-pili, such as high rates of Fe(III) oxide reduction and high current densities on graphite anodes. Individual pili prepared at physiologically relevant pH 7 had conductivities of 277 ± 18.9 S/cm (mean ± standard deviation), which is 5,000-fold higher than the conductivity of G. sulfurreducens pili at pH 7 and nearly 1 million-fold higher than the conductivity of G. uraniireducens pili at the same pH. A potential explanation for the higher conductivity of the G. metallireducens pili is their greater density of aromatic amino acids, which are known to be important components in electron transport along the length of the pilus. The G. metallireducens pili represent the most highly conductive pili found to date and suggest strategies for designing synthetic pili with even higher conductivities. PMID:28096491

  12. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

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    Aklujkar Muktak

    2009-05-01

    Full Text Available Abstract Background The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.

  13. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

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    Aklujkar, Muktak; Krushkal, Julia; DiBartolo, Genevieve; Lapidus, Alla; Land, Miriam L.; Lovley, Derek R.

    2008-12-01

    Background: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion: The genomic evidence suggests that metabolism, physiology and regulation of gene expression in G. metallireducens may be dramatically different from other Geobacteraceae.

  14. Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling

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    Tang, Yinjie J.; Chakraborty, Romy; Martin, Hector Garcia; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

    2007-08-13

    We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The model indicated that over 90 percent of the acetate wascompletely oxidized to CO2 via a complete tricarboxylic acid (TCA) cyclewhile reducing iron. Pyruvate carboxylase and phosphoenolpyruvatecarboxykinase were present under these conditions, but enzymes in theglyoxylate shunt and malic enzyme were absent. Gluconeogenesis and thepentose phosphate pathway were mainly employed for biosynthesis andaccounted for less than 3 percent of total carbon consumption. The modelalso indicated surprisingly high reversibility in the reaction betweenoxoglutarate and succinate. This step operates close to the thermodynamicequilibrium possibly because succinate is synthesized via a transferasereaction, and its product, acetyl-CoA, inhibits the conversion ofoxoglutarate to succinate. These findings enable a better understandingof the relationship between genome annotation and extant metabolicpathways in G. metallireducens.

  15. The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Aklujkar, Muktak [University of Massachusetts, Amherst; Krushkal, Julia [University of Texas, Austin; DiBartolo, Genevieve [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lovley, Derek [University of Massachusetts, Amherst

    2009-01-01

    Background. The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. Results. The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until recently in its evolutionary history. Vestiges of the molybdate (ModE) regulon of G. sulfurreducens can be detected in G. metallireducens, which has lost the global regulatory protein ModE but retained some putative ModE-binding sites and multiplied certain genes of molybdenum cofactor biosynthesis. Several enzymes of amino acid metabolism are of different origin in the two species, but significant patterns of gene organization are conserved. Whereas most Geobacteraceae are predicted to obtain biosynthetic reducing equivalents from electron transfer pathways via a ferredoxin oxidoreductase, G. metallireducens can derive them from the oxidative pentose phosphate pathway. In addition to the evidence of greater metabolic versatility, the G. metallireducens genome is also remarkable for the abundance of multicopy nucleotide sequences found in intergenic regions and even within genes. Conclusion. The genomic evidence suggests that metabolism, physiology Background. The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and

  16. Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Liu, Fanghua;

    2014-01-01

    Direct interspecies electron transfer (DIET) is potentially an effective form of syntrophy in methanogenic communities, but little is known about the diversity of methanogens capable of DIET. The ability of Methanosarcina barkeri, to participate in DIET was evaluated in co-culture with Geobacter...

  17. Outer cell surface components essential for Fe(III) oxide reduction by Geobacter metallireducens.

    Science.gov (United States)

    Smith, Jessica A; Lovley, Derek R; Tremblay, Pier-Luc

    2013-02-01

    Geobacter species are important Fe(III) reducers in a diversity of soils and sediments. Mechanisms for Fe(III) oxide reduction have been studied in detail in Geobacter sulfurreducens, but a number of the most thoroughly studied outer surface components of G. sulfurreducens, particularly c-type cytochromes, are not well conserved among Geobacter species. In order to identify cellular components potentially important for Fe(III) oxide reduction in Geobacter metallireducens, gene transcript abundance was compared in cells grown on Fe(III) oxide or soluble Fe(III) citrate with whole-genome microarrays. Outer-surface cytochromes were also identified. Deletion of genes for c-type cytochromes that had higher transcript abundance during growth on Fe(III) oxides and/or were detected in the outer-surface protein fraction identified six c-type cytochrome genes, that when deleted removed the capacity for Fe(III) oxide reduction. Several of the c-type cytochromes which were essential for Fe(III) oxide reduction in G. metallireducens have homologs in G. sulfurreducens that are not important for Fe(III) oxide reduction. Other genes essential for Fe(III) oxide reduction included a gene predicted to encode an NHL (Ncl-1-HT2A-Lin-41) repeat-containing protein and a gene potentially involved in pili glycosylation. Genes associated with flagellum-based motility, chemotaxis, and pili had higher transcript abundance during growth on Fe(III) oxide, consistent with the previously proposed importance of these components in Fe(III) oxide reduction. These results demonstrate that there are similarities in extracellular electron transfer between G. metallireducens and G. sulfurreducens but the outer-surface c-type cytochromes involved in Fe(III) oxide reduction are different.

  18. Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens

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    Tian eZhang

    2014-05-01

    Full Text Available Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter metallireducens can anaerobically oxidize benzene to carbon dioxide with Fe(III as the sole electron acceptor and that phenol is an intermediate in benzene oxidation. In an attempt to identify enzymes that might be involved in the conversion of benzene to phenol, whole-genome gene transcript abundance was compared in cells metabolizing benzene and cells metabolizing phenol. Eleven genes had significantly higher transcript abundance in benzene-metabolizing cells. Five of these genes had annotations suggesting that they did not encode proteins that could be involved in benzene metabolism and were not further studied. Strains were constructed in which one of the remaining six genes was deleted. The strain in which the monocistronic gene Gmet 0232 was deleted metabolized phenol, but not benzene. Transcript abundance of the adjacent monocistronic gene, Gmet 0231, predicted to encode a zinc-containing oxidoreductase, was elevated in cells metabolizing benzene, although not at a statistically significant level. However, deleting Gmet 0231 also yielded a strain that could metabolize phenol, but not benzene. Although homologs of Gmet 0231 and Gmet 0232 are found in microorganisms not known to anaerobically metabolize benzene, the adjacent localization of these genes is unique to G. metallireducens. The discovery of genes that are specifically required for the metabolism of benzene, but not phenol in G. metallireducens is an important step in potentially identifying the mechanisms for anaerobic benzene activation.

  19. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

    Science.gov (United States)

    Lovley, D.R.; Giovannoni, S.J.; White, D.C.; Champine, J.E.; Phillips, E.J.P.; Gorby, Y.A.; Goodwin, S.

    1993-01-01

    The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn(IV), U(VI), and nitrate. In whole cell suspensions, the c-type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans. The name Geobacter metallireducens is proposed.

  20. Structural characterization of a β-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity.

    Science.gov (United States)

    Zhang, Yanfeng; Zheng, Yi; Qin, Ling; Wang, Shihua; Buchko, Garry W; Garavito, R Michael

    2014-09-01

    Beta-hydroxyacid dehydrogenase (β-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD(+)- or NADP(+)-dependent oxidation of various β-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple β-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential β-HAD genes. The protein sequences of one pair of these genes, Gs-βHAD (Q74DE4) and Gm-βHAD (Q39R98), have 65% sequence identity and 77% sequence similarity with each other. Both proteins are observed to reduce succinic semialdehyde, a 4-carbon substrate instead of the typical β-HAD 3-carbon substrate, to γ-hydroxybutyric acid. To further explore the structural and functional characteristics of these two β-HADs with a less frequently observed substrate specificity, crystal structures for Gs-βHAD and Gm-βHAD in complex with NADP(+) were determined to a resolution of 1.89 Å and 2.07 Å, respectively. The structures of both proteins are similar, composed of 14 α-helices and nine β-strands organized into two domains. Domain 1 (1-165) adopts a typical Rossmann fold composed of two α/β units: a six-strand parallel β-sheet surrounded by six α-helices (α1-α6) followed by a mixed three-strand β-sheet surrounded by two α-helices (α7 and α8). Domain 2 (166-287) is composed of a bundle of seven α-helices (α9-α14). Four functional regions conserved in all β-HADs are spatially located near each other, with a buried molecule of NADP(+), at the interdomain cleft. Comparison of these Geobacter structures to a closely related β-HAD from Arabidopsis thaliana in the apo-NADP(+) and apo-substrate bound state suggests that NADP(+) binding effects a rigid body rotation between Domains 1 and 2. Bound

  1. Structural characterization of a β-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanfeng; Zheng, Yi; Qin, Ling; Wang, Shihua; Buchko, Garry W.; Garavito, Michael R.

    2014-07-30

    Beta-hydroxyacid dehydrogenase (β-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD+- or NADP+-dependent oxidation of various β-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple β-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential β-HAD genes. The protein sequences of one pair of these genes, Gs-βHAD (Q74DE4) and Gm-βHAD (Q39R98), have 65% sequence identity and 77% sequence similarity with each other. Both proteins reduce succinic semialdehyde, a metabolite of the GABA shunt. To further explore the structural and functional characteristics of these two β-HADs with a potentially unique substrate specificity, crystal structures for Gs-βHAD and Gm-βHAD in complex with NADP+ were determined to a resolution of 1.89 Å and 2.07 Å, respectively. The structure of both proteins are similar, composed of 14 α-helices and nine β-strands organized into two domains. Domain One (1-165) adopts a typical Rossmann fold composed of two α/β units: a six-strand parallel β-sheet surrounded by six α-helices (α1 – α6) followed by a mixed three-strand β-sheet surrounded by two α-helices (α7 and α8). Domain Two (166-287) is composed of a bundle of seven α-helices (α9 – α14). Four functional regions conserved in all β-HADs are spatially located near each other at the interdomain cleft in both Gs-βHAD and Gm-βHAD with a buried molecule of NADP+. The structural features of Gs-βHAD and Gm-βHAD are described in relation to the four conserved consensus sequences characteristic of β-HADs and the potential biochemical importance of these enzymes as an alternative pathway for the degradation of succinic semialdehyde.

  2. Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

    OpenAIRE

    Joyner, Dominique

    2010-01-01

    The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organis...

  3. Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

    Directory of Open Access Journals (Sweden)

    Zhou Jizhong

    2007-06-01

    Full Text Available Abstract Background Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known. Results The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold

  4. Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part II. Mimicking environmental conditions during cultivation in retentostats.

    Science.gov (United States)

    Marozava, Sviatlana; Röling, Wilfred F M; Seifert, Jana; Küffner, Robert; von Bergen, Martin; Meckenstock, Rainer U

    2014-06-01

    The strict anaerobe Geobacter metallireducens was cultivated in retentostats under acetate and acetate plus benzoate limitation in the presence of Fe(III) citrate in order to investigate its physiology under close to natural conditions. Growth rates below 0.003h(-1) were achieved in the course of cultivation. A nano-liquid chromatography-tandem mass spectrometry-based proteomic approach (nano-LC-MS/MS) with subsequent label-free quantification was performed on proteins extracted from cells sampled at different time points during retentostat cultivation. Proteins detected at low (0.002h(-1)) and high (0.06h(-1)) growth rates were compared between corresponding growth conditions (acetate or acetate plus benzoate). Carbon limitation significantly increased the abundances of several catabolic proteins involved in the degradation of substrates not present in the medium (ethanol, butyrate, fatty acids, and aromatic compounds). Growth rate-specific physiology was reflected in the changed abundances of energy-, chemotaxis-, oxidative stress-, and transport-related proteins. Mimicking natural conditions by extremely slow bacterial growth allowed to show how G. metallireducens optimized its physiology in order to survive in its natural habitats, since it was prepared to consume several carbon sources simultaneously and to withstand various environmental stresses.

  5. Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part I. Batch cultivation with excess of carbon sources.

    Science.gov (United States)

    Marozava, Sviatlana; Röling, Wilfred F M; Seifert, Jana; Küffner, Robert; von Bergen, Martin; Meckenstock, Rainer U

    2014-06-01

    For microorganisms that play an important role in bioremediation, the adaptation to swift changes in the availability of various substrates is a key for survival. The iron-reducing bacterium Geobacter metallireducens was hypothesized to repress utilization of less preferred substrates in the presence of high concentrations of easily degradable compounds. In our experiments, acetate and ethanol were preferred over benzoate, but benzoate was co-consumed with toluene and butyrate. To reveal overall physiological changes caused by different single substrates and a mixture of acetate plus benzoate, a nano-liquid chromatography-tandem mass spectrometry-based proteomic approach (nano-LC-MS/MS) was performed using label-free quantification. Significant differential expression during growth on different substrates was observed for 155 out of 1477 proteins. The benzoyl-CoA pathway was found to be subjected to incomplete repression during exponential growth on acetate in the presence of benzoate and on butyrate as a single substrate. Peripheral pathways of toluene, ethanol, and butyrate degradation were highly expressed only during growth on the corresponding substrates. However, low expression of these pathways was detected in all other tested conditions. Therefore, G. metallireducens seems to lack strong carbon catabolite repression under high substrate concentrations, which might be advantageous for survival in habitats rich in fatty acids and aromatic hydrocarbons.

  6. Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens

    DEFF Research Database (Denmark)

    Zhang, Tian; Tremblay, Pier-Luc; Chaurasia, Akhilesh Kumar;

    2014-01-01

    Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter...

  7. Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

    Energy Technology Data Exchange (ETDEWEB)

    Joyner, Dominique; Fortney, Julian; Chakraborty, Romy; Hazen, Terry

    2010-05-17

    The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not

  8. Genetic evidence that the degradation of para-cresol by Geobacter metallireducens is catalyzed by the periplasmic para-cresol methylhydroxylase.

    Science.gov (United States)

    Chaurasia, Akhilesh Kumar; Tremblay, Pier-Luc; Holmes, Dawn E; Zhang, Tian

    2015-10-01

    Two pathways for para-cresol (p-cresol) degradation by anaerobic bacteria have been elucidated; one involves fumarate addition at the methyl group of p-cresol by a hydroxylbenzylsuccinate synthase protein while the other utilizes a methylhydroxylase protein (PCMH) to catalyze hydroxylation of the methyl group of p-cresol. In Geobacter metallireducens, in vitro enzymatic assays showed that p-cresol is degraded via the methylhydroxylation pathway. However, prior to this study these results had not been confirmed by genetic analyses. In this work, the gene coding for benzylsuccinate-CoA dehydrogenase (bbsG), an enzyme required for toluene degradation by G. metallireducens that is homologous to the p-hydroxybenzylsuccinyl-CoA dehydrogenase involved in p-cresol degradation by Desulfobacula toluolica Tol2 via fumarate addition, and the gene encoding the alpha prime subunit of PCMH (pcmI), were deleted to investigate the possibility of co-existing p-cresol degradation pathways in G. metallireducens. The absence of a functional PcmI protein completely inhibited p-cresol degradation, while deletion of the bbsG gene had little impact. These results further support the observation that G. metallireducens utilizes a PCMH-initiated pathway for p-cresol degradation.

  9. Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.

    Science.gov (United States)

    Fang, Yilin; Wilkins, Michael J; Yabusaki, Steven B; Lipton, Mary S; Long, Philip E

    2012-12-01

    Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens-specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

  10. Geobacter

    DEFF Research Database (Denmark)

    Lovley, Derek R; Ueki, Toshiyuki; Zhang, Tian

    2011-01-01

    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...... 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...

  11. Three paths to reduce ferric oxides taken by Geobacter metallireducens%Geobacter metallireducens异化还原铁氧化物三种方式

    Institute of Scientific and Technical Information of China (English)

    冯雅丽; 周良; 祝学远; 连静; 李少华

    2006-01-01

    异化金属还原菌通过络和剂、电子传递中间体、直接接触三种方式异化还原金属氧化矿.以Geobacter metallireducens还原铁氧化物为实验体系,利用微生物燃料电池考察了以上三种方式对异化还原铁氧化物的影响.结果表明,微生物异化还原铁氧化矿时,NTA,AQDS在初始阶段显著加速铁氧化物的还原,但也加速磁铁矿的生成,阻碍反应继续进行;直接接触方式起着重要作用,吸附形成的生物膜是一个关键因素,其形成是一个相对较长的过程.生物膜的形成阻碍电子传递中间体发挥作用.

  12. Glutaryl-coenzyme A dehydrogenase from Geobacter metallireducens - interaction with electron transferring flavoprotein and kinetic basis of unidirectional catalysis.

    Science.gov (United States)

    Estelmann, Sebastian; Boll, Matthias

    2014-11-01

    Glutaryl-CoA dehydrogenases (GDHs) are FAD containing acyl-CoA dehydrogenases that usually catalyze the dehydrogenation and decarboxylation of glutaryl-CoA to crotonyl-CoA with an electron transferring flavoprotein (ETF) acting as natural electron acceptor. In anaerobic bacteria, GDHs play an important role in the benzoyl-CoA degradation pathway of monocyclic aromatic compounds. In the present study, we identified, purified and characterized the benzoate-induced BamOP as the electron accepting ETF of GDH (BamM) from the Fe(III)-respiring Geobacter metallireducens. The BamOP heterodimer contained FAD and AMP as cofactors. In the absence of an artificial electron acceptor, at pH values above 8, the BamMOP-components catalyzed the expected glutaryl-CoA oxidation to crotonyl-CoA and CO2 ; however, at pH values below 7, the redox-neutral glutaryl-CoA conversion to butyryl-CoA and CO2 became the dominant reaction. This previously unknown, strictly ETF-dependent coupled glutaryl-CoA oxidation/crotonyl-CoA reduction activity was facilitated by an unexpected two-electron transfer between FAD(BamM) and FAD(BamOP) , as well as by the similar redox potentials of the two FAD cofactors in the substrate-bound state. The strict order of electron/proton transfer and C-C-cleavage events including transient charge-transfer complexes did not allow an energetic coupling of electron transfer and decarboxylation. This explains why it was difficult to release the glutaconyl-CoA intermediate from reduced GDH. Moreover, it provides a kinetic rational for the apparent inability of BamM to catalyze the reverse reductive crotonyl-CoA carboxylation, even under thermodynamically favourable conditions. For this reason reductive crotonyl-CoA carboxylation, a key reaction in C2-assimilation via the ethylmalonyl-CoA pathway, is accomplished by a different crotonyl-CoA carboxylase/reductase via a covalent NADPH/ene-adduct.

  13. Arsenic dissolution from Japanese paddy soil by a dissimilatory arsenate-reducing bacterium Geobacter sp. OR-1.

    Science.gov (United States)

    Ohtsuka, Toshihiko; Yamaguchi, Noriko; Makino, Tomoyuki; Sakurai, Kazuhiro; Kimura, Kenta; Kudo, Keitaro; Homma, Eri; Dong, Dian Tao; Amachi, Seigo

    2013-06-18

    Dissimilatory As(V) (arsenate)-reducing bacteria may play an important role in arsenic release from anoxic sediments in the form of As(III) (arsenite). Although respiratory arsenate reductase genes (arrA) closely related to Geobacter species have been frequently detected in arsenic-rich sediments, it is still unclear whether they directly participate in arsenic release, mainly due to lack of pure cultures capable of arsenate reduction. In this study, we isolated a novel dissimilatory arsenate-reducing bacterium, strain OR-1, from Japanese paddy soil, and found that it was phylogenetically closely related to Geobacter pelophilus. OR-1 also utilized soluble Fe(III), ferrihydrite, nitrate, and fumarate as electron acceptors. OR-1 catalyzed dissolution of arsenic from arsenate-adsorbed ferrihydrite, while Geobacter metallireducens GS-15 did not. Furthermore, inoculation of washed cells of OR-1 into sterilized paddy soil successfully restored arsenic release. Arsenic K-edge X-ray absorption near-edge structure analysis revealed that strain OR-1 reduced arsenate directly on the soil solid phase. Analysis of putative ArrA sequences from paddy soils suggested that Geobacter-related bacteria, including those closely related to OR-1, play an important role in arsenic release from paddy soils. Our results provide direct evidence for arsenic dissolution by Geobacter species and support the hypothesis that Geobacter species play a significant role in reduction and mobilization of arsenic in flooded soils and anoxic sediments.

  14. Anaerobic benzene oxidation by Geobacter species.

    Science.gov (United States)

    Zhang, Tian; Bain, Timothy S; Nevin, Kelly P; Barlett, Melissa A; Lovley, Derek R

    2012-12-01

    The abundance of Geobacter species in contaminated aquifers in which benzene is anaerobically degraded has led to the suggestion that some Geobacter species might be capable of anaerobic benzene degradation, but this has never been documented. A strain of Geobacter, designated strain Ben, was isolated from sediments from the Fe(III)-reducing zone of a petroleum-contaminated aquifer in which there was significant capacity for anaerobic benzene oxidation. Strain Ben grew in a medium with benzene as the sole electron donor and Fe(III) oxide as the sole electron acceptor. Furthermore, additional evaluation of Geobacter metallireducens demonstrated that it could also grow in benzene-Fe(III) medium. In both strain Ben and G. metallireducens the stoichiometry of benzene metabolism and Fe(III) reduction was consistent with the oxidation of benzene to carbon dioxide with Fe(III) serving as the sole electron acceptor. With benzene as the electron donor, and Fe(III) oxide (strain Ben) or Fe(III) citrate (G. metallireducens) as the electron acceptor, the cell yields of strain Ben and G. metallireducens were 3.2 × 10(9) and 8.4 × 10(9) cells/mmol of Fe(III) reduced, respectively. Strain Ben also oxidized benzene with anthraquinone-2,6-disulfonate (AQDS) as the sole electron acceptor with cell yields of 5.9 × 10(9) cells/mmol of AQDS reduced. Strain Ben serves as model organism for the study of anaerobic benzene metabolism in petroleum-contaminated aquifers, and G. metallireducens is the first anaerobic benzene-degrading organism that can be genetically manipulated.

  15. 徕卡GS15-GPS RTK测量的应用研究%Study on the Application of RTK Surveying by Laika GS15 - GPS

    Institute of Scientific and Technical Information of China (English)

    贾涛

    2012-01-01

    文章通过实测控制网及工程放样,在静态观测数据的基准下,以某校园GPS控制网为例,利用徕卡GS15 - GPS接收机进行RTK模式测量控制点坐标,与静态观测数据进行对比分析;同时利用CORS的单基准站模式,测量控制点的坐标,与静态观测数据进行对比分析;通过一系列的实践和对比分析,不仅正确掌握了徕卡GS15 - GPS接收机的操作及应用,而且证明了其精度完全可以满足各项工程的要求.

  16. Influence of Anode Potentials on Current Generation and Extracellular Electron Transfer Paths of Geobacter Species

    Directory of Open Access Journals (Sweden)

    Souichiro Kato

    2017-01-01

    Full Text Available Geobacter species are capable of utilizing solid-state compounds, including anodic electrodes, as electron acceptors of respiration via extracellular electron transfer (EET and have attracted considerable attention for their crucial role as biocatalysts of bioelectrochemical systems (BES’s. Recent studies disclosed that anode potentials affect power output and anodic microbial communities, including selection of dominant Geobacter species, in various BES’s. However, the details in current-generating properties and responses to anode potentials have been investigated only for a model species, namely Geobacter sulfurreducens. In this study, the effects of anode potentials on the current generation and the EET paths were investigated by cultivating six Geobacter species with different anode potentials, followed by electrochemical analyses. The electrochemical cultivation demonstrated that the G. metallireducens clade species (G. sulfurreducens and G. metallireducens constantly generate high current densities at a wide range of anode potentials (≥−0.3 or −0.2 V vs. Ag/AgCl, while the subsurface clades species (G. daltonii, G. bemidjensis, G. chapellei, and G. pelophilus generate a relatively large current only at limited potential regions (−0.1 to −0.3 V vs. Ag/AgCl. The linear sweep voltammetry analyses indicated that the G. metallireducens clade species utilize only one EET path irrespective of the anode potentials, while the subsurface clades species utilize multiple EET paths, which can be optimized depending on the anode potentials. These results clearly demonstrate that the response features to anode potentials are divergent among species (or clades of Geobacter.

  17. Anaerobic oxidation of toluene, phenol, and p-cresol by the dissimilatory iron-reducing organism, GS-15

    Science.gov (United States)

    Lovley, D.R.; Lonergan, D.J.

    1990-01-01

    The dissimilatory Fe(III) reducer, GS-15, is the first microorganism known to couple the oxidation of aromatic compounds to the reduction of Fe(III) and the first example of a pure culture of any kind known to anaerobically oxidize an aromatic hydrocarbon, toluene. In this study, the metabolism of toluene, phenol, and p-cresol by GS-15 was investigated in more detail. GS-15 grew in an anaerobic medium with toluene as the sole electron donor and Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. [ring-14C]toluene was oxidized to 14CO2, and the stoichiometry of 14CO2 production and Fe(III) reduction indicated that GS-15 completely oxidized toluene to carbon dioxide with Fe(III) as the electron acceptor. Magnetite was the primary iron end product during toluene oxidation. Phenol and p-cresol were also completely oxidized to carbon dioxide with Fe(III) as the sole electron acceptor, and GS-15 could obtain energy to support growth by oxidizing either of these compounds as the sole electron donor. p-Hydroxybenzoate was a transitory extracellular intermediate of phenol and p-cresol metabolism but not of toluene metabolism. GS-15 oxidized potential aromatic intermediates in the oxidation of toluene (benzylalcohol and benzaldehyde) and p-cresol (p-hydroxybenzylalcohol and p-hydroxybenzaldehyde). The metabolism described here provides a model for how aromatic hydrocarbons and phenols may be oxidized with the reduction of Fe(III) in contaminated aquifers and petroleum-containing sediments.

  18. Hydrogen production by geobacter species and a mixed consortium in a microbial electrolysis cell.

    Science.gov (United States)

    Call, Douglas F; Wagner, Rachel C; Logan, Bruce E

    2009-12-01

    A hydrogen utilizing exoelectrogenic bacterium (Geobacter sulfurreducens) was compared to both a nonhydrogen oxidizer (Geobacter metallireducens) and a mixed consortium in order to compare the hydrogen production rates and hydrogen recoveries of pure and mixed cultures in microbial electrolysis cells (MECs). At an applied voltage of 0.7 V, both G. sulfurreducens and the mixed culture generated similar current densities (ca. 160 A/m3), resulting in hydrogen production rates of ca. 1.9 m(3) H2/m3/day, whereas G. metallireducens exhibited lower current densities and production rates of 110 +/- 7 A/m3 and 1.3 +/- 0.1 m3 H2/m3/day, respectively. Before methane was detected in the mixed-culture MEC, the mixed consortium achieved the highest overall energy recovery (relative to both electricity and substrate energy inputs) of 82% +/- 8% compared to G. sulfurreducens (77% +/- 2%) and G. metallireducens (78% +/- 5%), due to the higher coulombic efficiency of the mixed consortium. At an applied voltage of 0.4 V, methane production increased in the mixed-culture MEC and, as a result, the hydrogen recovery decreased and the overall energy recovery dropped to 38% +/- 16% compared to 80% +/- 5% for G. sulfurreducens and 76% +/- 0% for G. metallireducens. Internal hydrogen recycling was confirmed since the mixed culture generated a stable current density of 31 +/- 0 A/m3 when fed hydrogen gas, whereas G. sulfurreducens exhibited a steady decrease in current production. Community analysis suggested that G. sulfurreducens was predominant in the mixed-culture MEC (72% of clones) despite its relative absence in the mixed-culture inoculum obtained from a microbial fuel cell reactor (2% of clones). These results demonstrate that Geobacter species are capable of obtaining similar hydrogen production rates and energy recoveries as mixed cultures in an MEC and that high coulombic efficiencies in mixed culture MECs can be attributed in part to the recycling of hydrogen into current.

  19. Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function

    Directory of Open Access Journals (Sweden)

    Antommattei Frances M

    2008-10-01

    Full Text Available Abstract Background Geobacter species are δ-Proteobacteria and are often the predominant species in a variety of sedimentary environments where Fe(III reduction is important. Their ability to remediate contaminated environments and produce electricity makes them attractive for further study. Cell motility, biofilm formation, and type IV pili all appear important for the growth of Geobacter in changing environments and for electricity production. Recent studies in other bacteria have demonstrated that signaling pathways homologous to the paradigm established for Escherichia coli chemotaxis can regulate type IV pili-dependent motility, the synthesis of flagella and type IV pili, the production of extracellular matrix material, and biofilm formation. The classification of these pathways by comparative genomics improves the ability to understand how Geobacter thrives in natural environments and better their use in microbial fuel cells. Results The genomes of G. sulfurreducens, G. metallireducens, and G. uraniireducens contain multiple (~70 homologs of chemotaxis genes arranged in several major clusters (six, seven, and seven, respectively. Unlike the single gene cluster of E. coli, the Geobacter clusters are not all located near the flagellar genes. The probable functions of some Geobacter clusters are assignable by homology to known pathways; others appear to be unique to the Geobacter sp. and contain genes of unknown function. We identified large numbers of methyl-accepting chemotaxis protein (MCP homologs that have diverse sensing domain architectures and generate a potential for sensing a great variety of environmental signals. We discuss mechanisms for class-specific segregation of the MCPs in the cell membrane, which serve to maintain pathway specificity and diminish crosstalk. Finally, the regulation of gene expression in Geobacter differs from E. coli. The sequences of predicted promoter elements suggest that the alternative sigma factors

  20. RDX Transformation In Biotic and Abiotic Systems Under Poised Redox Potentials

    Science.gov (United States)

    2011-03-30

    continued 5 Mixed Culture:  Pseudomonas aeruginosa – nitrate reducer  Geobacter metallireducens GS-15 – iron reducer  Desulfovibrio desulfuricans...100 mV Geobacter sp. R e d o x P o t e n t i a l ( m V ) Aerobic (600 to 400 mV) Fermentative (< -200 mV) Anaerobic (400 to -250 mV

  1. Geobacter sp. SD-1 with enhanced electrochemical activity in high-salt concentration solutions.

    Science.gov (United States)

    Sun, Dan; Call, Douglas; Wang, Aijie; Cheng, Shaoan; Logan, Bruce E

    2014-12-01

    An isolate, designated strain SD-1, was obtained from a biofilm dominated by Geobacter sulfurreducens in a microbial fuel cell. The electrochemical activity of strain SD-1 was compared with type strains, G. sulfurreducens PCA and Geobacter metallireducens GS-15, and a mixed culture in microbial electrolysis cells. SD-1 produced a maximum current density of 290 ± 29 A m−3 in a high-concentration phosphate buffer solution (PBS-H, 200 mM). This current density was significantly higher than that produced by the mixed culture (189 ± 44 A m−3) or the type strains (Geobacter strains and mixed cultures in terms of its salt tolerance.

  2. Isolation of Geobacter species from diverse sedimentary environments

    Science.gov (United States)

    Coaxes, J.D.; Phillips, E.J.P.; Lonergan, D.J.; Jenter, H.; Lovley, D.R.

    1996-01-01

    In an attempt to better understand the microorganisms responsible for Fe(III) reduction in sedimentary environments, Fe(III)-reducing microorganisms were enriched for and isolated from freshwater aquatic sediments, a pristine deep aquifer, and a petroleum-contaminated shallow aquifer. Enrichments were initiated with acetate or toluene as the electron donor and Fe(III) as the electron acceptor. Isolations were made with acetate or benzoate. Five new strains which could obtain energy for growth by dissimilatory Fe(III) reduction were isolated. All five isolates are gram- negative strict anaerobes which grow with acetate as the electron donor and Fe(III) as the electron acceptor. Analysis of the 16S rRNA sequence of the isolated organisms demonstrated that they all belonged to the genus Geobacter in the delta subdivision of the Proteobacteria. Unlike the type strain, Geobacter metallireducens, three of the five isolates could use H2 as an electron donor fur Fe(III) reduction. The deep subsurface isolate is the first Fe(III) reducer shown to completely oxidize lactate to carbon dioxide, while one of the freshwater sediment isolates is only the second Fe(III) reducer known that can oxidize toluene. The isolation of these organisms demonstrates that Geobacter species are widely distributed in a diversity of sedimentary environments in which Fe(III) reduction is an important process.

  3. N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species

    Science.gov (United States)

    Bazylinski, D.A.; Dean, A.J.; Schuler, D.; Phillips, E.J.P.; Lovley, D.R.

    2000-01-01

    Cells of Geobacter metallireducens, Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2-dependent growth, the first anaerobically with Fe(lll) as the electron acceptor, and the latter three species micro-aerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5 ?? 5.9nmol C2H4 produced min-1 mg-1 cell protein) while growing with Fe(lll) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.

  4. Link Between Capacity for Current Production and Syntrophic Growth in Geobacter species

    Directory of Open Access Journals (Sweden)

    Amelia-Elena eRotaru

    2015-07-01

    Full Text Available Electrodes are unnatural electron acceptors, and it is yet unknown how some Geobacter species evolved to use electrodes as terminal electron acceptors. Analysis of different Geobacter species revealed that they varied in their capacity for current production. G. metallireducens and G. hydrogenophilus generated high current densities (ca. 0.05 mA/cm2, comparable to G. sulfurreducens. G. bremensis, G. chapellei, G. humireducens, and G. uranireducens, produced much lower currents (ca. 0.05 mA/cm2 and G. bemidjiensis was previously found to not produce current. There was no correspondence between the effectiveness of current generation and Fe(III oxide reduction rates. Some high-current-density strains (G. metallireducens and G. hydrogenophilus reduced Fe(III-oxides as fast as some low-current-density strains (G. bremensis, G. humireducens, and G. uranireducens whereas other low-current-density strains (G. bemidjiensis and G. chapellei reduced Fe(III oxide as slowly as G. sulfurreducens, a high-current-density strain. However, there was a correspondence between the ability to produce higher currents and the ability to grow syntrophically. G. hydrogenophilius was found to grow in co-culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET, but not with Methanospirillium hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron exchange via DIET. These findings, coupled with the previous finding that G. metallireducens and G. sulfurreducens are also capable of DIET, suggest that evolution to optimize DIET has fortuitiously conferred the capability for high-density current production to some Geobacter species.

  5. Conjugated oligoelectrolyte represses hydrogen oxidation by Geobacter sulfurreducens in microbial electrolysis cells

    KAUST Repository

    Liu, Jia

    2015-12-01

    © 2015 Elsevier B.V. A conjugated oligoelectrolyte (COE), which spontaneously aligns within cell membranes, was shown to completely inhibit H2 uptake by Geobacter sulfurreducens in microbial electrolysis cells. Coulombic efficiencies that were 490±95%, due to H2 recycling between the cathode and microorganisms on the anode, were reduced to 86±2% with COE addition. The use of the COE resulted in a 67-fold increase in H2 gas recovery, and a 4.4-fold increase in acetate removal. Current generation, H2 recovery and COD removals by Geobacter metallireducens, which cannot use H2, were unaffected by COE addition. These results show that this COE is an effective H2 uptake inhibitor, and that it can enable improved and sustained H2 gas recovery in this bioelectrochemical system.

  6. Link between capacity for current production and syntrophic growth in Geobacter species

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Woodard, Trevor; Nevin, Kelly;

    2015-01-01

    -culture with Methanosarcina barkeri, which is capable of direct interspecies electron transfer (DIET), but not with Methanospirillium hungatei capable only of H2 or formate transfer. Conductive granular activated carbon (GAC) stimulated metabolism of the G. hydrogenophilus - M. barkeri co-culture, consistent with electron......Electrodes are unnatural electron acceptors, and it is yet unknown how some Geobacter species evolved to use electrodes as terminal electron acceptors. Analysis of different Geobacter species revealed that they varied in their capacity for current production. G. metallireducens and G....... hydrogenophilus generated high current densities (ca. 0.05 mA/cm2), comparable to G. sulfurreducens. G. bremensis, G. chapellei, G. humireducens, and G. uranireducens, produced much lower currents (ca. 0.05 mA/cm2) and G. bemidjiensis was previously found to not produce current. There was no correspondence...

  7. Conjugated oligoelectrolyte represses hydrogen oxidation by Geobacter sulfurreducens in microbial electrolysis cells.

    Science.gov (United States)

    Liu, Jia; Hou, Huijie; Chen, Xiaofen; Bazan, Guillermo C; Kashima, Hiroyuki; Logan, Bruce E

    2015-12-01

    A conjugated oligoelectrolyte (COE), which spontaneously aligns within cell membranes, was shown to completely inhibit H2 uptake by Geobacter sulfurreducens in microbial electrolysis cells. Coulombic efficiencies that were 490±95%, due to H2 recycling between the cathode and microorganisms on the anode, were reduced to 86±2% with COE addition. The use of the COE resulted in a 67-fold increase in H2 gas recovery, and a 4.4-fold increase in acetate removal. Current generation, H2 recovery and COD removals by Geobacter metallireducens, which cannot use H2, were unaffected by COE addition. These results show that this COE is an effective H2 uptake inhibitor, and that it can enable improved and sustained H2 gas recovery in this bioelectrochemical system.

  8. Hydrogen Production by Geobacter Species and a Mixed Consortium in a Microbial Electrolysis Cell▿

    Science.gov (United States)

    Call, Douglas F.; Wagner, Rachel C.; Logan, Bruce E.

    2009-01-01

    A hydrogen utilizing exoelectrogenic bacterium (Geobacter sulfurreducens) was compared to both a nonhydrogen oxidizer (Geobacter metallireducens) and a mixed consortium in order to compare the hydrogen production rates and hydrogen recoveries of pure and mixed cultures in microbial electrolysis cells (MECs). At an applied voltage of 0.7 V, both G. sulfurreducens and the mixed culture generated similar current densities (ca. 160 A/m3), resulting in hydrogen production rates of ca. 1.9 m3 H2/m3/day, whereas G. metallireducens exhibited lower current densities and production rates of 110 ± 7 A/m3 and 1.3 ± 0.1 m3 H2/m3/day, respectively. Before methane was detected in the mixed-culture MEC, the mixed consortium achieved the highest overall energy recovery (relative to both electricity and substrate energy inputs) of 82% ± 8% compared to G. sulfurreducens (77% ± 2%) and G. metallireducens (78% ± 5%), due to the higher coulombic efficiency of the mixed consortium. At an applied voltage of 0.4 V, methane production increased in the mixed-culture MEC and, as a result, the hydrogen recovery decreased and the overall energy recovery dropped to 38% ± 16% compared to 80% ± 5% for G. sulfurreducens and 76% ± 0% for G. metallireducens. Internal hydrogen recycling was confirmed since the mixed culture generated a stable current density of 31 ± 0 A/m3 when fed hydrogen gas, whereas G. sulfurreducens exhibited a steady decrease in current production. Community analysis suggested that G. sulfurreducens was predominant in the mixed-culture MEC (72% of clones) despite its relative absence in the mixed-culture inoculum obtained from a microbial fuel cell reactor (2% of clones). These results demonstrate that Geobacter species are capable of obtaining similar hydrogen production rates and energy recoveries as mixed cultures in an MEC and that high coulombic efficiencies in mixed culture MECs can be attributed in part to the recycling of hydrogen into current. PMID:19820150

  9. Hydrogen Production by Geobacter Species and a Mixed Consortium in a Microbial Electrolysis Cell

    KAUST Repository

    Call, D. F.

    2009-10-09

    A hydrogen utilizing exoelectrogenic bacterium (Geobacter sulfurreducens) was compared to both a nonhydrogen oxidizer (Geobacter metallireducens) and a mixed consortium in order to compare the hydrogen production rates and hydrogen recoveries of pure and mixed cultures in microbial electrolysis cells (MECs). At an applied voltage of 0.7 V, both G. sulfurreducens and the mixed culture generated similar current densities (ca. 160 A/m3), resulting in hydrogen production rates of ca. 1.9 m3 H2/m 3/day, whereas G. metallireducens exhibited lower current densities and production rates of 110 ± 7 A/m3 and 1.3 ± 0.1 m3 H2/m3/day, respectively. Before methane was detected in the mixed-culture MEC, the mixed consortium achieved the highest overall energy recovery (relative to both electricity and substrate energy inputs) of 82% ± 8% compared to G. sulfurreducens (77% ± 2%) and G. metallireducens (78% ± 5%), due to the higher coulombic efficiency of the mixed consortium. At an applied voltage of 0.4 V, methane production increased in the mixed-culture MEC and, as a result, the hydrogen recovery decreased and the overall energy recovery dropped to 38% ± 16% compared to 80% ± 5% for G. sulfurreducens and 76% ± 0% for G. metallireducens. Internal hydrogen recycling was confirmed since the mixed culture generated a stable current density of 31 ± 0 A/m3 when fed hydrogen gas, whereas G. sulfurreducens exhibited a steady decrease in current production. Community analysis suggested that G. sulfurreducens was predominant in the mixed-culture MEC (72% of clones) despite its relative absence in the mixed-culture inoculum obtained from a microbial fuel cell reactor (2% of clones). These results demonstrate that Geobacter species are capable of obtaining similar hydrogen production rates and energy recoveries as mixed cultures in an MEC and that high coulombic efficiencies in mixed culture MECs can be attributed in part to the recycling of hydrogen into current. Copyright

  10. Carboxydotrophic growth of Geobacter sulfurreducens

    NARCIS (Netherlands)

    Geelhoed, J.S.; Henstra, A.M.; Stams, A.J.M.

    2016-01-01

    This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 P

  11. Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens.

    Science.gov (United States)

    Rotaru, Amelia-Elena; Shrestha, Pravin M; Liu, Fanghua; Ueki, Toshiyuki; Nevin, Kelly; Summers, Zarath M; Lovley, Derek R

    2012-11-01

    Direct interspecies electron transfer (DIET) is an alternative to interspecies H(2)/formate transfer as a mechanism for microbial species to cooperatively exchange electrons during syntrophic metabolism. To understand what specific properties contribute to DIET, studies were conducted with Pelobacter carbinolicus, a close relative of Geobacter metallireducens, which is capable of DIET. P. carbinolicus grew in coculture with Geobacter sulfurreducens with ethanol as the electron donor and fumarate as the electron acceptor, conditions under which G. sulfurreducens formed direct electrical connections with G. metallireducens. In contrast to the cell aggregation associated with DIET, P. carbinolicus and G. sulfurreducens did not aggregate. Attempts to initiate cocultures with a genetically modified strain of G. sulfurreducens incapable of both H(2) and formate utilization were unsuccessful, whereas cocultures readily grew with mutant strains capable of formate but not H(2) uptake or vice versa. The hydrogenase mutant of G. sulfurreducens compensated, in cocultures, with significantly increased formate dehydrogenase gene expression. In contrast, the transcript abundance of a hydrogenase gene was comparable in cocultures with that for the formate dehydrogenase mutant of G. sulfurreducens or the wild type, suggesting that H(2) was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of G. sulfurreducens that could not produce pili or OmcS, two essential components for DIET. The finding that P. carbinolicus exchanged electrons with G. sulfurreducens via interspecies transfer of H(2)/formate rather than DIET demonstrates that not all microorganisms that can grow syntrophically are capable of DIET and that closely related microorganisms may use significantly different strategies for interspecies electron exchange.

  12. Orenia metallireducens sp. nov. strain Z6, a Novel Metal-reducing Firmicute from the Deep Subsurface

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Yiran; Sanford, Robert A.; Boyanov, Maxim I.; Kemner, Kenneth M.; Flynn, Theodore M.; O' Loughlin, Edward J.; Chang, Yun-juan; Locke, Randall A.; Weber, Joseph R.; Egan, Sheila M.; Mackie, Roderick I.; Cann, Isaac; Fouke, Bruce W.

    2016-08-26

    A novel halophilic and metal-reducing bacterium,Orenia metallireducensstrain Z6, was isolated from briny groundwater extracted from a 2.02 km-deep borehole in the Illinois Basin, IL. This organism shared 96% 16S rRNA gene similarity withOrenia marismortui, but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of genusOrenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)] using H2as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6-9.6), salinity (0.4-3.5 M NaCl) and temperature (20-60 °C). At pH 6.5, strain Z6 also reduced more crystalline iron oxides such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH) and hematite (α-Fe2O3). Analysis of X-ray absorption fine structure (XAFS) following Fe(III) reduction by strain Z6 revealed spectra from ferrous secondary mineral phases consistent with the precipitation of vivianite [Fe3(PO4)2] and siderite (FeCO3). The draft genome assembled for strain Z6 is 3.47 Mb in size and contains 3,269 protein-coding genes. Unlike the well understood iron-reducingShewanellaandGeobacterspecies, this organism lacks thec-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genusOrenia(orderHalanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scope of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from otherOreniaspp. support the designation of strain Z6 as a new species,Orenia metallireducenssp. nov.

  13. Carboxydotrophic growth of Geobacter sulfurreducens.

    Science.gov (United States)

    Geelhoed, Jeanine S; Henstra, Anne M; Stams, Alfons J M

    2016-01-01

    This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 Pa). In assays with cell-free extract of cells grown with CO and fumarate, production of hydrogen from CO was not observed, and hydrogenase activity with benzyl viologen as electron acceptor was very low. Taken together, this suggested that CO is not utilized via hydrogen as intermediate. In the presence of CO, reduction of NADP(+) was observed at a rate comparable to CO oxidation coupled to fumarate reduction in vivo. The G. sulfurreducens genome contains a single putative carbon monoxide dehydrogenase-encoding gene. The gene is part of a predicted operon also comprising a putative Fe-S cluster-binding subunit (CooF) and a FAD-NAD(P) oxidoreductase and is preceded by a putative CO-sensing transcription factor. This cluster may be involved in a novel pathway for CO oxidation, but further studies are necessary to ascertain this. Similar gene clusters are present in several other species belonging to the Deltaproteobacteria and Firmicutes, for which CO utilization is currently not known.

  14. Identification of succinic semialdehyde reductases from Geobacter: expression,purification, crystallization, preliminary functional, and crystallographic analysis

    Institute of Scientific and Technical Information of China (English)

    Yanfeng Zhang; Xiaoli Gao; Yi Zheng; R. Michae; Garavito

    2011-01-01

    Succinic semialdehyde reductase (SSAR) is an important enzyme involved in γ-aminobutyrate (GABA) metabolism.By converting succinic semialdehyde (SSA) to γ-hydroxybutyrate (GHB),the SSAR facilitates an alternative pathway for GABA degradation.In this study,we identified SSARs from Geobacter sulfurreducens and Geobacter metallireducens (GsSSAR and GmSSAR,respectively).The enzymes were over-expressed in Escherichia coil and purified to near homogeneity.Both GsSSAR and GmSSAR showed the activity of reducing SSA using nicotinamide adenine dinucleotide phosphate as a co-factor.The oligomeric sizes of GsSSAR and GmSSAR,as determined by analytical size exclusion chromatography,suggest that the enzymes presumably exist as tetramers in solution.The recombinant GsSSAR and GmSSAR crystallized in the presence of NADP+,and the resulting crystals diffracted to 1.89 (A) (GsSSAR) and 2.25 (A)(GmSSAR) resolution.The GsSSAR and GmSSAR crystals belong to the space groups P21221 (a =99.61 (A),b =147.49 (A),c =182.47 A) and P1 (a =75.97 (A) b =79.14 (A) c =95.47 (A),α =82.15°,β =88.80°,γ=87.66°),respectively.Preliminary crystallographic data analysis suggests the presence of eight protein monomers in the asymmetric units for both GsSSAR and GmSSAR.

  15. Identification of succinic semialdehyde reductases from Geobacter: expression, purification, crystallization, preliminary functional, and crystallographic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanfeng; Gao, Xiaoli; Zheng, Yi; Garavito, R. Michael (MSU)

    2012-04-30

    Succinic semialdehyde reductase (SSAR) is an important enzyme involved in {gamma}-aminobutyrate (GABA) metabolism. By converting succinic semialdehyde (SSA) to {gamma}-hydroxybutyrate (GHB), the SSAR facilitates an alternative pathway for GABA degradation. In this study, we identified SSARs from Geobacter sulfurreducens and Geobacter metallireducens (GsSSAR and GmSSAR, respectively). The enzymes were over-expressed in Escherichia coli and purified to near homogeneity. Both GsSSAR and GmSSAR showed the activity of reducing SSA using nicotinamide adenine dinucleotide phosphate as a co-factor. The oligomeric sizes of GsSSAR and GmSSAR, as determined by analytical size exclusion chromatography, suggest that the enzymes presumably exist as tetramers in solution. The recombinant GsSSAR and GmSSAR crystallized in the presence of NADP{sup +}, and the resulting crystals diffracted to 1.89 {angstrom} (GsSSAR) and 2.25 {angstrom} (GmSSAR) resolution. The GsSSAR and GmSSAR crystals belong to the space groups P2{sub 1}22{sub 1} (a = 99.61 {angstrom}, b = 147.49 {angstrom}, c = 182.47 {angstrom}) and P1 (a = 75.97 {angstrom}, b = 79.14 {angstrom}, c = 95.47 {angstrom}, {alpha} = 82.15{sup o}, {beta} = 88.80{sup o}, {gamma} = 87.66{sup o}), respectively. Preliminary crystallographic data analysis suggests the presence of eight protein monomers in the asymmetric units for both GsSSAR and GmSSAR.

  16. Mechanisms for Electron Transfer Through Pili to Fe(III) Oxide in Geobacter

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R. [Univ. of Massachusetts, Amherst, MA (United States)

    2015-03-09

    The purpose of these studies was to aid the Department of Energy in its goal of understanding how microorganisms involved in the bioremediation of metals and radionuclides sustain their activity in the subsurface. This information is required in order to incorporate biological processes into decision making for environmental remediation and long-term stewardship of contaminated sites. The proposed research was designed to elucidate the mechanisms for electron transfer to Fe(III) oxides in Geobacter species because Geobacter species are abundant dissimilatory metal-reducing microorganisms in a diversity of sites in which uranium is undergoing natural attenuation via the reduction of soluble U(VI) to insoluble U(IV) or when this process is artificially stimulated with the addition of organic electron donors. This study investigated the novel, but highly controversial, concept that the final conduit for electron transfer to Fe(III) oxides are electrically conductive pili. The specific objectives were to: 1) further evaluate the conductivity along the pili of Geobacter sulfurreducens and related organisms; 2) determine the mechanisms for pili conductivity; and 3) investigate the role of pili in Fe(III) oxide reduction. The studies demonstrated that the pili of G. sulfurreducens are conductive along their length. Surprisingly, the pili possess a metallic-like conductivity similar to that observed in synthetic organic conducting polymers such as polyaniline. Detailed physical analysis of the pili, as well as studies in which the structure of the pili was genetically modified, demonstrated that the metallic-like conductivity of the pili could be attributed to overlapping pi-pi orbitals of aromatic amino acids. Other potential mechanisms for conductivity, such as electron hopping between cytochromes associated with the pili were definitively ruled out. Pili were also found to be essential for Fe(III) oxide reduction in G. metallireducens. Ecological studies demonstrated

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

    Science.gov (United States)

    Lovley, Derek R; Ueki, Toshiyuki; Zhang, Tian; Malvankar, Nikhil S; Shrestha, Pravin M; Flanagan, Kelly A; Aklujkar, Muktak; Butler, Jessica E; Giloteaux, Ludovic; Rotaru, Amelia-Elena; Holmes, Dawn E; Franks, Ashley E; Orellana, Roberto; Risso, Carla; Nevin, Kelly P

    2011-01-01

    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

  18. Genetic evidence that the degradation of para-cresol by Geobacter metallireducens is catalyzed by the periplasmic para-cresol methylhydroxylase

    DEFF Research Database (Denmark)

    Chaurasia, Akhilesh Kumar; Tremblay, Pier-Luc; Holmes, Dawn E.

    2015-01-01

    Two pathways for para-cresol (p-cresol) degradation by anaerobic bacteria have been elucidated; one involves fumarate addition at the methyl group of p-cresol by a hydroxylbenzylsuccinate synthase protein while the other utilizes a methylhydroxylase protein (PCMH) to catalyze hydroxylation of the...

  19. Microbial fuel cell used in study on dissimilatory ferric oxides reduction by Geobacter metallireducens%利用微生物燃料电池研究Geobacter metallireducens异化还原铁氧化物

    Institute of Scientific and Technical Information of China (English)

    周良; 刘志丹; 连静; 李福生; 杜竹玮; 李浩然

    2005-01-01

    微生物异化还原金属氧化物的过程中,关键问题是微生物如何把电子传递给最终的固态电子受体.利用新颖的微生物燃料电池体系,可以更细致、准确地研究这一胞外电子传递过程.实验结果表明在Geobacter metallireducens还原铁氧化物过程中, 直接接触是一种重要的电子传递方式; 而电子传递中间体,在金属氧化物表面完全被微生物细胞覆盖后, 也即在金属氧化物表面形成成熟的生物膜后, 其加速电子传递速率的作用减弱.

  20. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation.

    Science.gov (United States)

    Wilkins, Michael J; Verberkmoes, Nathan C; Williams, Kenneth H; Callister, Stephen J; Mouser, Paula J; Elifantz, Hila; N'guessan, A Lucie; Thomas, Brian C; Nicora, Carrie D; Shah, Manesh B; Abraham, Paul; Lipton, Mary S; Lovley, Derek R; Hettich, Robert L; Long, Philip E; Banfield, Jillian F

    2009-10-01

    Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

  1. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, M.J.; VerBerkmoes, N.C.; Williams, K.H.; Callister, S.J.; Mouser, P.J.; Elifantz, H.; N' Guessan, A.L.; Thomas, B.C.; Nicora, C.D.; Shah, M.B.; Lipton, M.S.; Lovley, D.R.; Hettich, R.L.; Long, P.E.; Banfield, J.F.; Abraham, P.

    2009-08-01

    Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

  2. Evidence of Geobacter-associated phage in a uranium-contaminated aquifer

    OpenAIRE

    2014-01-01

    Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were ...

  3. Extracellular Palladium Nanoparticle Production using Geobacter sulfurreducens

    KAUST Repository

    Yates, Matthew D.

    2013-09-03

    Sustainable methods are needed to recycle precious metals and synthesize catalytic nanoparticles. Palladium nanoparticles can be produced via microbial reduction of soluble Pd(II) to Pd(0), but in previous tests using dissimilatory metal reducing bacteria (DMRB), the nanoparticles were closely associated with the cells, occupying potential reductive sites and eliminating the potential for cell reuse. The DMRB Geobacter sulfurreducens was shown here to reduce soluble Pd(II) to Pd(0) nanoparticles primarily outside the cell, reducing the toxicity of metal ions, and allowing nanoparticle recovery without cell destruction that has previously been observed using other microorganisms. Cultures reduced 50 ± 3 mg/L Pd(II) with 1% hydrogen gas (v/v headspace) in 6 h incubation tests [100 mg/L Pd(II) initially], compared to 8 ± 3 mg/L (10 mM acetate) without H2. Acetate was ineffective as an electron donor for palladium removal in the presence or absence of fumarate as an electron acceptor. TEM imaging verified that Pd(0) nanoparticles were predominantly in the EPS surrounding cells in H2-fed cultures, with only a small number of particles visible inside the cell. Separation of the cells and EPS by centrifugation allowed reuse of the cell suspensions and effective nanoparticle recovery. These results demonstrate effective palladium recovery and nanoparticle production using G. sulfurreducens cell suspensions and renewable substrates such as H2 gas. © 2013 American Chemical Society.

  4. Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems.

    Science.gov (United States)

    Sun, Dan; Wang, Aijie; Cheng, Shaoan; Yates, Matthew; Logan, Bruce E

    2014-10-01

    A previously isolated exoelectrogenic bacterium, strain SD-1(T), was further characterized and identified as a representative of a novel species of the genus Geobacter. Strain SD-1(T) was Gram-negative, aerotolerant, anaerobic, non-spore-forming, non-fermentative and non-motile. Cells were short, curved rods (0.8-1.3 µm long and 0.3 µm in diameter). Growth of strain SD-1(T) was observed at 15-42 °C and pH 6.0-8.5, with optimal growth at 30-35 °C and pH 7. Analysis of 16S rRNA gene sequences indicated that the isolate was a member of the genus Geobacter, with the closest known relative being Geobacter sulfurreducens PCA(T) (98% similarity). Similar to other members of the genus Geobacter, strain SD-1(T) used soluble or insoluble Fe(III) as the sole electron acceptor coupled with the oxidation of acetate. However, SD-1(T) could not reduce fumarate as an electron acceptor with acetate oxidization, which is an important physiological trait for G. sulfurreducens. Moreover, SD-1(T) could grow in media containing as much as 3% NaCl, while G. sulfurreducens PCA(T) can tolerate just half this concentration, and this difference in salt tolerance was even more obvious when cultivated in bioelectrochemical systems. DNA-DNA hybridization analysis of strain SD-1(T) and its closest relative, G. sulfurreducens ATCC 51573(T), showed a relatedness of 61.6%. The DNA G+C content of strain SD-1(T) was 58.9 mol%. Thus, on the basis of these characteristics, strain SD-1(T) was not assigned to G. sulfurreducens, and was instead classified in the genus Geobacter as a representative of a novel species. The name Geobacter anodireducens sp. nov. is proposed, with the type strain SD-1(T) ( = CGMCC 1.12536(T) = KCTC 4672(T)).

  5. Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems

    KAUST Repository

    Sun, D.

    2014-07-22

    © 2014 IUMS. A previously isolated exoelectrogenic bacterium, strain SD-1(T), was further characterized and identified as a representative of a novel species of the genus Geobacter. Strain SD-1(T) was Gram-negative, aerotolerant, anaerobic, non-spore-forming, non-fermentative and non-motile. Cells were short, curved rods (0.8-1.3 µm long and 0.3 µm in diameter). Growth of strain SD-1(T) was observed at 15-42 °C and pH 6.0-8.5, with optimal growth at 30-35 °C and pH 7. Analysis of 16S rRNA gene sequences indicated that the isolate was a member of the genus Geobacter, with the closest known relative being Geobacter sulfurreducens PCA(T) (98% similarity). Similar to other members of the genus Geobacter, strain SD-1(T) used soluble or insoluble Fe(III) as the sole electron acceptor coupled with the oxidation of acetate. However, SD-1(T) could not reduce fumarate as an electron acceptor with acetate oxidization, which is an important physiological trait for G. sulfurreducens. Moreover, SD-1(T) could grow in media containing as much as 3% NaCl, while G. sulfurreducens PCA(T) can tolerate just half this concentration, and this difference in salt tolerance was even more obvious when cultivated in bioelectrochemical systems. DNA-DNA hybridization analysis of strain SD-1(T) and its closest relative, G. sulfurreducens ATCC 51573(T), showed a relatedness of 61.6%. The DNA G+C content of strain SD-1(T) was 58.9 mol%. Thus, on the basis of these characteristics, strain SD-1(T) was not assigned to G. sulfurreducens, and was instead classified in the genus Geobacter as a representative of a novel species. The name Geobacter anodireducens sp. nov. is proposed, with the type strain SD-1(T) ( = CGMCC 1.12536(T) = KCTC 4672(T)).

  6. Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.

    Science.gov (United States)

    Holmes, Dawn E; Giloteaux, Ludovic; Chaurasia, Akhilesh K; Williams, Kenneth H; Luef, Birgit; Wilkins, Michael J; Wrighton, Kelly C; Thompson, Courtney A; Comolli, Luis R; Lovley, Derek R

    2015-02-01

    Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.

  7. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Mike [University of California, Berkeley; Verberkmoes, Nathan C [ORNL; Williams, Ken [Lawrence Berkeley National Laboratory (LBNL); Callister, Stephen J [Pacific Northwest National Laboratory (PNNL); Mouser, Paula J [University of Massachusetts, Amherst; Elifantz, Hila [University of Massachusetts, Amherst; N' Guessan, A. Lucie [University of Massachusetts, Amherst; Thomas, Brian [University of California, Berkeley; Nicora, Carrie D. [Pacific Northwest National Laboratory (PNNL); Shah, Manesh B [ORNL; Abraham, Paul E [ORNL; Lipton, Mary S [Pacific Northwest National Laboratory (PNNL); Lovley, Derek [University of Massachusetts, Amherst; Hettich, Robert {Bob} L [ORNL; Long, Phil [Pacific Northwest National Laboratory (PNNL); Banfield, Jillian F. [University of California, Berkeley

    2009-01-01

    Implementation of uranium bioremediation requires methods to monitor the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here we report a proteomics-based approach to simultaneously document strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching LC MS/MS spectra to peptides predicted from 7 isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and G. bemidjiensis like strains and later possible emergence of M21 and G. bemidjiensis like strains more closely related to G. lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-CoA and pyruvate for central metabolism while abundant peptides matching TCA cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

  8. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; VerBerkmoes, Nathan C.; Williams, Kenneth H.; Callister, Stephen J.; Mouser, Paula; Elifantz, H.; N' Guessan, A. Lucie; Thomas, Brian C.; Nicora, Carrie D.; Shah, Manesh B.; Abraham, Paul; Lipton, Mary S.; Lovely, Derek R.; Hettich, Robert L.; Long, Philip E.; Banfield, Jillian F.

    2009-10-01

    Implementation of uranium bioremediation requires methods to monitor the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here we report a proteomics-based approach to simultaneously document strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching LC MS/MS spectra to peptides predicted from 7 isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and G. bemidjiensis–like strains and later possible emergence of M21 and G. bemidjiensis–like strains more closely related to G. lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-CoA and pyruvate for central metabolism while abundant peptides matching TCA cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

  9. Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies.

    Science.gov (United States)

    Yun, Jiae; Ueki, Toshiyuki; Miletto, Marzia; Lovley, Derek R

    2011-07-01

    Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.

  10. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    Science.gov (United States)

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)).

  11. Enhanced uranium immobilization and reduction by Geobacter sulfurreducens biofilms.

    Science.gov (United States)

    Cologgi, Dena L; Speers, Allison M; Bullard, Blair A; Kelly, Shelly D; Reguera, Gemma

    2014-11-01

    Biofilms formed by dissimilatory metal reducers are of interest to develop permeable biobarriers for the immobilization of soluble contaminants such as uranium. Here we show that biofilms of the model uranium-reducing bacterium Geobacter sulfurreducens immobilized substantially more U(VI) than planktonic cells and did so for longer periods of time, reductively precipitating it to a mononuclear U(IV) phase involving carbon ligands. The biofilms also tolerated high and otherwise toxic concentrations (up to 5 mM) of uranium, consistent with a respiratory strategy that also protected the cells from uranium toxicity. The enhanced ability of the biofilms to immobilize uranium correlated only partially with the biofilm biomass and thickness and depended greatly on the area of the biofilm exposed to the soluble contaminant. In contrast, uranium reduction depended on the expression of Geobacter conductive pili and, to a lesser extent, on the presence of the c cytochrome OmcZ in the biofilm matrix. The results support a model in which the electroactive biofilm matrix immobilizes and reduces the uranium in the top stratum. This mechanism prevents the permeation and mineralization of uranium in the cell envelope, thereby preserving essential cellular functions and enhancing the catalytic capacity of Geobacter cells to reduce uranium. Hence, the biofilms provide cells with a physically and chemically protected environment for the sustained immobilization and reduction of uranium that is of interest for the development of improved strategies for the in situ bioremediation of environments impacted by uranium contamination.

  12. Identification of a Transcriptional Repressor Involved in Benzoate Metabolism in Geobacter bemidjiensis ▿

    OpenAIRE

    2011-01-01

    Subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species. A transcription factor that represses expression of bamA, a benzoate-inducible gene, in Geobacter bemidjiensis during growth with acetate was identified. It is likely that this repressor also regulates other genes involved in aromatic compound metabolism.

  13. G eobacter sp. SD-1 with enhanced electrochemical activity in high-salt concentration solutions

    KAUST Repository

    Sun, Dan

    2014-07-16

    © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd. Summary: An isolate, designated strain SD-1, was obtained from a biofilm dominated by Geobacter sulfurreducens in a microbial fuel cell. The electrochemical activity of strain SD-1 was compared with type strains, G.sulfurreducensPCA and Geobacter metallireducensGS-15, and a mixed culture in microbial electrolysis cells. SD-1 produced a maximum current density of 290±29Am-3 in a high-concentration phosphate buffer solution (PBS-H, 200mM). This current density was significantly higher than that produced by the mixed culture (189±44Am-3) or the type strains (<70Am-3). In a highly saline water (SW; 50mM PBS and 650mM NaCl), current by SD-1 (158±4Am-3) was reduced by 28% compared with 50mM PBS (220±4Am-3), but it was still higher than that of the mixed culture (147±19Am-3), and strains PCA and GS-15 did not produce any current. Electrochemical tests showed that the improved performance of SD-1 was due to its lower charge transfer resistance and more negative potentials produced at higher current densities. These results show that the electrochemical activity of SD-1 was significantly different than other Geobacter strains and mixed cultures in terms of its salt tolerance.

  14. Harvesting electricity with Geobacter bremensis isolated from compost.

    Directory of Open Access Journals (Sweden)

    Olivier Nercessian

    Full Text Available Electrochemically active (EA biofilms were formed on metallic dimensionally stable anode-type electrode (DSA, embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m(2 on DSA, 2490 mA/m(2 on graphite than the original multi-species biofilms (in average 300 mA/m(2 on DSA and the G. bremensis DSM type strain (100-300 A/m(2 on DSA; 2485 mA/m(2 on graphite. FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes.

  15. Harvesting electricity with Geobacter bremensis isolated from compost.

    Science.gov (United States)

    Nercessian, Olivier; Parot, Sandrine; Délia, Marie-Line; Bergel, Alain; Achouak, Wafa

    2012-01-01

    Electrochemically active (EA) biofilms were formed on metallic dimensionally stable anode-type electrode (DSA), embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m(2) on DSA, 2490 mA/m(2) on graphite) than the original multi-species biofilms (in average 300 mA/m(2) on DSA) and the G. bremensis DSM type strain (100-300 A/m(2) on DSA; 2485 mA/m(2) on graphite). FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes.

  16. The Complex Conductivity Signature of Geobacter Species in Geological Media

    Science.gov (United States)

    Brown, I.; Atekwana, E. A.; Sarkisova, S.; Achang, M.

    2013-12-01

    The Complex Conductivity (CC) technique is a promising biogeophysical approach for sensing microbially-induced changes in geological media because of its low-invasive character and sufficient sensitivity to enhanced microbial activity in the near subsurface. Geobacter species have been shown to play important roles in the bioremediation of groundwater contaminated with petroleum and landfill leachate. This capability is based on the ability of Geobacter species to reduce Fe(III) by transferring of electrons from the reduced equivalents to Fe(III) rich minerals through respiration chain and special metallic-like conductors - pili. Only the cultivation of Geobacter species on Fe(III) oxides specifically express pili biosynthesis. Moreover, mutants that cannot produce pili are unable to reduce Fe(III) oxides. However, little is known about the contribution of these molecular conductors (nanowires) to the generation of complex conductivity signatures in geological media. Here, we present the results about the modulation of CC signatures in geological media by Geobacter sulfurreducens (G.s.). Cultures of wild strain G.s. and its pilA(-) mutant were anaerobically cultivated in the presence of the pair of such donors and acceptors of electrons: acetate - fumarate, and acetate - magnetite under anaerobic conditions. Each culture was injected in CC sample holders filled either with N2-CO2 mix (planktonic variant) or with this gases mix and glass beads, d=1 mm, (porous medium variant). Both strains of G.s. proliferated well in a medium supplemented with acetate-fumarate. However, pilA(-) mutant did not multiply in a medium supplemented with ox-red pair yeast extract - magnetite. This observation confirmed that only wild pilA(+) strain is capable of the dissimilatory reduction of Fe(III) within magnetite molecule. The measurement of CC responses from planktonic culture of G.s. wild strain grown with acetate-fumarate did not show linear correlation with their magnitudes but

  17. Hematite Reduction Buffers Acid Generation and Enhances Nutrient Uptake by a Fermentative Iron Reducing Bacterium, Orenia metallireducens Strain Z6.

    Science.gov (United States)

    Dong, Yiran; Sanford, Robert A; Chang, Yun-Juan; McInerney, Michael J; Fouke, Bruce W

    2017-01-03

    Fermentative iron-reducing organisms have been identified in a variety of environments. Instead of coupling iron reduction to respiration, they have been consistently observed to use ferric iron minerals as an electron sink for fermentation. In the present study, a fermentative iron reducer, Orenia metallireducens strain Z6, was shown to use iron reduction to enhance fermentation not only by consuming electron equivalents, but also by generating alkalinity that effectively buffers the pH. Fermentation of glucose by this organism in the presence of a ferric oxide mineral, hematite (Fe2O3), resulted in enhanced glucose decomposition compared with fermentation in the absence of an iron source. Parallel evidence (i.e., genomic reconstruction, metabolomics, thermodynamic analyses, and calculation of electron transfer) suggested hematite reduction as a proton-consuming reaction effectively consumed acid produced by fermentation. The buffering effect of hematite was further supported by a greater extent of glucose utilization by strain Z6 in media with increasing buffer capacity. Such maintenance of a stable pH through hematite reduction for enhanced glucose fermentation complements the thermodynamic interpretation of interactions between microbial iron reduction and other biogeochemical processes. This newly discovered feature of iron reducer metabolism also has significant implications for groundwater management and contaminant remediation by providing microbially mediated buffering systems for the associated microbial and/or chemical reactions.

  18. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments.

    Science.gov (United States)

    Zhuang, Kai; Izallalen, Mounir; Mouser, Paula; Richter, Hanno; Risso, Carla; Mahadevan, Radhakrishnan; Lovley, Derek R

    2011-02-01

    The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected under natural conditions at the site, Rhodoferax will outcompete Geobacter as long as sufficient ammonium is available. The model also predicted that when high concentrations of acetate are added during in situ bioremediation, Geobacter species would predominate, consistent with field-scale observations. This can be attributed to the higher expected growth yields of Rhodoferax and the ability of Geobacter to fix nitrogen. The modeling predicted relative proportions of Geobacter and Rhodoferax in geochemically distinct zones of the Rifle site that were comparable to those that were previously documented with molecular techniques. The model also predicted that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium zones. These results show that genome-scale modeling can be a useful tool for predicting microbial interactions in subsurface environments and shows promise for designing bioremediation strategies.

  19. Biochemical Mechanisms and Energy Strategies of Geobacter Sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Tien, Ming; Brantley, Susan L.

    2013-10-28

    To provide the scientific understanding required to allow DOE sites to incorporate relevant biological, chemical, and physical processes into decisions concerning environmental remediation, a fundamental understanding of the controls on micro-organism growth in the subsurface is necessary. Specifically, mobility of metals in the environment, including chromium, technetium and uranium, is greatly affected by the process of dissimilatory metal reduction (DMR), which has been shown to be an important biological activity controlling contaminant mobility in the subsurface at many DOE sites. Long-term maintenance of DMR at constant rates must rely upon steady fluxes of electron donors to provide the maintenance energy needed by organisms such as Geobacter sulfurreducens to maintain steady state populations in the subsurface.

  20. Physiological stratification in electricity-producing biofilms of Geobacter sulfurreducens.

    Science.gov (United States)

    Schrott, Germán David; Ordoñez, María Victoria; Robuschi, Luciana; Busalmen, Juan Pablo

    2014-02-01

    The elucidation of mechanisms and limitations in electrode respiration by electroactive biofilms is significant for the development of rapidly emerging clean energy production and wastewater treatment technologies. In Geobacter sulfurreducens biofilms, the controlling steps in current production are thought to be the metabolic activity of cells, but still remain to be determined. By quantifying the DNA, RNA, and protein content during the long-term growth of biofilms on polarized graphite electrodes, we show in this work that current production becomes independent of DNA accumulation immediately after a maximal current is achieved. Indeed, the mean respiratory rate of biofilms rapidly decreases after this point, which indicates the progressive accumulation of cells that do not contribute to current production or contribute to a negligible extent. These results support the occurrence of physiological stratification within biofilms as a consequence of respiratory limitations imposed by limited biofilm conductivity.

  1. Iron-oxide minerals affect extracellular electron-transfer paths of Geobacter spp.

    Science.gov (United States)

    Kato, Souichiro; Hashimoto, Kazuhito; Watanabe, Kazuya

    2013-01-01

    Some bacteria utilize (semi)conductive iron-oxide minerals as conduits for extracellular electron transfer (EET) to distant, insoluble electron acceptors. A previous study demonstrated that microbe/mineral conductive networks are constructed in soil ecosystems, in which Geobacter spp. share dominant populations. In order to examine how (semi)conductive iron-oxide minerals affect EET paths of Geobacter spp., the present study grew five representative Geobacter strains on electrodes as the sole electron acceptors in the absence or presence of (semi)conductive iron oxides. It was found that iron-oxide minerals enhanced current generation by three Geobacter strains, while no effect was observed in another strain. Geobacter sulfurreducens was the only strain that generated substantial amounts of currents both in the presence and absence of the iron oxides. Microscopic, electrochemical and transcriptomic analyses of G. sulfurreducens disclosed that this strain constructed two distinct types of EET path; in the absence of iron-oxide minerals, bacterial biofilms rich in extracellular polymeric substances were constructed, while composite networks made of mineral particles and microbial cells (without polymeric substances) were developed in the presence of iron oxides. It was also found that uncharacterized c-type cytochromes were up-regulated in the presence of iron oxides that were different from those found in conductive biofilms. These results suggest the possibility that natural (semi)conductive minerals confer energetic and ecological advantages on Geobacter, facilitating their growth and survival in the natural environment.

  2. The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III-reducing subsurface environments.

    Directory of Open Access Journals (Sweden)

    Aklujkar Muktak

    2010-09-01

    Full Text Available Abstract Background Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. Results Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. Conclusion Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of

  3. Flux analysis of central metabolic pathways in Geobactermetallireducens during reduction of solubleFe(III)-NTA

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Chakraborty, Romy; Garcia-Martin, Hector; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

    We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were present under theseconditions, but enzymes in the glyoxylate shunt and malic enzyme wereabsent. Gluconeogenesis and the pentose phosphate pathway were mainlyemployed for biosynthesis and accounted for less than 3 percent of totalcarbon consumption. The model also indicated surprisingly highreversibility in the reaction between oxoglutarate and succinate. Thisstep operates close to the thermodynamic equilibrium possibly becausesuccinate is synthesized via a transferase reaction, and the conversionof oxoglutarate to succinate is a rate limiting step for carbonmetabolism. These findings enable a better understanding of therelationship between genome annotation and extant metabolic pathways inG. metallireducens.

  4. Integrative analysis of the interactions between Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    Directory of Open Access Journals (Sweden)

    D. R. Lovley

    2011-11-01

    Full Text Available Enhancing microbial U(VI reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI-reducing Geobacter predominated and U(VI was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB predominated and U(VI reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III was depleted whereas the SRB grow more slowly and reached dominance after 30–40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  5. Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    Science.gov (United States)

    Barlett, M.; Zhuang, K.; Mahadevan, R.; Lovley, D.

    2012-03-01

    Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing Geobacter predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30-40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  6. Integrative analysis of the interactions between Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    Science.gov (United States)

    Barlett, M.; Zhuang, K.; Mahadevan, R.; Lovley, D. R.

    2011-11-01

    Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing Geobacter predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30-40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  7. Molecular analysis of the in situ growth rates of subsurface Geobacter species.

    Science.gov (United States)

    Holmes, Dawn E; Giloteaux, Ludovic; Barlett, Melissa; Chavan, Milind A; Smith, Jessica A; Williams, Kenneth H; Wilkins, Michael; Long, Philip; Lovley, Derek R

    2013-03-01

    Molecular tools that can provide an estimate of the in situ growth rate of Geobacter species could improve understanding of dissimilatory metal reduction in a diversity of environments. Whole-genome microarray analyses of a subsurface isolate of Geobacter uraniireducens, grown under a variety of conditions, identified a number of genes that are differentially expressed at different specific growth rates. Expression of two genes encoding ribosomal proteins, rpsC and rplL, was further evaluated with quantitative reverse transcription-PCR (qRT-PCR) in cells with doubling times ranging from 6.56 h to 89.28 h. Transcript abundance of rpsC correlated best (r(2) = 0.90) with specific growth rates. Therefore, expression patterns of rpsC were used to estimate specific growth rates of Geobacter species during an in situ uranium bioremediation field experiment in which acetate was added to the groundwater to promote dissimilatory metal reduction. Initially, increased availability of acetate in the groundwater resulted in higher expression of Geobacter rpsC, and the increase in the number of Geobacter cells estimated with fluorescent in situ hybridization compared well with specific growth rates estimated from levels of in situ rpsC expression. However, in later phases, cell number increases were substantially lower than predicted from rpsC transcript abundance. This change coincided with a bloom of protozoa and increased attachment of Geobacter species to solid phases. These results suggest that monitoring rpsC expression may better reflect the actual rate that Geobacter species are metabolizing and growing during in situ uranium bioremediation than changes in cell abundance.

  8. Integrative analysis of Geobacter spp. and sulfate-reducing bacteria during uranium bioremediation

    Directory of Open Access Journals (Sweden)

    D. Lovley

    2012-03-01

    Full Text Available Enhancing microbial U(VI reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI-reducing Geobacter predominated and U(VI was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB predominated and U(VI reduction was poor. The interaction of Geobacter and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, Geobacter grew quickly but then declined in numbers as the microbially reducible Fe(III was depleted whereas the SRB grow more slowly and reached dominance after 30–40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the Geobacter and SRB were varied indicated that there was little to no competitive interaction between Geobacter and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III would revive the Geobacter, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III availability, rather than competition with SRB, is the key factor limiting the activity of Geobacter during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies.

  9. Structural and Operational Complexity of the Geobacter Sulfurreducens Genome

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Yu; Cho, Byung-Kwan; Park, Young S.; Lovley, Derek R.; Palsson, Bernhard O.; Zengler, Karsten

    2010-06-30

    Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale, such as metabolism and transcriptional regulation. Here, we describe a systems approach to simultaneously determine the structural and operational annotation of the Geobacter sulfurreducens genome. Integration of proteomics, transcriptomics, RNA polymerase, and sigma factor-binding information with deep-sequencing-based analysis of primary 59-end transcripts allowed for a most precise annotation. The structural annotation is comprised of numerous previously undetected genes, noncoding RNAs, prevalent leaderless mRNA transcripts, and antisense transcripts. When compared with other prokaryotes, we found that the number of antisense transcripts reversely correlated with genome size. The operational annotation consists of 1453 operons, 22% of which have multiple transcription start sites that use different RNA polymerase holoenzymes. Several operons with multiple transcription start sites encoded genes with essential functions, giving insight into the regulatory complexity of the genome. The experimentally determined structural and operational annotations can be combined with functional annotation, yielding a new three-level annotation that greatly expands our understanding of prokaryotic genomes.

  10. Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem.

    Science.gov (United States)

    Lu, Xia; Liu, Yurong; Johs, Alexander; Zhao, Linduo; Wang, Tieshan; Yang, Ziming; Lin, Hui; Elias, Dwayne A; Pierce, Eric M; Liang, Liyuan; Barkay, Tamar; Gu, Baohua

    2016-04-19

    Microbial methylation and demethylation are two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems. Although mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjiensis Bem. Here we report, for the first time, that the strain G. bemidjiensis Bem can mediate a suite of Hg transformations, including Hg(II) reduction, Hg(0) oxidation, MeHg production and degradation under anoxic conditions. Results suggest that G. bemidjiensis utilizes a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) as the major reaction product, possibly due to the presence of genes encoding homologues of an organomercurial lyase (MerB) and a mercuric reductase (MerA). In addition, the cells can strongly sorb Hg(II) and MeHg, reduce or oxidize Hg, resulting in both time and concentration-dependent Hg species transformations. Moderate concentrations (10-500 μM) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of Hg methylation and demethylation among anaerobic bacteria, thereby influencing net MeHg production in anoxic water and sediments.

  11. Anaerobes unleashed: Aerobic fuel cells of Geobacter sulfurreducens

    Science.gov (United States)

    Nevin, Kelly P.; Zhang, Pei; Franks, Ashley E.; Woodard, Trevor L.; Lovley, Derek R.

    One of the limitations of power generation with microbial fuel cells is that the anode must typically be maintained under anaerobic conditions. When oxygen is present in the anode chamber microorganisms oxidize the fuel with the reduction of oxygen rather than electron transfer to the anode. A system in which fuel is provided from within a graphite anode and diffuses out to the outer surface of the anode was designed to overcome these limitations. A biofilm of Geobacter sulfurreducens strain KN400, pregrown on the surface of a graphite electrode in a traditional two-chambered system with an anaerobic anode chamber and acetate as an external fuel source, produced current just as well under aerobic conditions when acetate was provided via diffusion from an internal concentrated acetate solution. No acetate was detectable in the external medium. In contrast, aerobic systems in which acetate was provided in the external medium completely failed within 48 h. Internally fed anodes colonized by a strain of KN400 adapted to grow at marine salinities produced current in aerobic seawater as well as an anaerobic anode system. The ability to generate current with an anode under aerobic conditions increases the potential applications and design options for microbial fuel cells.

  12. Studies of multi-heme cytochromes from Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Pokkuluri, P. Raj; Londer, Yuri, Y.; Orshonsky, Valerie; Orshonsky, Lisa; Duke, Norma; Schiffer, Marianne

    2006-04-05

    The Geobacteraceae family predominates in the reduction of uranium in subsurface environments. We are focusing on the model organism, Geobacter sulfurreducens; its genome contains a large number (>100) of cytochromes c that function in metal reduction pathways. Intensive functional genomics and physiological studies are in progress in Prof. Derek Lovley's laboratory, and the complete genome sequence of this organism has been determined by Methe et al. 2003. We are studying cytochromes from the c{sub 7} family that are required for the reduction of Fe(III). Previously, we expressed in E. coli (Londer et al., 2002) and determined the three-dimensional structure at 1.45 {angstrom} resolution (Pokkuluri et al., 2004a) of the three-heme cytochrome c{sub 7} (PpcA, coded by ORF01023) characterized by Lloyd et al., 2003. Further we identified in the G. sulfurreducens genome ORFs for several of its homologs (Pokkuluri et al., 2004a). Four of the ORFs are the same size as PpcA; three other ORFs are polymers of c7-type domains, two of which consist of four domains and one of nine domains, that contain 12 and 27 hemes respectively.

  13. Proteins involved in electron transfer to Fe(III) and Mn(IV) oxides by Geobacter sulfurreducens and Geobacter uraniireducens.

    Science.gov (United States)

    Aklujkar, M; Coppi, M V; Leang, C; Kim, B C; Chavan, M A; Perpetua, L A; Giloteaux, L; Liu, A; Holmes, D E

    2013-03-01

    Whole-genome microarray analysis of Geobacter sulfurreducens grown on insoluble Fe(III) oxide or Mn(IV) oxide versus soluble Fe(III) citrate revealed significantly different expression patterns. The most upregulated genes, omcS and omcT, encode cell-surface c-type cytochromes, OmcS being required for Fe(III) and Mn(IV) oxide reduction. Other electron transport genes upregulated on both metal oxides included genes encoding putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc4 and Cbc5, periplasmic c-type cytochromes Dhc2 and PccF, outer membrane c-type cytochromes OmcC, OmcG and OmcV, multicopper oxidase OmpB, the structural components of electrically conductive pili, PilA-N and PilA-C, and enzymes that detoxify reactive oxygen/nitrogen species. Genes upregulated on Fe(III) oxide encode putative menaquinol : ferricytochrome c oxidoreductase complexes Cbc3 and Cbc6, periplasmic c-type cytochromes, including PccG and PccJ, and outer membrane c-type cytochromes, including OmcA, OmcE, OmcH, OmcL, OmcN, OmcO and OmcP. Electron transport genes upregulated on Mn(IV) oxide encode periplasmic c-type cytochromes PccR, PgcA, PpcA and PpcD, outer membrane c-type cytochromes OmaB/OmaC, OmcB and OmcZ, multicopper oxidase OmpC and menaquinone-reducing enzymes. Genetic studies indicated that MacA, OmcB, OmcF, OmcG, OmcH, OmcI, OmcJ, OmcM, OmcV and PccH, the putative Cbc5 complex subunit CbcC and the putative Cbc3 complex subunit CbcV are important for reduction of Fe(III) oxide but not essential for Mn(IV) oxide reduction. Gene expression patterns for Geobacter uraniireducens were similar. These results demonstrate that the physiology of Fe(III)-reducing bacteria differs significantly during growth on different insoluble and soluble electron acceptors and emphasize the importance of c-type cytochromes for extracellular electron transfer in G. sulfurreducens.

  14. Probing single- to multi-cell level charge transport in Geobacter sulfurreducens DL-1

    Science.gov (United States)

    Jiang, Xiaocheng; Hu, Jinsong; Petersen, Emily R.; Fitzgerald, Lisa A.; Jackan, Charles S.; Lieber, Alexander M.; Ringeisen, Bradley R.; Lieber, Charles M.; Biffinger, Justin C.

    2013-11-01

    Microbial fuel cells, in which living microorganisms convert chemical energy into electricity, represent a potentially sustainable energy technology for the future. Here we report the single-bacterium level current measurements of Geobacter sulfurreducens DL-1 to elucidate the fundamental limits and factors determining maximum power output from a microbial fuel cell. Quantized stepwise current outputs of 92(±33) and 196(±20) fA are generated from microelectrode arrays confined in isolated wells. Simultaneous cell imaging/tracking and current recording reveals that the current steps are directly correlated with the contact of one or two cells with the electrodes. This work establishes the amount of current generated by an individual Geobacter cell in the absence of a biofilm and highlights the potential upper limit of microbial fuel cell performance for Geobacter in thin biofilms.

  15. A long way to the electrode: how do Geobacter cells transport their electrons?

    Science.gov (United States)

    Bonanni, Pablo Sebastián; Schrott, Germán David; Busalmen, Juan Pablo

    2012-12-01

    The mechanism of electron transport in Geobacter sulfurreducens biofilms is a topic under intense study and debate. Although some proteins were found to be essential for current production, the specific role that each one plays in electron transport to the electrode remains to be elucidated and a consensus on the mechanism of electron transport has not been reached. In the present paper, to understand the state of the art in the topic, electron transport from inside of the cell to the electrode in Geobacter sulfurreducens biofilms is analysed, reviewing genetic studies, biofilm conductivity assays and electrochemical and spectro-electrochemical experiments. Furthermore, crucial data still required to achieve a deeper understanding are highlighted.

  16. Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies

    Directory of Open Access Journals (Sweden)

    Joana M Dantas

    2015-07-01

    Full Text Available Multiheme cytochromes have been implicated in Geobacter sulfurreducens (Gs extracellular electron transfer (EET. These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by Gs. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of Gs multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of Gs by characterizing a family of five triheme cytochromes (PpcA-E. These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell’s outer surface. The results obtained suggested that PpcA can couple e-/H+ transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e-/H+ transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of Gs. For the first time Gs strains have been manipulated by the introduction of mutant forms of essential proteins with the aim to develop and improve

  17. Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies.

    Science.gov (United States)

    Dantas, Joana M; Morgado, Leonor; Aklujkar, Muktak; Bruix, Marta; Londer, Yuri Y; Schiffer, Marianne; Pokkuluri, P Raj; Salgueiro, Carlos A

    2015-01-01

    Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e(-)/H(+) transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e(-)/H(+) transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential

  18. Rational engineering of Geobacter sulfurreducens electron transfer components: a foundation for building improved Geobacter-based bioelectrochemical technologies

    Science.gov (United States)

    Dantas, Joana M.; Morgado, Leonor; Aklujkar, Muktak; Bruix, Marta; Londer, Yuri Y.; Schiffer, Marianne; Pokkuluri, P. Raj; Salgueiro, Carlos A.

    2015-01-01

    Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Over the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. In previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e−/H+ transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e−/H+ transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential

  19. Proteogenomic Analysis of Geobacter Populations in a low Nutrient Contaminated Aquifer Under Stimulated Conditions.

    Science.gov (United States)

    Wilkins, M. J.; Williams, K. H.; Verberkmoes, N. C.; Hettich, R. L.; Lipton, M. S.; Callister, S. J.; Long, P. E.; Banfield, J. F.

    2008-12-01

    Proteogenomic samples were obtained from a U(VI)-contaminated aquifer undergoing acetate-stimulated bioreduction at the U.S. Department of Energy Integrated Field Challenge (IFC) site in Western Colorado. Analysis of these samples using ICP-MS/MS indicated that they were dominated by Geobacter species, with over 2,500 proteins identified per sample. The detected proteins revealed a wealth of information about how Geobacter species are able to dominate subsurface environments under nutrient-poor conditions such as those at Rifle. The presence of nitrogenase proteins indicates that the Geobacter populations are fixing nitrogen, although the absence of other proteins indicative of nitrogen stress, such as the uridylylated version of the P-II regulatory protein and NtrB, suggests that low-level N2 fixation occurs without the community undergoing extreme nitrogen stress. The detection of a large number of proteins involved in two- component sensor and chemotaxis systems, along with flagella subunits, indicates that Geobacter species are able to rapidly detect and respond to chemical gradients in the environment. Pathways for the efficient utilization of the elevated acetate concentrations in the subsurface have also been elucidated, with an important role suggested for acetyl-CoA transferase in controlling flux between succinyl-CoA and succinate. Other proteins detected that are clearly important for growth in the subsurface include those involved in phosphate acquisition and heavy-metal efflux.

  20. Use of a Coculture To Enable Current Production by Geobacter sulfurreducens

    KAUST Repository

    Qu, Y.

    2012-02-17

    Microbial fuel cells often produce more electrical power with mixed cultures than with pure cultures. Here, we show that a coculture of a nonexoelectrogen (Escherichia coli) and Geobacter sulfurreducens improved system performance relative to that of a pure culture of the exoelectrogen due to the consumption of oxygen leaking into the reactor.

  1. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis

    Energy Technology Data Exchange (ETDEWEB)

    Merkley, Eric D.; Wrighton, Kelly C.; Castelle, Cindy; Anderson, Brian J.; Wilkins, Michael J.; Shah, Vega; Arbour, Tyler; Brown, Joseph N.; Singer, Steven W.; Smith, Richard D.; Lipton, Mary S.

    2015-03-06

    Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of Geobacter bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely-related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.

  2. Influence of anode potentials on selection of Geobacter strains in microbial electrolysis cells.

    Science.gov (United States)

    Commault, Audrey S; Lear, Gavin; Packer, Michael A; Weld, Richard J

    2013-07-01

    Through their ability to directly transfer electrons to electrodes, Geobacter sp. are key organisms for microbial fuel cell technology. This study presents a simple method to reproducibly select Geobacter-dominated anode biofilms from a mixed inoculum of bacteria using graphite electrodes initially poised at -0.25, -0.36 and -0.42 V vs. Ag/AgCl. The biofilms all produced maximum power density of approximately 270 m Wm(-2) (projected anode surface area). Analysis of 16S rRNA genes and intergenic spacer (ITS) sequences found that the biofilm communities were all dominated by bacteria closely related to Geobacter psychrophilus. Anodes initially poised at -0.25 V reproducibly selected biofilms that were dominated by a strain of G. psychrophilus that was genetically distinct from the strain that dominated the -0.36 and -0.42 V biofilms. This work demonstrates for the first time that closely related strains of Geobacter can have very different competitive advantages at different anode potentials.

  3. Maintenance of Geobacter-dominated biofilms in microbial fuel cells treating synthetic wastewater.

    Science.gov (United States)

    Commault, Audrey S; Lear, Gavin; Weld, Richard J

    2015-12-01

    Geobacter-dominated biofilms can be selected under stringent conditions that limit the growth of competing bacteria. However, in many practical applications, such stringent conditions cannot be maintained and the efficacy and stability of these artificial biofilms may be challenged. In this work, biofilms were selected on low-potential anodes (-0.36 V vs Ag/AgCl, i.e. -0.08 V vs SHE) in minimal acetate or ethanol media. Selection conditions were then relaxed by transferring the biofilms to synthetic wastewater supplemented with soil as a source of competing bacteria. We tracked community succession and functional changes in these biofilms. The Geobacter-dominated biofilms showed stability in their community composition and electrochemical properties, with Geobacter sp. being still electrically active after six weeks in synthetic wastewater with power densities of 100±19 mW·m(-2) (against 74±14 mW·m(-2) at week 0) for all treatments. After six weeks, the ethanol-selected biofilms, despite their high taxon richness and their efficiency at removing the chemical oxygen demand (0.8 g·L(-1) removed against the initial 1.3 g·L(-1) injected), were the least stable in terms of community structure. These findings have important implications for environmental microbial fuel cells based on Geobacter-dominated biofilms and suggest that they could be stable in challenging environments.

  4. Electricity-Assisted Biological Hydrogen Production from Acetate by Geobacter sulfurreducens

    NARCIS (Netherlands)

    Geelhoed, J.S.; Stams, A.J.M.

    2011-01-01

    Geobacter sulfurreducens is a well-known current-producing microorganism in microbial fuel cells, and is able to use acetate and hydrogen as electron donor. We studied the functionality of G. sulfurreducens as biocatalyst for hydrogen formation at the cathode of a microbial electrolysis cell (MEC).

  5. Scanning probe studies of the pilus nanowires in Geobacter sulfurreducens

    Science.gov (United States)

    Veazey, Joshua P.

    In microbial organisms like bacteria, pili (singular: pilus) are filament-like appendages that are nanometers in diameter and microns long. The sizes and structures of the different types of pili found in nature are adapted to serve one of many distinct functions for the organism from which they come. The pili expressed by the bacterium Geobacter sulfurreducens act as electrically conductive nanowires that provide conduits for electrons to leave the cell during its respiratory cycle. Biological experiments have suggested that long range electron transfer across micron distances may proceed along the protein matrix, rather than by metal cofactors (metal atoms bound to the protein). Protein conductivity across such distances would require a novel transport mechanism. In an effort to elucidate this mechanism, our lab has used two electronically sensitive scanning probe techniques: Scanning Tunneling Microscopy (STM) and Conductive Probe Atomic Force Microscopy (CP-AFM). I employed the high resolution imaging and electronic sensitivity of STM to resolve the molecular sub-structure and local electronic density of states (LDOS) at different points above pili from purified preparations, deposited onto a conducting substrate. The significant and stable tunneling currents achieved for biologically relevant voltages, in the absence of metal cofactors, demonstrated conduction between tip and substrate via the protein matrix. We observed periodicity of roughly 10 nm and 2.5 nm in topographs of the pili. In our acquisition of LDOS, we observed gap-like asymmetric energy spectra that were dependent upon the location of the tip above the pilus, suggestive of easier current flow out of one side of the cylindrical pilus and into the opposite side. Voltage-dependent STM imaging, which also contains information about the LDOS at each pixel, was consistent with this interpretation. The asymmetry in spectra observed on one pilus edge had a slightly larger magnitude than the other edge

  6. Modeling and sensitivity analysis of electron capacitance for Geobacter in sedimentary environments.

    Science.gov (United States)

    Zhao, Jiao; Fang, Yilin; Scheibe, Timothy D; Lovley, Derek R; Mahadevan, R

    2010-03-01

    In situ stimulation of the metabolic activity of Geobacter species through acetate amendment has been shown to be a promising bioremediation strategy to reduce and immobilize hexavalent uranium [U(VI)] as insoluble U(IV). Although Geobacter species are reducing U(VI), they primarily grow via Fe(III) reduction. Unfortunately, the biogeochemistry and the physiology of simultaneous reduction of multiple metals are still poorly understood. A detailed model is therefore required to better understand the pathways leading to U(VI) and Fe(III) reduction by Geobacter species. Based on recent experimental evidence of temporary electron capacitors in Geobacter we propose a novel kinetic model that physically distinguishes planktonic cells into electron-loaded and -unloaded states. Incorporation of an electron load-unload cycle into the model provides insight into U(VI) reduction efficiency, and elucidates the relationship between U(VI)- and Fe(III)-reducing activity and further explains the correlation of high U(VI) removal with high fractions of planktonic cells in subsurface environments. Global sensitivity analysis was used to determine the level of importance of geochemical and microbial processes controlling Geobacter growth and U(VI) reduction, suggesting that the electron load-unload cycle and the resulting repartition of the microbes between aqueous and attached phases are critical for U(VI) reduction. As compared with conventional Monod modeling approaches without inclusion of the electron capacitance, the new model attempts to incorporate a novel cellular mechanism that has a significant impact on the outcome of in situ bioremediation.

  7. The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu.

    Science.gov (United States)

    Shanmugam, Raghuvaran; Aklujkar, Muktak; Schäfer, Matthias; Reinhardt, Richard; Nickel, Olaf; Reuter, Gunter; Lovley, Derek R; Ehrenhofer-Murray, Ann; Nellen, Wolfgang; Ankri, Serge; Helm, Mark; Jurkowski, Tomasz P; Jeltsch, Albert

    2014-06-01

    Dnmt2 enzymes are conserved in eukaryotes, where they methylate C38 of tRNA-Asp with high activity. Here, the activity of one of the very few prokaryotic Dnmt2 homologs from Geobacter species (GsDnmt2) was investigated. GsDnmt2 was observed to methylate tRNA-Asp from flies and mice. Unexpectedly, it had only a weak activity toward its matching Geobacter tRNA-Asp, but methylated Geobacter tRNA-Glu with good activity. In agreement with this result, we show that tRNA-Glu is methylated in Geobacter while the methylation is absent in tRNA-Asp. The activities of Dnmt2 enzymes from Homo sapiens, Drosophila melanogaster, Schizosaccharomyces pombe and Dictyostelium discoideum for methylation of the Geobacter tRNA-Asp and tRNA-Glu were determined showing that all these Dnmt2s preferentially methylate tRNA-Asp. Hence, the GsDnmt2 enzyme has a swapped transfer ribonucleic acid (tRNA) specificity. By comparing the different tRNAs, a characteristic sequence pattern was identified in the variable loop of all preferred tRNA substrates. An exchange of two nucleotides in the variable loop of murine tRNA-Asp converted it to the corresponding variable loop of tRNA-Glu and led to a strong reduction of GsDnmt2 activity. Interestingly, the same loss of activity was observed with human DNMT2, indicating that the variable loop functions as a specificity determinant in tRNA recognition of Dnmt2 enzymes.

  8. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture.

    Science.gov (United States)

    Esteve-Núñez, Abraham; Rothermich, Mary; Sharma, Manju; Lovley, Derek

    2005-05-01

    A system for growing Geobacter sulfurreducens under anaerobic conditions in chemostats was developed in order to study the physiology of this organism under conditions that might more closely approximate those found in the subsurface than batch cultures. Geobacter sulfurreducens could be cultured under acetate-limiting conditions with fumarate or Fe(III)-citrate as the electron acceptor at growth rates between 0.04 and 0.09 h(-1). The molar growth yield was threefold higher with fumarate as the electron acceptor than with Fe(III), despite the lower mid-point potential of the fumarate/succinate redox couple. When growth was limited by availability of fumarate, high steady-state concentrations were detected, suggesting that fumarate is unlikely to be an important electron acceptor in sedimentary environments. The half-saturation constant, Ks, for acetate in Fe(III)-grown cultures (10 microM) suggested that the growth of Geobacter species is likely to be acetate limited in most subsurface sediments, but that when millimolar quantities of acetate are added to the subsurface in order to promote the growth of Geobacter for bioremediation applications, this should be enough to overcome any acetate limitations. When the availability of electron acceptors, rather than acetate, limited growth, G. sulfurreducens was less efficient in incorporating acetate into biomass but had higher respiration rates, a desirable physiological characteristic when adding acetate to stimulate the activity of Geobacter species during in situ uranium bioremediation. These results demonstrate that the ability to study the growth of G. sulfurreducens under steady-state conditions can provide insights into its physiological characteristics that have relevance for its activity in a diversity of sedimentary environments.

  9. Identification of multicomponent histidine-aspartate phosphorelay system controlling flagellar and motility gene expression in Geobacter species.

    Science.gov (United States)

    Ueki, Toshiyuki; Leang, Ching; Inoue, Kengo; Lovley, Derek R

    2012-03-30

    Geobacter species play an important role in the natural biogeochemical cycles of aquatic sediments and subsurface environments as well as in subsurface bioremediation by oxidizing organic compounds with the reduction of insoluble Fe(III) oxides. Flagellum-based motility is considered to be critical for Geobacter species to locate fresh sources of Fe(III) oxides. Functional and comparative genomic approaches, coupled with genetic and biochemical methods, identified key regulators for flagellar gene expression in Geobacter species. A master transcriptional regulator, designated FgrM, is a member of the enhancer-binding protein family. The fgrM gene in the most studied strain of Geobacter species, Geobacter sulfurreducens strain DL-1, is truncated by a transposase gene, preventing flagellar biosynthesis. Integrating a functional FgrM homolog restored flagellar biosynthesis and motility in G. sulfurreducens DL-1 and enhanced the ability to reduce insoluble Fe(III) oxide. Interrupting the fgrM gene in G. sulfurreducens strain KN400, which is motile, removed the capacity for flagellar production and inhibited Fe(III) oxide reduction. FgrM, which is also a response regulator of the two-component His-Asp phosphorelay system, was phosphorylated by histidine kinase GHK4, which was essential for flagellar production and motility. GHK4, which is a hybrid kinase with a receiver domain at the N terminus, was phosphorylated by another histidine kinase, GHK3. Therefore, the multicomponent His-Asp phosphorelay system appears to control flagellar gene expression in Geobacter species.

  10. Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species.

    Science.gov (United States)

    Ueki, Toshiyuki; Lovley, Derek R

    2010-01-01

    Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic and biochemical assays, identified a novel transcription factor termed HgtR that acts as a repressor for gltA. Further analysis revealed that HgtR is a global regulator for genes involved in biosynthesis and energy generation in Geobacter species. The hgtR gene was essential for growth with hydrogen, during which hgtR expression was induced. These findings provide important new insights into the mechanisms by which Geobacter species regulate their central metabolism under different environmental conditions.

  11. Influence of inoculum and anode surface properties on the selection of Geobacter-dominated biofilms.

    Science.gov (United States)

    Commault, Audrey S; Barrière, Frédéric; Lapinsonnière, Laure; Lear, Gavin; Bouvier, Solène; Weld, Richard J

    2015-11-01

    This study evaluated the impact of inoculum source and anode surface modification (carboxylate -COO(-) and sulfonamide -SO2NH2 groups) on the microbial composition of anode-respiring biofilms. These two factors have not previously been considered in detail. Three different inoculum sources were investigated, a dry aerobic soil, brackish estuarine mud and freshwater sediment. The biofilms were selected using a poised anode (-0.36 V vs Ag/AgCl) and acetate as the electron donor in a three-electrode configuration microbial fuel cell (MFC). Population profiling and cloning showed that all biofilms selected were dominated by Geobacter sp., although their electrochemical properties varied depending on the source inoculum and electrode surface modification. These findings suggest that Geobacter sp. are widespread in soils, even those that do not provide a continuously anaerobic environment, and are better at growing in the MFC conditions than other bacteria.

  12. Probing Single- to Multi-Cell Level Charge Transport in Geobacter sulfurreducens DL-1

    Science.gov (United States)

    2013-11-08

    experiment for analysis by HPLC (Varian, Inc.) with a refractive index detector. The mobile phase was a 5-mM sulphuric acid solution and the column was PL...thick; VWR) were cleaned in Piranha solution (3:1 concentrated sulphuric acid to 30% hydrogen peroxide) for 30min, rinsed with deionized water (15 s...due to secondary p-stacking of amino acids comprising the pilin itself25. Most conductivity and gene expression experiments with Geobacter sp. are

  13. Localization and Solubilization of the Iron(III) Reductase of Geobacter sulfurreducens

    OpenAIRE

    1998-01-01

    The iron(III) reductase activity of Geobacter sulfurreducens was determined with the electron donor NADH and the artificial electron donor horse heart cytochrome c. The highest reduction rates were obtained with Fe(III) complexed by nitrilotriacetic acid as an electron acceptor. Fractionation experiments indicated that no iron(III) reductase activity was present in the cytoplasm, that approximately one-third was found in the periplasmic fraction, and that two-thirds were associated with the m...

  14. Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.

    Science.gov (United States)

    Viulu, Samson; Nakamura, Kohei; Okada, Yurina; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-02-01

    A novel species of Fe(III)-reducing bacterium, designated strain OSK6(T), belonging to the genus Geobacter, was isolated from lotus field mud in Japan. Strain OSK6(T) was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, gram-negative, motile, straight rod-shaped bacterium, 0.6-1.9 µm long and 0.2-0.4 µm wide. The growth of the isolate occurred at 20-40 °C with optima of 30-37 °C and pH 6.5-7.5 in the presence of up to 0.5 g NaCl l(-1). The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6(T) was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6(T) is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6(T) is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6(T) ( = DSM 24905(T) = JCM 17780(T)).

  15. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil.

    Science.gov (United States)

    Zhou, Shungui; Yang, Guiqin; Lu, Qin; Wu, Min

    2014-11-01

    A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)).

  16. Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes

    Directory of Open Access Journals (Sweden)

    Young Nelson D

    2010-01-01

    Full Text Available Abstract Background Geobacter species grow by transferring electrons out of the cell - either to Fe(III-oxides or to man-made substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments. Results The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species. Conclusions These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor.

  17. Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism.

    Science.gov (United States)

    Cologgi, Dena L; Lampa-Pastirk, Sanela; Speers, Allison M; Kelly, Shelly D; Reguera, Gemma

    2011-09-13

    The in situ stimulation of Fe(III) oxide reduction by Geobacter bacteria leads to the concomitant precipitation of hexavalent uranium [U(VI)] from groundwater. Despite its promise for the bioremediation of uranium contaminants, the biological mechanism behind this reaction remains elusive. Because Fe(III) oxide reduction requires the expression of Geobacter's conductive pili, we evaluated their contribution to uranium reduction in Geobacter sulfurreducens grown under pili-inducing or noninducing conditions. A pilin-deficient mutant and a genetically complemented strain with reduced outer membrane c-cytochrome content were used as controls. Pili expression significantly enhanced the rate and extent of uranium immobilization per cell and prevented periplasmic mineralization. As a result, pili expression also preserved the vital respiratory activities of the cell envelope and the cell's viability. Uranium preferentially precipitated along the pili and, to a lesser extent, on outer membrane redox-active foci. In contrast, the pilus-defective strains had different degrees of periplasmic mineralization matching well with their outer membrane c-cytochrome content. X-ray absorption spectroscopy analyses demonstrated the extracellular reduction of U(VI) by the pili to mononuclear tetravalent uranium U(IV) complexed by carbon-containing ligands, consistent with a biological reduction. In contrast, the U(IV) in the pilin-deficient mutant cells also required an additional phosphorous ligand, in agreement with the predominantly periplasmic mineralization of uranium observed in this strain. These findings demonstrate a previously unrecognized role for Geobacter conductive pili in the extracellular reduction of uranium, and highlight its essential function as a catalytic and protective cellular mechanism that is of interest for the bioremediation of uranium-contaminated groundwater.

  18. Lactate Oxidation Coupled to Iron or Electrode Reduction by Geobacter sulfurreducens PCA

    KAUST Repository

    Call, D. F.

    2011-10-14

    Geobacter sulfurreducens PCA completely oxidized lactate and reduced iron or an electrode, producing pyruvate and acetate intermediates. Compared to the current produced by Shewanella oneidensis MR-1, G. sulfurreducens PCA produced 10-times-higher current levels in lactate-fed microbial electrolysis cells. The kinetic and comparative analyses reported here suggest a prominent role of G. sulfurreducens strains in metaland electrode-reducing communities supplied with lactate. © 2011, American Society for Microbiology.

  19. Cooperative growth of Geobacter sulfurreducens and Clostridium pasteurianum with subsequent metabolic shift in glycerol fermentation

    Science.gov (United States)

    Moscoviz, Roman; de Fouchécour, Florence; Santa-Catalina, Gaëlle; Bernet, Nicolas; Trably, Eric

    2017-01-01

    Interspecies electron transfer is a common way to couple metabolic energy balances between different species in mixed culture consortia. Direct interspecies electron transfer (DIET) mechanism has been recently characterised with Geobacter species which couple the electron balance with other species through physical contacts. Using this mechanism could be an efficient and cost-effective way to directly control redox balances in co-culture fermentation. The present study deals with a co-culture of Geobacter sulfurreducens and Clostridium pasteurianum during glycerol fermentation. As a result, it was shown that Geobacter sulfurreducens was able to grow using Clostridium pasteurianum as sole electron acceptor. C. pasteurianum metabolic pattern was significantly altered towards improved 1,3-propanediol and butyrate production (+37% and +38% resp.) at the expense of butanol and ethanol production (−16% and −20% resp.). This metabolic shift was clearly induced by a small electron uptake that represented less than 0.6% of the electrons consumed by C. pasteurianum. A non-linear relationship was found between G. sulfurreducens growth (i.e the electrons transferred between the two species) and the changes in C. pasteurianum metabolite distribution. This study opens up new possibilities for controlling and increasing specificity in mixed culture fermentation. PMID:28287150

  20. Electron donors supporting growth and electroactivity of Geobacter sulfurreducens anode biofilms.

    Science.gov (United States)

    Speers, Allison M; Reguera, Gemma

    2012-01-01

    Geobacter bacteria efficiently oxidize acetate into electricity in bioelectrochemical systems, yet the range of fermentation products that support the growth of anode biofilms and electricity production has not been thoroughly investigated. Here, we show that Geobacter sulfurreducens oxidized formate and lactate with electrodes and Fe(III) as terminal electron acceptors, though with reduced efficiency compared to acetate. The structure of the formate and lactate biofilms increased in roughness, and the substratum coverage decreased, to alleviate the metabolic constraints derived from the assimilation of carbon from the substrates. Low levels of acetate promoted formate carbon assimilation and biofilm growth and increased the system's performance to levels comparable to those with acetate only. Lactate carbon assimilation also limited biofilm growth and led to the partial oxidization of lactate to acetate. However, lactate was fully oxidized in the presence of fumarate, which redirected carbon fluxes into the tricarboxylic acid (TCA) cycle, and by acetate-grown biofilms. These results expand the known ranges of electron donors for Geobacter-driven fuel cells and identify microbial constraints that can be targeted to develop better-performing strains and increase the performance of bioelectrochemical systems.

  1. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis.

    Science.gov (United States)

    Merkley, Eric D; Wrighton, Kelly C; Castelle, Cindy J; Anderson, Brian J; Wilkins, Michael J; Shah, Vega; Arbour, Tyler; Brown, Joseph N; Singer, Steven W; Smith, Richard D; Lipton, Mary S

    2015-03-06

    Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of G. bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.

  2. Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens.

    Science.gov (United States)

    Ueki, Toshiyuki; Lovley, Derek R

    2010-11-01

    Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of nitrogen-fixation genes and represses a gene encoding glutamate dehydrogenase during nitrogen fixation. The other system whose expression is directly activated by the master regulatory system appears to control by antitermination the expression of a subset of the nitrogen-fixation genes whose transcription is activated by the master regulatory system and whose promoter contains transcription termination signals. This study provides a new paradigm for nitrogen-fixation gene regulation.

  3. Electron transfer at the cell-uranium interface in Geobacter spp.

    Science.gov (United States)

    Reguera, Gemma

    2012-12-01

    The in situ stimulation of Fe(III) oxide reduction in the subsurface stimulates the growth of Geobacter spp. and the precipitation of U(VI) from groundwater. As with Fe(III) oxide reduction, the reduction of uranium by Geobacter spp. requires the expression of their conductive pili. The pili bind the soluble uranium and catalyse its extracellular reductive precipitation along the pili filaments as a mononuclear U(IV) complexed by carbon-containing ligands. Although most of the uranium is immobilized by the pili, some uranium deposits are also observed in discreet regions of the outer membrane, consistent with the participation of redox-active foci, presumably c-type cytochromes, in the extracellular reduction of uranium. It is unlikely that cytochromes released from the outer membrane could associate with the pili and contribute to the catalysis, because scanning tunnelling microscopy spectroscopy did not reveal any haem-specific electronic features in the pili, but, rather, showed topographic and electronic features intrinsic to the pilus shaft. Pili not only enhance the rate and extent of uranium reduction per cell, but also prevent the uranium from traversing the outer membrane and mineralizing the cell envelope. As a result, pili expression preserves the essential respiratory activities of the cell envelope and the cell's viability. Hence the results support a model in which the conductive pili function as the primary mechanism for the reduction of uranium and cellular protection in Geobacter spp.

  4. Enhanced methane production in an anaerobic digestion and microbial electrolysis cell coupled system with co-cultivation of Geobacter and Methanosarcina.

    Science.gov (United States)

    Yin, Qi; Zhu, Xiaoyu; Zhan, Guoqiang; Bo, Tao; Yang, Yanfei; Tao, Yong; He, Xiaohong; Li, Daping; Yan, Zhiying

    2016-04-01

    The anaerobic digestion (AD) and microbial electrolysis cell (MEC) coupled system has been proved to be a promising process for biomethane production. In this paper, it was found that by co-cultivating Geobacter with Methanosarcina in an AD-MEC coupled system, methane yield was further increased by 24.1%, achieving to 360.2 mL/g-COD, which was comparable to the theoretical methane yield of an anaerobic digester. With the presence of Geobacter, the maximum chemical oxygen demand (COD) removal rate (216.8 mg COD/(L·hr)) and current density (304.3A/m(3)) were both increased by 1.3 and 1.8 fold compared to the previous study without Geobacter, resulting in overall energy efficiency reaching up to 74.6%. Community analysis demonstrated that Geobacter and Methanosarcina could coexist together in the biofilm, and the electrochemical activities of both were confirmed by cyclic voltammetry. Our study observed that the carbon dioxide content in total gas generated from the AD reactor with Geobacter was only half of that generated from the same reactor without Geobacter, suggesting that Methanosarcina may obtain the electron transferred from Geobacter for the reduction of carbon dioxide to methane. Taken together, Geobacter not only can improve the performance of the MEC system, but also can enhance methane production.

  5. Scarless Genome Editing and Stable Inducible Expression Vectors for Geobacter sulfurreducens.

    Science.gov (United States)

    Chan, Chi Ho; Levar, Caleb E; Zacharoff, Lori; Badalamenti, Jonathan P; Bond, Daniel R

    2015-10-01

    Metal reduction by members of the Geobacteraceae is encoded by multiple gene clusters, and the study of extracellular electron transfer often requires biofilm development on surfaces. Genetic tools that utilize polar antibiotic cassette insertions limit mutant construction and complementation. In addition, unstable plasmids create metabolic burdens that slow growth, and the presence of antibiotics such as kanamycin can interfere with the rate and extent of Geobacter biofilm growth. We report here genetic system improvements for the model anaerobic metal-reducing bacterium Geobacter sulfurreducens. A motile strain of G. sulfurreducens was constructed by precise removal of a transposon interrupting the fgrM flagellar regulator gene using SacB/sucrose counterselection, and Fe(III) citrate reduction was eliminated by deletion of the gene encoding the inner membrane cytochrome imcH. We also show that RK2-based plasmids were maintained in G. sulfurreducens for over 15 generations in the absence of antibiotic selection in contrast to unstable pBBR1 plasmids. Therefore, we engineered a series of new RK2 vectors containing native constitutive Geobacter promoters, and modified one of these promoters for VanR-dependent induction by the small aromatic carboxylic acid vanillate. Inducible plasmids fully complemented ΔimcH mutants for Fe(III) reduction, Mn(IV) oxide reduction, and growth on poised electrodes. A real-time, high-throughput Fe(III) citrate reduction assay is described that can screen numerous G. sulfurreducens strain constructs simultaneously and shows the sensitivity of imcH expression by the vanillate system. These tools will enable more sophisticated genetic studies in G. sulfurreducens without polar insertion effects or need for multiple antibiotics.

  6. Proteome of Geobacter sulfurreducens in the presence of U(VI).

    Science.gov (United States)

    Orellana, Roberto; Hixson, Kim K; Murphy, Sean; Mester, Tünde; Sharma, Manju L; Lipton, Mary S; Lovley, Derek R

    2014-12-01

    Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 µM U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance-nodulation-cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.

  7. Long-range electron transport in Geobacter sulfurreducens biofilms is redox gradient-driven.

    Science.gov (United States)

    Snider, Rachel M; Strycharz-Glaven, Sarah M; Tsoi, Stanislav D; Erickson, Jeffrey S; Tender, Leonard M

    2012-09-18

    Geobacter spp. can acquire energy by coupling intracellular oxidation of organic matter with extracellular electron transfer to an anode (an electrode poised at a metabolically oxidizing potential), forming a biofilm extending many cell lengths away from the anode surface. It has been proposed that long-range electron transport in such biofilms occurs through a network of bound redox cofactors, thought to involve extracellular matrix c-type cytochromes, as occurs for polymers containing discrete redox moieties. Here, we report measurements of electron transport in actively respiring Geobacter sulfurreducens wild type biofilms using interdigitated microelectrode arrays. Measurements when one electrode is used as an anode and the other electrode is used to monitor redox status of the biofilm 15 μm away indicate the presence of an intrabiofilm redox gradient, in which the concentration of electrons residing within the proposed redox cofactor network is higher farther from the anode surface. The magnitude of the redox gradient seems to correlate with current, which is consistent with electron transport from cells in the biofilm to the anode, where electrons effectively diffuse from areas of high to low concentration, hopping between redox cofactors. Comparison with gate measurements, when one electrode is used as an electron source and the other electrode is used as an electron drain, suggests that there are multiple types of redox cofactors in Geobacter biofilms spanning a range in oxidation potential that can engage in electron transport. The majority of these redox cofactors, however, seem to have oxidation potentials too negative to be involved in electron transport when acetate is the electron source.

  8. Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens.

    Science.gov (United States)

    Fernandes, Ana P; Nunes, Tiago C; Paquete, Catarina M; Salgueiro, Carlos A

    2017-02-20

    Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  9. Set potential regulation reveals additional oxidation peaks of Geobacter sulfurreducens anodic biofilms

    KAUST Repository

    Zhu, Xiuping

    2012-08-01

    Higher current densities produced in microbial fuel cells and other bioelectrochemical systems are associated with the presence of various Geobacter species. A number of electron transfer components are involved in extracellular electron transfer by the model exoelectrogen, Geobacter sulfurreducens. It has previously been shown that 5 main oxidation peaks can be identified in cyclic voltammetry scans. It is shown here that 7 separate oxidation peaks emerged over relatively long periods of time when a larger range of set potentials was used to acclimate electroactive biofilms. The potentials of oxidation peaks obtained with G. sulfurreducens biofilms acclimated at 0.60 V (vs. Ag/AgCl) were different from those that developed at - 0.46 V, and both of their peaks were different from those obtained for biofilms incubated at - 0.30 V, 0 V, and 0.30 V. These results expand the known range of potentials for which G. sulfurreducens produces identifiable oxidation peaks that could be important for extracellular electron transfer. © 2012 Elsevier B.V.

  10. The iron stimulon and fur regulon of Geobacter sulfurreducens and their role in energy metabolism.

    Science.gov (United States)

    Embree, Mallory; Qiu, Yu; Shieu, Wendy; Nagarajan, Harish; O'Neil, Regina; Lovley, Derek; Zengler, Karsten

    2014-05-01

    Iron plays a critical role in the physiology of Geobacter species. It serves as both an essential component for proteins and cofactors and an electron acceptor during anaerobic respiration. Here, we investigated the iron stimulon and ferric uptake regulator (Fur) regulon of Geobacter sulfurreducens to examine the coordination between uptake of Fe(II) and the reduction of Fe(III) at the transcriptional level. Gene expression studies across a variety of different iron concentrations in both the wild type and a Δfur mutant strain were used to determine the iron stimulon. The stimulon consists of a broad range of gene products, ranging from iron-utilizing to central metabolism and iron reduction proteins. Integration of gene expression and chromatin immunoprecipitation (ChIP) data sets assisted in the identification of the Fur transcriptional regulatory network and Fur's role as a regulator of the iron stimulon. Additional physiological and transcriptional analyses of G. sulfurreducens grown with various Fe(II) concentrations revealed the depth of Fur's involvement in energy metabolism and the existence of redundancy within the iron-regulatory network represented by IdeR, an alternative iron transcriptional regulator. These characteristics enable G. sulfurreducens to thrive in environments with fluctuating iron concentrations by providing it with a robust mechanism to maintain tight and deliberate control over intracellular iron homeostasis.

  11. Acetate oxidation by syntrophic association between Geobacter sulfurreducens and a hydrogen-utilizing exoelectrogen.

    Science.gov (United States)

    Kimura, Zen-ichiro; Okabe, Satoshi

    2013-08-01

    Anodic microbial communities in acetate-fed microbial fuel cells (MFCs) were analyzed using stable-isotope probing of 16S rRNA genes followed by denaturing gradient gel electrophoresis. The results revealed that Geobacter sulfurreducens and Hydrogenophaga sp. predominated in the anodic biofilm. Although the predominance of Geobacter sp. as acetoclastic exoelectrogens in acetate-fed MFC systems has been often reported, the ecophysiological role of Hydrogenophaga sp. is unknown. Therefore, we isolated and characterized a bacterium closely related to Hydrogenophaga sp. (designated strain AR20). The newly isolated strain AR20 could use molecular hydrogen (H2), but not acetate, with carbon electrode as the electron acceptor, indicating that the strain AR20 was a hydrogenotrophic exoelectrogen. This evidence raises a hypothesis that acetate was oxidized by G. sulfurreducens in syntrophic cooperation with the strain AR20 as a hydrogen-consuming partner in the acetate-fed MFC. To prove this hypothesis, G. sulfurreducens strain PCA was cocultivated with the strain AR20 in the acetate-fed MFC without any dissolved electron acceptors. In the coculture MFC of G. sulfurreducens and strain AR20, current generation and acetate degradation were the highest, and the growth of strain AR20 was observed. No current generation, acetate degradation and cell growth occurred in the strain AR20 pure culture MFC. These results show for the first time that G. sulfurreducens can oxidize acetate in syntrophic cooperation with the isolated Hydrogenophaga sp. strain AR20, with electrode as the electron acceptor.

  12. Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer.

    Science.gov (United States)

    Arkhipova, Oksana V; Meer, Margarita V; Mikoulinskaia, Galina V; Zakharova, Marina V; Galushko, Alexander S; Akimenko, Vasilii K; Kondrashov, Fyodor A

    2015-01-01

    The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome с (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.

  13. Recent Origin of the Methacrylate Redox System in Geobacter sulfurreducens AM-1 through Horizontal Gene Transfer.

    Directory of Open Access Journals (Sweden)

    Oksana V Arkhipova

    Full Text Available The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd and tetraheme cytochrome с (Mcc in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.

  14. Structural insights into the modulation of the redox properties of two Geobacter sulfurreducens homologous triheme cytochromes.

    Energy Technology Data Exchange (ETDEWEB)

    Morgado, L.; Bruix, M.; Orshonsky, V.; Londer, Y. Y.; Duke, N. E. C.; Yang, X.; Pokkuluri, P. R.; Schiffer, M.; Salgueiro, C. A.; Biosciences Division; Univ. Nova de Lisboa; Insti. de Quimica-Fisica

    2008-09-01

    The redox properties of a periplasmic triheme cytochrome, PpcB from Geobacter sulfurreducens, were studied by NMR and visible spectroscopy. The structure of PpcB was determined by X-ray diffraction. PpcB is homologous to PpcA (77% sequence identity), which mediates cytoplasmic electron transfer to extracellular acceptors and is crucial in the bioenergetic metabolism of Geobacter spp. The heme core structure of PpcB in solution, probed by 2D-NMR, was compared to that of PpcA. The results showed that the heme core structures of PpcB and PpcA in solution are similar, in contrast to their crystal structures where the heme cores of the two proteins differ from each other. NMR redox titrations were carried out for both proteins and the order of oxidation of the heme groups was determined. The microscopic properties of PpcB and PpcA redox centers showed important differences: (1) the order in which hemes become oxidized is III-I-IV for PpcB, as opposed to I-IV-III for PpcA; (2) the redox-Bohr effect is also different in the two proteins. The different redox features observed between PpcB and PpcA suggest that each protein uniquely modulates the properties of their co-factors to assure effectiveness in their respective metabolic pathways. The origins of the observed differences are discussed.

  15. Electricity-assisted biological hydrogen production from acetate by Geobacter sulfurreducens.

    Science.gov (United States)

    Geelhoed, Jeanine S; Stams, Alfons J M

    2011-01-15

    Geobacter sulfurreducens is a well-known current-producing microorganism in microbial fuel cells, and is able to use acetate and hydrogen as electron donor. We studied the functionality of G. sulfurreducens as biocatalyst for hydrogen formation at the cathode of a microbial electrolysis cell (MEC). Geobacter sulfurreducens was grown in the bioelectrode compartment of a MFC with acetate as the substrate and reduction of complexed Fe(III) at the counter electrode. After depletion of the acetate the electrode potential of the bioelectrode was decreased stepwise to -1.0 V vs Ag/AgCl reference. Production of negative current was observed, which increased in time, indicating that the bioelectrode was now acting as biocathode. Headspace analyses carried out at electrode potentials ranging from -0.8 to -1.0 V showed that hydrogen was produced, with higher rates at more negative cathode potentials. Subsequently, the metabolic properties of G. sulfurreducens for acetate oxidation at the anode and hydrogen production at the cathode were combined in one-compartment membraneless MECs operated at applied voltages of 0.8 and 0.65 V. After two days, current densities were 0.44 A m(-2) at 0.8 V applied voltage and 0.22 A m(-2) at 0.65 V, using flat-surface carbon electrodes for both anode and cathode. The cathodic hydrogen recovery ranged from 23% at 0.5 V applied voltage to 43% at 0.9 V.

  16. The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Y-H R.; Hixson, Kim K.; Giometti, Carol S.; Stanley, A; Esteve-Nunez, A; Khare, Tripti; Tollaksen, Sandra L.; Zhu, Wenhong; Adkins, Joshua N.; Lipton, Mary S.; Smith, Richard D.; Mester, Tunde; Lovley, Derek R.

    2006-05-16

    The global protein analysis of Geobacter sulfurreducens, a model for the Geobacter species that predominate in many Fe(III)-reducing subsurface environments, was characterized with ultra high pressure liquid chromatography and mass spectrometry using accurate mass and time (AMT) tags as well as with more traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Cells were grown under eight different growth conditions in order to enhance the potential that genes would be expressed. Over 3,187 gene products, representing about 92% of the total predicted gene products in the genome, were detected. The AMT approach was able to identify a much higher number of proteins than could be detected with the 2-D PAGE approach. A high proportion of predicted proteins in most protein role categories were detected with the highest number of proteins identified in the hypothetical protein role category. Furthermore, 91 c-type cytochromes of 111 predicted genes in the G. sulfurreducens genome were identified. Localization studies indicated that computational predictions of cytochrome location were limited. Differences in the abundance of cytochromes and other proteins under different growth conditions provided information for future functional analysis of these proteins. These results demonstrate that a high percentage of the predicted proteins in the G. sulfurreducens genome are produced and that the AMT approach provides a rapid method for comparing differential expression of proteins under different growth conditions in this organism.

  17. The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions.

    Science.gov (United States)

    Ding, Yan-Huai R; Hixson, Kim K; Giometti, Carol S; Stanley, Ann; Esteve-Núñez, Abraham; Khare, Tripti; Tollaksen, Sandra L; Zhu, Wenhong; Adkins, Joshua N; Lipton, Mary S; Smith, Richard D; Mester, Tünde; Lovley, Derek R

    2006-07-01

    The proteome of Geobacter sulfurreducens, a model for the Geobacter species that predominate in many Fe(III)-reducing subsurface environments, was characterized with ultra high-pressure liquid chromatography and mass spectrometry using accurate mass and time (AMT) tags as well as with more traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Cells were grown under six different growth conditions in order to enhance the potential that a wide range of genes would be expressed. The AMT tag approach was able to identify a much greater number of proteins than could be detected with the 2-D PAGE approach. With the AMT approach over 3,000 gene products were identified, representing about 90% of the total predicted gene products in the genome. A high proportion of predicted proteins in most protein role categories were detected; the highest number of proteins was identified in the hypothetical protein role category. Furthermore, 91 c-type cytochromes of 111 predicted genes in the G. sulfurreducens genome were identified. Differences in the abundance of cytochromes and other proteins under different growth conditions provided information for future functional analysis of these proteins. These results demonstrate that a high percentage of the predicted proteins in the G. sulfurreducens genome are produced and that the AMT tag approach provides a rapid method for comparing differential expression of proteins under different growth conditions in this organism.

  18. Charge transport in films of Geobacter sulfurreducens on graphite electrodes as a function of film thickness

    KAUST Repository

    Jana, Partha Sarathi

    2014-01-01

    Harnessing, and understanding the mechanisms of growth and activity of, biofilms of electroactive bacteria (EAB) on solid electrodes is of increasing interest, for application to microbial fuel and electrolysis cells. Microbial electrochemical cell technology can be used to generate electricity, or higher value chemicals, from organic waste. The capability of biofilms of electroactive bacteria to transfer electrons to solid anodes is a key feature of this emerging technology, yet the electron transfer mechanism is not fully characterized as yet. Acetate oxidation current generated from biofilms of an EAB, Geobacter sulfurreducens, on graphite electrodes as a function of time does not correlate with film thickness. Values of film thickness, and the number and local concentration of electrically connected redox sites within Geobacter sulfurreducens biofilms as well as a charge transport diffusion co-efficient for the biofilm can be estimated from non-turnover voltammetry. The thicker biofilms, of 50 ± 9 μm, display higher charge transport diffusion co-efficient than that in thinner films, as increased film porosity of these films improves ion transport, required to maintain electro-neutrality upon electrolysis. This journal is © the Partner Organisations 2014.

  19. Production of gold nanoparticles by electrode-respiring Geobacter sulfurreducens biofilms

    Energy Technology Data Exchange (ETDEWEB)

    Tanzil, Abid H.; Sultana, Sujala T.; Saunders, Steven R.; Dohnalkova, Alice C.; Shi, Liang; Davenport, Emily; Ha, Phuc; Beyenal, Haluk

    2016-12-01

    Current chemical syntheses of nanoparticles (NP) has had limited success due to the relatively high environmental cost caused by the use of harsh chemicals requiring necessary purification and size-selective fractionation. Therefore, biological approaches have received recent attention for their potential to overcome these obstacles as a benign synthetic approach. The intrinsic nature of biomolecules present in microorganisms has intrigued researchers to design bottom-up approaches to biosynthesize metal nanoparticles using microorganisms. Most of the literature work has focused on NP synthesis using planktonic cells while the use of biofilms are limited. The goal of this work was to synthesize gold nanoparticles (AuNPs) using electrode respiring Geobacter sulfurreducens biofilms. We found that most of the AuNPs are generated in the extracellular matrix of Geobacter biofilms with an average particle size of 20 nm. The formation of AuNPs was verified using TEM, FTIR and EDX. We also found that the extracellular substances extracted from electrode respiring G. sulfurreducens biofilms can reduce Au3+ to AuNPs. It appears that reducing sugars were involved in bioreduction and synthesis of AuNPs and amine groups acted as the major biomolecules involved in binding. This is first demonstration of AuNPs formation from the extracellular matrix of electrode respiring biofilms.

  20. From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    REGUERA, GEMMA [Michigan State University

    2014-01-16

    One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilms than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.

  1. Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae

    Directory of Open Access Journals (Sweden)

    Wagner Darlene D

    2012-05-01

    Full Text Available Abstract Background Geobacter lovleyi is a unique member of the Geobacteraceae because strains of this species share the ability to couple tetrachloroethene (PCE reductive dechlorination to cis-1,2-dichloroethene (cis-DCE with energy conservation and growth (i.e., organohalide respiration. Strain SZ also reduces U(VI to U(IV and contributes to uranium immobilization, making G. lovleyi relevant for bioremediation at sites impacted with chlorinated ethenes and radionuclides. G. lovleyi is the only fully sequenced representative of this distinct Geobacter clade, and comparative genome analyses identified genetic elements associated with organohalide respiration and elucidated genome features that distinguish strain SZ from other members of the Geobacteraceae. Results Sequencing the G. lovleyi strain SZ genome revealed a 3.9 Mbp chromosome with 54.7% GC content (i.e., the percent of the total guanines (Gs and cytosines (Cs among the four bases within the genome, and average amino acid identities of 53–56% compared to other sequenced Geobacter spp. Sequencing also revealed the presence of a 77 kbp plasmid, pSZ77 (53.0% GC, with nearly half of its encoded genes corresponding to chromosomal homologs in other Geobacteraceae genomes. Among these chromosome-derived features, pSZ77 encodes 15 out of the 24 genes required for de novo cobalamin biosynthesis, a required cofactor for organohalide respiration. A plasmid with 99% sequence identity to pSZ77 was subsequently detected in the PCE-dechlorinating G. lovleyi strain KB-1 present in the PCE-to-ethene-dechlorinating consortium KB-1. Additional PCE-to-cis-DCE-dechlorinating G. lovleyi strains obtained from the PCE-contaminated Fort Lewis, WA, site did not carry a plasmid indicating that pSZ77 is not a requirement (marker for PCE respiration within this species. Chromosomal genomic islands found within the G. lovleyi strain SZ genome encode two reductive dehalogenase (RDase homologs and a putative

  2. Effect of Dynamic Magnetic Field on Electricity Production of Geobacter sulfurreducens%动态磁场对Geobacter sulfurreducens产电特性的影响

    Institute of Scientific and Technical Information of China (English)

    狄梦洁; 李伟新; 薛诚; 殷瑶; 黄光团

    2015-01-01

    Geobacter sulfurreducens为产电菌构建双室微生物燃料电池(MFC).产电茵液分别在0、100、200mT的垂直磁场下动态处理lh,然后接种到MFC1、MFC2和MFC3中,研究动态磁场处理对MFC产电性能的影响.实验结果表明:动态磁场处理使产电茵反应器的启动时间延长、稳定电压降低、表观内阻增大,MFC1、MFC2和MFC3的表观内阻依次为329、507、353 Ω;通过电化学阻抗谱测试可知,相比对照组MFC活化内阻,经磁场处理的产电菌MFC全电池的活化内阻变大,其中MFC1、MFC2和MFC3的活化内阻依次为12.34、28.29、16.87 Ω;循环伏安测试发现经过动态磁场处理的产电菌其电化学活性降低.

  3. Effects of Anode Potential on the Electricity Generation Performance of Geobacter Sulfurreducens%阳极电势对Geobacter sulfurreducens产电性能的影响

    Institute of Scientific and Technical Information of China (English)

    曹效鑫; 范明志; 梁鹏; 黄霞

    2009-01-01

    以产电模式菌Geobacter sulfurreducens为研究对象接种两瓶型微生物燃料电池(MFC)阳极室,利用恒电位仪控制阳极电势,考察了7种电势条件下MFC的启动期、最大功率密度和阳极生物量的变化情况.研究结果表明,当阳极电势为-250,-100和50 mV(vs.SCE)时,MFC启动较快, CV曲线和极化曲线表明,在这3种电势条件下,MFC产电性能增强,其中阳极电势为-100 mV时,MFC最大功率密度为1.67 W/m3,比固定外阻条件下启动的MFC最大功率密度提高了5倍.控制合适的阳极电势可以使阳极生物量提高 2.5~3倍.

  4. NMR studies of the interaction between inner membrane-associated and periplasmic cytochromes from Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Brausemann, Anton; Einsle, Oliver; Salgueiro, Carlos A

    2017-06-01

    Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium with notable properties and significance in biotechnological applications. Biochemical studies suggest that the inner membrane-associated diheme cytochrome MacA and the periplasmic triheme cytochrome PpcA from G. sulfurreducens can exchange electrons. In this work, NMR chemical shift perturbation measurements were used to map the interface region and to measure the binding affinity between PpcA and MacA. The results show that MacA binds to PpcA in a cleft defined by hemes I and IV, favoring the contact between PpcA heme IV and the MacA high-potential heme. The dissociation constant values indicate the formation of a low-affinity complex between the proteins, which is consistent with the transient interaction observed in electron transfer complexes. © 2017 Federation of European Biochemical Societies.

  5. Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens

    Science.gov (United States)

    Yu, Linpeng; Yuan, Yong; Tang, Jia; Wang, Yueqiang; Zhou, Shungui

    2015-11-01

    The reductive dechlorination of pentachlorophenol (PCP) by Geobacter sulfurreducens in the presence of different biochars was investigated to understand how biochars affect the bioreduction of environmental contaminants. The results indicated that biochars significantly accelerate electron transfer from cells to PCP, thus enhancing reductive dechlorination. The promotion effects of biochar (as high as 24-fold) in this process depend on its electron exchange capacity (EEC) and electrical conductivity (EC). A kinetic model revealed that the surface redox-active moieties (RAMs) and EC of biochar (900 °C) contributed to 56% and 41% of the biodegradation rate, respectively. This work demonstrates that biochars are efficient electron mediators for the dechlorination of PCP and that both the EC and RAMs of biochars play important roles in the electron transfer process.

  6. Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens

    Science.gov (United States)

    Yu, Linpeng; Yuan, Yong; Tang, Jia; Wang, Yueqiang; Zhou, Shungui

    2015-01-01

    The reductive dechlorination of pentachlorophenol (PCP) by Geobacter sulfurreducens in the presence of different biochars was investigated to understand how biochars affect the bioreduction of environmental contaminants. The results indicated that biochars significantly accelerate electron transfer from cells to PCP, thus enhancing reductive dechlorination. The promotion effects of biochar (as high as 24-fold) in this process depend on its electron exchange capacity (EEC) and electrical conductivity (EC). A kinetic model revealed that the surface redox-active moieties (RAMs) and EC of biochar (900 °C) contributed to 56% and 41% of the biodegradation rate, respectively. This work demonstrates that biochars are efficient electron mediators for the dechlorination of PCP and that both the EC and RAMs of biochars play important roles in the electron transfer process. PMID:26592958

  7. Mechanistic stratification in electroactive biofilms of Geobacter sulfurreducens mediated by pilus nanowires

    Science.gov (United States)

    Steidl, Rebecca J.; Lampa-Pastirk, Sanela; Reguera, Gemma

    2016-08-01

    Electricity generation by Geobacter sulfurreducens biofilms grown on electrodes involves matrix-associated electron carriers, such as c-type cytochromes. Yet, the contribution of the biofilm's conductive pili remains uncertain, largely because pili-defective mutants also have cytochrome defects. Here we report that a pili-deficient mutant carrying an inactivating mutation in the pilus assembly motor PilB has no measurable defects in cytochrome expression, yet forms anode biofilms with reduced electroactivity and is unable to grow beyond a threshold distance (~10 μm) from the underlying electrode. The defects are similar to those of a Tyr3 mutant, which produces poorly conductive pili. The results support a model in which the conductive pili permeate the biofilms to wire the cells to the conductive biofilm matrix and the underlying electrode, operating coordinately with cytochromes until the biofilm reaches a threshold thickness that limits the efficiency of the cytochrome pathway but not the functioning of the conductive pili network.

  8. Unexpected specificity of interspecies cobamide transfer from Geobacter spp. to organohalide-respiring Dehalococcoides mccartyi strains.

    Science.gov (United States)

    Yan, Jun; Ritalahti, Kirsti M; Wagner, Darlene D; Löffler, Frank E

    2012-09-01

    Dehalococcoides mccartyi strains conserve energy from reductive dechlorination reactions catalyzed by corrinoid-dependent reductive dehalogenase enzyme systems. Dehalococcoides lacks the ability for de novo corrinoid synthesis, and pure cultures require the addition of cyanocobalamin (vitamin B(12)) for growth. In contrast, Geobacter lovleyi, which dechlorinates tetrachloroethene to cis-1,2-dichloroethene (cis-DCE), and the nondechlorinating species Geobacter sulfurreducens have complete sets of cobamide biosynthesis genes and produced 12.9 ± 2.4 and 24.2 ± 5.8 ng of extracellular cobamide per liter of culture suspension, respectively, during growth with acetate and fumarate in a completely synthetic medium. G. lovleyi-D. mccartyi strain BAV1 or strain FL2 cocultures provided evidence for interspecies corrinoid transfer, and cis-DCE was dechlorinated to vinyl chloride and ethene concomitant with Dehalococcoides growth. In contrast, negligible increase in Dehalococcoides 16S rRNA gene copies and insignificant dechlorination occurred in G. sulfurreducens-D. mccartyi strain BAV1 or strain FL2 cocultures. Apparently, G. lovleyi produces a cobamide that complements Dehalococcoides' nutritional requirements, whereas G. sulfurreducens does not. Interestingly, Dehalococcoides dechlorination activity and growth could be restored in G. sulfurreducens-Dehalococcoides cocultures by adding 10 μM 5',6'-dimethylbenzimidazole. Observations made with the G. sulfurreducens-Dehalococcoides cocultures suggest that the exchange of the lower ligand generated a cobalamin, which supported Dehalococcoides activity. These findings have implications for in situ bioremediation and suggest that the corrinoid metabolism of Dehalococcoides must be understood to faithfully predict, and possibly enhance, reductive dechlorination activities.

  9. Spatially resolved confocal resonant Raman microscopic analysis of anode-grown Geobacter sulfurreducens biofilms.

    Science.gov (United States)

    Lebedev, Nikolai; Strycharz-Glaven, Sarah M; Tender, Leonard M

    2014-02-03

    When grown on the surface of an anode electrode, Geobacter sulfurreducens forms a multi-cell thick biofilm in which all cells appear to couple the oxidation of acetate with electron transport to the anode, which serves as the terminal metabolic electron acceptor. Just how electrons are transported through such a biofilm from cells to the underlying anode surface over distances that can exceed 20 microns remains unresolved. Current evidence suggests it may occur by electron hopping through a proposed network of redox cofactors composed of immobile outer membrane and/or extracellular multi-heme c-type cytochromes. In the present work, we perform a spatially resolved confocal resonant Raman (CRR) microscopic analysis to investigate anode-grown Geobacter biofilms. The results confirm the presence of an intra-biofilm redox gradient whereby the probability that a heme is in the reduced state increases with increasing distance from the anode surface. Such a gradient is required to drive electron transport toward the anode surface by electron hopping via cytochromes. The results also indicate that at open circuit, when electrons are expected to accumulate in redox cofactors involved in electron transport due to the inability of the anode to accept electrons, nearly all c-type cytochrome hemes detected in the biofilm are oxidized. The same outcome occurs when a comparable potential to that measured at open circuit (-0.30 V vs. SHE) is applied to the anode, whereas nearly all hemes are reduced when an exceedingly negative potential (-0.50 V vs. SHE) is applied to the anode. These results suggest that nearly all c-type cytochrome hemes detected in the biofilm can be electrochemically accessed by the electrode, but most have oxidation potentials too negative to transport electrons originating from acetate metabolism. The results also reveal a lateral heterogeneity (x-y dimensions) in the type of c-type cytochromes within the biofilm that may affect electron transport to the

  10. Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens

    Directory of Open Access Journals (Sweden)

    Núñez Cinthia

    2009-07-01

    Full Text Available Abstract Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a taclac promoter. Combining both the microarray transcriptome analysis and the computational prediction revealed that the G. sulfurreducens RpoN controls genes involved in a wide range of cellular functions. Most importantly, RpoN controls the expression of the dcuB gene encoding the fumarate/succinate exchanger, which is essential for cell growth with fumarate as the terminal electron acceptor in G. sulfurreducens. RpoN also controls genes, which encode enzymes for both pathways of ammonia assimilation that is predicted to be essential under all growth conditions in G. sulfurreducens. Other genes that were identified as part of the RpoN regulon using either the computational prediction or the microarray transcriptome analysis included genes involved in flagella biosynthesis, pili biosynthesis and genes involved in central metabolism enzymes and cytochromes involved in extracellular electron transfer to Fe(III, which are known to be important for growth in subsurface environment or electricity production in microbial fuel cells. The consensus sequence for the predicted RpoN-regulated promoter elements is TTGGCACGGTTTTTGCT. Conclusion The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of

  11. Geobacter Project

    Energy Technology Data Exchange (ETDEWEB)

    Derek Lovley; Maddalena Coppi; Stacy Ciufo; Barbara Methe; Pablo, Pomposiello; Steve Sandler; Cinthia Nunez; Daniel Bond; Susan Childers; Carol Giometti; Julia Krushkal; Christophe Shilling; Bernard Palsson

    2004-03-17

    Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter The primary goal of this research is to develop conceptual and computational models that can describe the functioning of complex microbial communities involved in microbial processes of interest to the Department of Energy. Microbial Communities to be Investigated: (1) Microbial community associated with the in situ bioremediation of uranium-contaminated groundwater; and (2) Microbial community that is capable of harvesting energy from waste organic matter in the form of electricity.

  12. Geobacter sulfurreducens对汞的甲基化及其影响因素研究%Research on Mercury Methylation by Geobacter sulfurreducens and Its Influencing Factors

    Institute of Scientific and Technical Information of China (English)

    邹嫣; 司友斌; 颜雪; 陈艳

    2012-01-01

    在实验室模拟条件下,研究了铁还原菌Geobacter sulfurreducens对汞的甲基化作用及其影响因素.结果表明,G.sulfurreducens在低浓度汞溶液中能够生长,但生长受到一定程度的抑制,主要表现在菌株生长曲线迟缓期的延长.G.sulfurreducens在生长过程中能同时将溶液中无机汞转化为甲基汞,甲基化过程受多种环境因素的制约.在初始HgCl2浓度为1 mg.L^-1、温度35℃、pH 6.0、0.9%盐度的厌氧环境条件下,G.sulfurreducens对汞的甲基化率可达38%.适当增加HgCl2初始浓度与盐度能提高甲基汞的转化率,但过高汞浓度和盐度会造成微生物的死亡;温度在4~35℃范围内,温度越高甲基汞转化率越高;弱酸性环境比酸性或中碱性环境更利于汞的甲基化.此外,腐殖酸和半胱氨酸等均影响甲基汞的转化效率,其中腐殖酸对汞甲基化有一定的抑制作用,而半胱氨酸有较强的促进作用.该研究为自然水体生态系统中铁还原菌参与汞甲基化的过程提供了直接证据.%Mercury methylation by Geobacter sulfurreducens and the effects of environmental factors were studied under laboratory conditions.The results showed that G.sulfurreducens could grow well in the presence of low concentrations of mercuric chloride,but its growth was inhibited to a certain extent,mainly expressed in the prolonged lag phase.G.sulfurreducens could transform inorganic mercury into methylmercury,and this process was affected by many environmental factors.The efficiency of mercury methylation reached 38% under anaerobic conditions with 1 mg·L^-1 HgCl2 and 0.9% salinity at 35℃,pH 6.0.Increasing the initial HgCl2 concentration or salinity in an appropriate manner improved mercury methylation,but the concentration of methylmercury reduced when the concentrations of HgCl2 and salinity were too high.The efficiency of mercury methylation increased with the increasing temperature in range of 4-35℃.Weakly acidic

  13. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture

    OpenAIRE

    2000-01-01

    Geobacter sulfurreducens strain PCA oxidized acetate to CO2 via citric acid cycle reactions during growth with acetate plus fumarate in pure culture, and with acetate plus nitrate in coculture with Wolinella succinogenes. Acetate was activated by succinyl-CoA:acetate CoA-transferase and also via acetate kinase plus phosphotransacetylase. Citrate was formed by citrate synthase. Soluble isocitrate and malate dehydrogenases reduced NADP+ and NAD+, respectively. Oxidation of 2-oxoglutarate was me...

  14. Expression of acetate permease-like (apl) genes in subsurface communities of Geobacter species under fluctuating acetate concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Elifantz, H.; N' Guessan, L.A.; Mouser, P.J.; Williams, K H.; Wilkins, M J.; Risso, C.; Holmes, D.E.; Long, P.E.; Lovley, D.R.

    2010-03-01

    The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high acetate) weakly correlated with the acetate concentration over time, the transcript levels for this gene were relatively constant in well D08 (low acetate). At the lowest acetate concentrations during the groundwater flush, the transcript levels of aplII were the highest. The expression of aplII decreased 2-10-fold upon acetate reintroduction. However, the overall instability of acetate concentrations throughout the experiment could not support a robust conclusion regarding the role of apl genes in response to acetate limitation under field conditions, in contrast to previous chemostat studies, suggesting that the function of a microbial community cannot be inferred based on lab experiments alone.

  15. A severe reduction in the cytochrome C content of Geobacter sulfurreducens eliminates its capacity for extracellular electron transfer.

    Science.gov (United States)

    Estevez-Canales, Marta; Kuzume, Akiyoshi; Borjas, Zulema; Füeg, Michael; Lovley, Derek; Wandlowski, Thomas; Esteve-Núñez, Abraham

    2015-04-01

    The ability of Geobacter species to transfer electrons outside the cell enables them to play an important role in a number of biogeochemical and bioenergy processes. Gene deletion studies have implicated periplasmic and outer-surface c-type cytochromes in this extracellular electron transfer. However, even when as many as five c-type cytochrome genes have been deleted, some capacity for extracellular electron transfer remains. In order to evaluate the role of c-type cytochromes in extracellular electron transfer, Geobacter sulfurreducens was grown in a low-iron medium that included the iron chelator (2,2'-bipyridine) to further sequester iron. Haem-staining revealed that the cytochrome content of cells grown in this manner was 15-fold lower than in cells exposed to a standard iron-containing medium. The low cytochrome abundance was confirmed by in situ nanoparticle-enhanced Raman spectroscopy (NERS). The cytochrome-depleted cells reduced fumarate to succinate as well as the cytochrome-replete cells do, but were unable to reduce Fe(III) citrate or to exchange electrons with a graphite electrode. These results demonstrate that c-type cytochromes are essential for extracellular electron transfer by G. sulfurreducens. The strategy for growing cytochrome-depleted G. sulfurreducens will also greatly aid future physiological studies of Geobacter species and other microorganisms capable of extracellular electron transfer.

  16. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili.

    Science.gov (United States)

    Xiao, Ke; Malvankar, Nikhil S; Shu, Chuanjun; Martz, Eric; Lovley, Derek R; Sun, Xiao

    2016-03-22

    The metallic-like electrical conductivity of Geobacter sulfurreducens pili has been documented with multiple lines of experimental evidence, but there is only a rudimentary understanding of the structural features which contribute to this novel mode of biological electron transport. In order to determine if it was feasible for the pilin monomers of G. sulfurreducens to assemble into a conductive filament, theoretical energy-minimized models of Geobacter pili were constructed with a previously described approach, in which pilin monomers are assembled using randomized structural parameters and distance constraints. The lowest energy models from a specific group of predicted structures lacked a central channel, in contrast to previously existing pili models. In half of the no-channel models the three N-terminal aromatic residues of the pilin monomer are arranged in a potentially electrically conductive geometry, sufficiently close to account for the experimentally observed metallic like conductivity of the pili that has been attributed to overlapping pi-pi orbitals of aromatic amino acids. These atomic resolution models capable of explaining the observed conductive properties of Geobacter pili are a valuable tool to guide further investigation of the metallic-like conductivity of the pili, their role in biogeochemical cycling, and applications in bioenergy and bioelectronics.

  17. Importance of c-Type cytochromes for U(VI reduction by Geobacter sulfurreducens

    Directory of Open Access Journals (Sweden)

    Leang Ching

    2007-03-01

    Full Text Available Abstract Background In order to study the mechanism of U(VI reduction, the effect of deleting c-type cytochrome genes on the capacity of Geobacter sulfurreducens to reduce U(VI with acetate serving as the electron donor was investigated. Results The ability of several c-type cytochrome deficient mutants to reduce U(VI was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50–60% the ability of G. sulfurreducens to reduce U(VI. Involvement in U(VI reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI reduction. A subpopulation of both wild type and U(VI reduction-impaired cells, 24–30%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI reduction-impaired and wild type G. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III revealed no correlation between the impact of cytochrome deletion on U(VI reduction and reduction of Fe(III hydroxide and chelated Fe(III. Conclusion This study indicates that c-type cytochromes are involved in U(VI reduction by Geobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction by G. sulfurreducens but do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium

  18. Functional Role of Infective Viral Particles on Metal Reduction

    Energy Technology Data Exchange (ETDEWEB)

    Coates, John D.

    2014-04-01

    A proposed strategy for the remediation of uranium (U) contaminated sites was based on the immobilization of U by reducing the oxidized soluble U, U(VI), to form a reduced insoluble end product, U(IV). Previous studies identified Geobacter sp., including G. sulfurreducens and G. metallireducens, as predominant U(VI)-reducing bacteria under acetate-oxidizing and U(VI)-reducing conditions. Examination of the finished genome sequence annotation of the canonical metal reducing species Geobacter sulfurreducens strain PCA and G. metallireduceans strain GS-15 as well as the draft genome sequence of G. uraniumreducens strain Rf4 identified phage related proteins. In addition, the completed genome for Anaeromyxobacter dehalogenans and the draft genome sequence of Desulfovibrio desulfuricans strain G20, two more model metal-reducing bacteria, also revealed phage related sequences. The presence of these gene sequences indicated that Geobacter spp., Anaeromyxobacter spp., and Desulfovibrio spp. are susceptible to viral infection. Furthermore, viral populations in soils and sedimentary environments in the order of 6.4×10{sup 6}–2.7×10{sup 10} VLP’s cm{sup -3} have been observed. In some cases, viral populations exceed bacterial populations in these environments suggesting that a relationship may exist between viruses and bacteria. Our preliminary screens of samples collected from the ESR FRC indicated that viral like particles were observed in significant numbers. The objective of this study was to investigate the potential functional role viruses play in metal reduction specifically Fe(III) and U(VI) reduction, the environmental parameters affecting viral infection of metal reducing bacteria, and the subsequent effects on U transport.

  19. Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Callister, Stephen J.; Miletto, Marzia; Williams, Kenneth H.; Nicora, Carrie D.; Lovely, Derek R.; Long, Philip E.; Lipton, Mary S.

    2011-01-01

    Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the U.S. Department of Energy’s Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

  20. Motile Geobacter dechlorinators migrate into a model source zone of trichloroethene dense non-aqueous phase liquid: Experimental evaluation and modeling

    Science.gov (United States)

    Philips, Jo; Miroshnikov, Alexey; Haest, Pieter Jan; Springael, Dirk; Smolders, Erik

    2014-12-01

    Microbial migration towards a trichloroethene (TCE) dense non-aqueous phase liquid (DNAPL) could facilitate the bioaugmentation of TCE DNAPL source zones. This study characterized the motility of the Geobacter dechlorinators in a TCE to cis-dichloroethene dechlorinating KB-1™ subculture. No chemotaxis towards or away from TCE was found using an agarose in-plug bridge method. A second experiment placed an inoculated aqueous layer on top of a sterile sand layer and showed that Geobacter migrated several centimeters in the sand layer in just 7 days. A random motility coefficient for Geobacter in water of 0.24 ± 0.02 cm2·day- 1 was fitted. A third experiment used a diffusion-cell setup with a 5.5 cm central sand layer separating a DNAPL from an aqueous top layer as a model source zone to examine the effect of random motility on TCE DNAPL dissolution. With top layer inoculation, Geobacter quickly colonized the sand layer, thereby enhancing the initial TCE DNAPL dissolution flux. After 19 days, the DNAPL dissolution enhancement was only 24% lower than with an homogenous inoculation of the sand layer. A diffusion-motility model was developed to describe dechlorination and migration in the diffusion-cells. This model suggested that the fast colonization of the sand layer by Geobacter was due to the combination of random motility and growth on TCE.

  1. Development of a biomarker for Geobacter activity and strain composition; proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI).

    Science.gov (United States)

    Wilkins, Michael J; Callister, Stephen J; Miletto, Marzia; Williams, Kenneth H; Nicora, Carrie D; Lovley, Derek R; Long, Philip E; Lipton, Mary S

    2011-01-01

    Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

  2. Development of a biomarker for Geobacter activity and strain composition: Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI)

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, M.J.; Callister, S.J.; Miletto, M.; Williams, K.H.; Nicora, C.D.; Lovley, D.R.; Long, P.E.; Lipton, M.S.

    2010-02-15

    Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired outcomes.

  3. Nanowires, Capacitors, and Other Novel Outer-Surface Components Involved in Electron Transfer to Fe(III) Oxides in Geobacter Species

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek, R.

    2008-12-22

    The overall goal of this project was to better understand the mechanisms by which Geobacter species transfer electrons outside the cell onto Fe(III) oxides. The rationale for this study was that Geobacter species are often the predominant microorganisms involved in in situ uranium bioremediation and the growth and activity of the Geobacter species during bioremediation is primarily supported by electron transfer to Fe(III) oxides. These studies greatly expanded the understanding of electron transfer to Fe(III). Novel concepts developed included the potential role of microbial nanowires for long range electron transfer in Geobacter species and the importance of extracytoplasmic cytochromes functioning as capacitors to permit continued electron transfer during the hunt for Fe(III) oxide. Furthermore, these studies provided target sequences that were then used in other studies to tract the activity of Geobacter species in the subsurface through monitoring the abundance of gene transcripts of the target genes. A brief summary of the major accomplishments of the project is provided.

  4. Diving into the redox properties of Geobacter sulfurreducens cytochromes: a model for extracellular electron transfer.

    Science.gov (United States)

    Santos, Telma C; Silva, Marta A; Morgado, Leonor; Dantas, Joana M; Salgueiro, Carlos A

    2015-05-28

    Geobacter bacteria have a remarkable respiratory versatility that includes the dissimilatory reduction of insoluble metal oxides in natural habitats and electron transfer to electrode surfaces from which electricity can be harvested. In both cases, electrons need to be exported from the cell interior to the exterior via a mechanism designated as extracellular electron transfer (EET). Several c-type cytochromes from G. sulfurreducens (Gs) were identified as key players in this process. Biochemical and biophysical data have been obtained for ten Gs cytochromes, including inner-membrane associated (MacA), periplasmic (PpcA, PpcB, PpcC, PpcD, PpcE and GSU1996) and outer membrane-associated (OmcF, OmcS and OmcZ). The redox properties of these cytochromes have been determined, except for PpcC and GSU1996. In this perspective, the reduction potentials of these two cytochromes were determined by potentiometric redox titrations followed by visible spectroscopy. The data obtained are taken together with those available for other key cytochromes to present a thorough overview of the current knowledge of Gs EET mechanisms and provide a possible rationalization for the existence of several multiheme cytochromes involved in the same respiratory pathways.

  5. High resolution AFM and single cell resonance Raman spectroscopy of Geobacter sulfurreducens biofilms early in growth.

    Directory of Open Access Journals (Sweden)

    Nikolai eLebedev

    2014-08-01

    Full Text Available AFM and confocal resonance Raman microscopy (CRRM of single-cells were used to study the transition of anode-grown Geobacter sulfurreducens biofilms from lag phase (initial period of low current to exponential phase (subsequent period of rapidly increasing current. Results reveal that lag phase biofilms consist of lone cells and tightly packed single-cell thick clusters crisscrossed with extracellular linear structures that appear to be comprised of nodules approximately 20 nm in diameter aligned end to end. By early exponential phase cell clusters expand laterally and a second layer of closely packed cells begins to form on top of the first. Abundance of c-type cytochromes (c-Cyt is > 3-fold greater in 2-cell thick regions than in 1-cell thick regions. The results indicate that early biofilm growth involves two transformations. The first is from lone cells to 2-dimensionally associated cells during lag phase when current remains low. This is accompanied by formation of extracellular linear structures. The second is from 2- to 3-dimensionally associated cells during early exponential phase when current begins to increases rapidly. This is accompanied by a dramatic increase in c-Cyt abundance.

  6. Microbial reduction of Fe(III) in hematite nanoparticles by Geobacter sulfurreducens.

    Science.gov (United States)

    Yan, Beizhan; Wrenn, Brian A; Basak, Soubir; Biswas, Pratim; Giammar, Daniel E

    2008-09-01

    The rates of microbial Fe(III) reduction of three sizes of hematite nanoparticles by Geobacter sulfurreducens were measured under two H2 partial pressures (0.01 and 1 atm) and three pH (7.0, 7.5, and 8.0) conditions. Hematite particles with mean primary particle sizes of 10, 30, and 50 nm were synthesized by a novel aerosol method that allows tight control of the particle size distribution. The mass-normalized reduction rates of the 10 and 30 nm particles were comparable to each other and higher than the rate for the 50 nm particles. However, the surface area-normalized rate was highest for the 30 nm particles. Consistent with a previously published model, the reduction rates are likely to be proportional to the bacteria-hematite contact area and not to the total hematite surface area. Surface area-normalized iron reduction rates were higher than those reported in previous studies, which may be due to the sequestration of Fe(II) through formation of vivianite. Similar initial reduction rates were observed under all pH and H2 conditions studied.

  7. Control of nanoparticle size, reactivity and magnetic properties during the bioproduction of magnetite by Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Byrne, J. M.; Telling, N. D.; Coker, V. S.; Pattrick, R. A. D.; Laan, G. van der; Arenholz, E.; Tuna, F.; Lloyd, J. R.

    2011-08-02

    The bioproduction of nano-scale magnetite by Fe(III)-reducing bacteria offers a potentially tunable, environmentally benign route to magnetic nanoparticle synthesis. Here, we demonstrate that it is possible to control the size of magnetite nanoparticles produced by Geobacter sulfurreducens, by adjusting the total biomass introduced at the start of the process. The particles have a narrow size distribution and can be controlled within the range of 10-50 nm. X-ray diffraction analysis indicates that controlled production of a number of different biominerals is possible via this method including goethite, magnetite and siderite, but their formation is strongly dependent upon the rate of Fe(III) reduction and total concentration and rate of Fe(II) produced by the bacteria during the reduction process. Relative cation distributions within the structure of the nanoparticles has been investigated by X-ray magnetic circular dichroism and indicates the presence of a highly reduced surface layer which is not observed when magnetite is produced through abiotic methods. The enhanced Fe(II)-rich surface, combined with small particle size, has important environmental applications such as in the reductive bioremediation of organics, radionuclides and metals. In the case of Cr(VI), as a model high-valence toxic metal, optimised biogenic magnetite is able to reduce and sequester the toxic hexavalent chromium very efficiently in the less harmful trivalent form.

  8. Control of nanoparticle size, reactivity and magnetic properties during the bioproduction of magnetite by Geobacter sulfurreducens.

    Science.gov (United States)

    Byrne, J M; Telling, N D; Coker, V S; Pattrick, R A D; van der Laan, G; Arenholz, E; Tuna, F; Lloyd, J R

    2011-11-11

    The bioproduction of nanoscale magnetite by Fe(III)-reducing bacteria offers a potentially tunable, environmentally benign route to magnetic nanoparticle synthesis. Here, we demonstrate that it is possible to control the size of magnetite nanoparticles produced by Geobacter sulfurreducens by adjusting the total biomass introduced at the start of the process. The particles have a narrow size distribution and can be controlled within the range of 10-50 nm. X-ray diffraction analysis indicates that controlled production of a number of different biominerals is possible via this method including goethite, magnetite and siderite, but their formation is strongly dependent upon the rate of Fe(III) reduction and total concentration and rate of Fe(II) produced by the bacteria during the reduction process. Relative cation distributions within the structure of the nanoparticles have been investigated by x-ray magnetic circular dichroism and indicate the presence of a highly reduced surface layer which is not observed when magnetite is produced through abiotic methods. The enhanced Fe(II)-rich surface, combined with small particle size, has important environmental applications such as in the reductive bioremediation of organics, radionuclides and metals. In the case of Cr(VI), as a model high-valence toxic metal, optimized biogenic magnetite is able to reduce and sequester the toxic hexavalent chromium very efficiently to the less harmful trivalent form.

  9. Geobacter strains that use alternate organic compounds, methods of making, and methods of use thereof

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R.; Summers, Zarath Morgan; Haveman, Shelley Annette; Izallalen, Mounir

    2016-03-01

    In preferred embodiments, the present invention provides new isolated strains of a Geobacter species that are capable of using a carbon source that is selected from C.sub.3 to C.sub.12 organic compounds selected from pyruvate or metabolic precursors of pyruvate as an electron donor in metabolism and in subsequent energy production. The wild type strain of the microorganisms has been shown to be unable to use these C.sub.3 to C.sub.12 organic compounds as electron donors. The inventive strains of microorganisms are useful for improving bioremediation applications, including in situ bioremediation (including uranium bioremediation and halogenated solvent bioremediation), microbial fuel cells, power generation from small and large-scale waste facilities (e.g., biomass waste from dairy, agriculture, food processing, brewery, or vintner industries, etc.) using microbial fuel cells, and other applications of microbial fuel cells, including, but not limited to, improved electrical power supplies for environmental sensors, electronic devices, and electric vehicles.

  10. Control of nanoparticle size, reactivity and magnetic properties during the bioproduction of magnetite by Geobacter sulfurreducens

    Science.gov (United States)

    Byrne, J. M.; Telling, N. D.; Coker, V. S.; Pattrick, R. A. D.; van der Laan, G.; Arenholz, E.; Tuna, F.; Lloyd, J. R.

    2011-11-01

    The bioproduction of nanoscale magnetite by Fe(III)-reducing bacteria offers a potentially tunable, environmentally benign route to magnetic nanoparticle synthesis. Here, we demonstrate that it is possible to control the size of magnetite nanoparticles produced by Geobacter sulfurreducens by adjusting the total biomass introduced at the start of the process. The particles have a narrow size distribution and can be controlled within the range of 10-50 nm. X-ray diffraction analysis indicates that controlled production of a number of different biominerals is possible via this method including goethite, magnetite and siderite, but their formation is strongly dependent upon the rate of Fe(III) reduction and total concentration and rate of Fe(II) produced by the bacteria during the reduction process. Relative cation distributions within the structure of the nanoparticles have been investigated by x-ray magnetic circular dichroism and indicate the presence of a highly reduced surface layer which is not observed when magnetite is produced through abiotic methods. The enhanced Fe(II)-rich surface, combined with small particle size, has important environmental applications such as in the reductive bioremediation of organics, radionuclides and metals. In the case of Cr(VI), as a model high-valence toxic metal, optimized biogenic magnetite is able to reduce and sequester the toxic hexavalent chromium very efficiently to the less harmful trivalent form.

  11. Unraveling the electron transfer processes of a nanowire protein from Geobacter sulfurreducens.

    Science.gov (United States)

    Alves, Mónica N; Fernandes, Ana P; Salgueiro, Carlos A; Paquete, Catarina M

    2016-01-01

    The extracellular electron transfer metabolism of Geobacter sulfurreducens is sustained by several multiheme c-type cytochromes. One of these is the dodecaheme cytochrome GSU1996 that belongs to a new sub-class of c-type cytochromes. GSU1996 is composed by four similar triheme domains (A–D). The C-terminal half of the molecule encompasses the domains C and D, which are connected by a small linker and the N-terminal half of the protein contains two domains (A and B) that form one structural unit. It was proposed that this protein works as an electrically conductive device in G. sulfurreducens, transferring electrons within the periplasm or to outer-membrane cytochromes. In this work, a novel strategy was applied to characterize in detail the thermodynamic and kinetic properties of the hexaheme fragment CD of GSU1996. This characterization revealed the electron transfer process of GSU1996 for the first time, showing that a heme at the edge of the C-terminal of the protein is thermodynamic and kinetically competent to receive electrons from physiological redox partners. This information contributes towards understanding how this new sub-class of cytochromes functions as nanowires, and also increases the current knowledge of the extracellular electron transfer mechanisms in G. sulfurreducens.

  12. Relevance of Aromatic Amino Acids for Electron Conduction along Geobacter Pili Protein

    Science.gov (United States)

    Adhikari, Ramesh; Malvankar, Nikhil; Tuominen, Mark; Lovley, Derek

    It has been proposed that the charge transport though Geobacter sulfurreducens pili protein occurs through the aromatic amino acids forming helical conducting chain within pili. X-ray studies of pili show that the aromatic amino acids are packed close enough (3-4 Å) for pi-stacking to occur. Conductivity of the pili network increases with lowering temperature indicating metallic-like transport mechanism. However due to the complexity of charge percolation path in 3D network, the intrinsic conductivity of an individual pili was not known. Here, we report transport measurements of individual pili of G. sulfurreducens. The conductivity, similar to that of organic polymers, shows that the pili may have implications in materials research. In addition, the conductivity value is sufficient to explain the respiration rate of the G. sulfurreducens. Further studies of pili from different natural and genetically modified species with varying amount of aromatic amino acid density demonstrate that it can play a decisive role on the magnitude of the conductivity. This research was supported by the Office of Naval Research (ONR) and National Science Foundation (NSF) Center for Hierarchical Manufacturing (CHM). Nikhil S. Malvankar holds a Career Award from the Burroughs Wellcome Fund.

  13. Structure of the type IVa major pilin from the electrically conductive bacterial nanowires of Geobacter sulfurreducens.

    Science.gov (United States)

    Reardon, Patrick N; Mueller, Karl T

    2013-10-11

    Several species of δ proteobacteria are capable of reducing insoluble metal oxides as well as other extracellular electron acceptors. These bacteria play a critical role in the cycling of minerals in subsurface environments, sediments, and groundwater. In some species of bacteria such as Geobacter sulfurreducens, the transport of electrons is proposed to be facilitated by filamentous fibers that are referred to as bacterial nanowires. These nanowires are polymeric assemblies of proteins belonging to the type IVa family of pilin proteins and are mainly comprised of one subunit protein, PilA. Here, we report the high resolution solution NMR structure of the PilA protein from G. sulfurreducens determined in detergent micelles. The protein is >85% α-helical and exhibits similar architecture to the N-terminal regions of other non-conductive type IVa pilins. The detergent micelle interacts with the first 21 amino acids of the protein, indicating that this region likely associates with the bacterial inner membrane prior to fiber formation. A model of the G. sulfurreducens pilus fiber is proposed based on docking of this structure into the fiber model of the type IVa pilin from Neisseria gonorrhoeae. This model provides insight into the organization of aromatic amino acids that are important for electrical conduction.

  14. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

  15. Crystallographic orientation and electrode nature are key factors for electric current generation by Geobacter sulfurreducens.

    Science.gov (United States)

    Maestro, Beatriz; Ortiz, Juan M; Schrott, Germán; Busalmen, Juan P; Climent, Víctor; Feliu, Juan M

    2014-08-01

    We have investigated the influence of electrode material and crystallographic structure on electron transfer and biofilm formation of Geobacter sulfurreducens. Single-crystal gold-Au(110), Au(111), Au(210)-and platinum-Pt(100), Pt(110), Pt(111), Pt(210)-electrodes were tested and compared to graphite rods. G. sulfurreducens electrochemically interacts with all these materials with different attachment kinetics and final current production, although redox species involved in the electron transfer to the anode are virtually the same in all cases. Initial bacterial colonization was fastest on graphite up to the monolayer level, whereas gold electrodes led to higher final current densities. Crystal geometry was shown to have an important influence, with Au(210) sustaining a current density of up to 1442±101μAcm(-2) at the steady state, over Au(111) with 961±94μAcm(-2) and Au(110) with 944±89μAcm(-2). On the other hand, the platinum electrodes displayed the lowest performances, including Pt(210). Our results indicate that both crystal geometry and electrode material are key parameters for the efficient interaction of bacteria with the substrate and should be considered for the design of novel materials and microbial devices to optimize energy production.

  16. Scale-up of the production of highly reactive biogenic magnetite nanoparticles using Geobacter sulfurreducens.

    Science.gov (United States)

    Byrne, J M; Muhamadali, H; Coker, V S; Cooper, J; Lloyd, J R

    2015-06-06

    Although there are numerous examples of large-scale commercial microbial synthesis routes for organic bioproducts, few studies have addressed the obvious potential for microbial systems to produce inorganic functional biomaterials at scale. Here we address this by focusing on the production of nanoscale biomagnetite particles by the Fe(III)-reducing bacterium Geobacter sulfurreducens, which was scaled up successfully from laboratory- to pilot plant-scale production, while maintaining the surface reactivity and magnetic properties which make this material well suited to commercial exploitation. At the largest scale tested, the bacterium was grown in a 50 l bioreactor, harvested and then inoculated into a buffer solution containing Fe(III)-oxyhydroxide and an electron donor and mediator, which promoted the formation of magnetite in under 24 h. This procedure was capable of producing up to 120 g of biomagnetite. The particle size distribution was maintained between 10 and 15 nm during scale-up of this second step from 10 ml to 10 l, with conserved magnetic properties and surface reactivity; the latter demonstrated by the reduction of Cr(VI). The process presented provides an environmentally benign route to magnetite production and serves as an alternative to harsher synthetic techniques, with the clear potential to be used to produce kilogram to tonne quantities.

  17. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP.

    Science.gov (United States)

    Kellenberger, Colleen A; Wilson, Stephen C; Hickey, Scott F; Gonzalez, Tania L; Su, Yichi; Hallberg, Zachary F; Brewer, Thomas F; Iavarone, Anthony T; Carlson, Hans K; Hsieh, Yu-Fang; Hammond, Ming C

    2015-04-28

    Cyclic dinucleotides are an expanding class of signaling molecules that control many aspects of bacterial physiology. A synthase for cyclic AMP-GMP (cAG, also referenced as 3'-5', 3'-5' cGAMP) called DncV is associated with hyperinfectivity of Vibrio cholerae but has not been found in many bacteria, raising questions about the prevalence and function of cAG signaling. We have discovered that the environmental bacterium Geobacter sulfurreducens produces cAG and uses a subset of GEMM-I class riboswitches (GEMM-Ib, Genes for the Environment, Membranes, and Motility) as specific receptors for cAG. GEMM-Ib riboswitches regulate genes associated with extracellular electron transfer; thus cAG signaling may control aspects of bacterial electrophysiology. These findings expand the role of cAG beyond organisms that harbor DncV and beyond pathogenesis to microbial geochemistry, which is important to environmental remediation and microbial fuel cell development. Finally, we have developed an RNA-based fluorescent biosensor for live-cell imaging of cAG. This selective, genetically encodable biosensor will be useful to probe the biochemistry and cell biology of cAG signaling in diverse bacteria.

  18. Mass transfer studies of Geobacter sulfurreducens biofilms on rotating disk electrodes.

    Science.gov (United States)

    Babauta, Jerome T; Beyenal, Haluk

    2014-02-01

    Electrochemical impedance spectroscopy has received significant attention recently as a method to measure electrochemical parameters of Geobacter sulfurreducens biofilms. Here, we use electrochemical impedance spectroscopy to demonstrate the effect of mass transfer processes on electron transfer by G. sulfurreducens biofilms grown in situ on an electrode that was subsequently rotated. By rotating the biofilms up to 530 rpm, we could control the microscale gradients formed inside G. sulfurreducens biofilms. A 24% increase above a baseline of 82 µA could be achieved with a rotation rate of 530 rpm. By comparison, we observed a 340% increase using a soluble redox mediator (ferrocyanide) limited by mass transfer. Control of mass transfer processes was also used to quantify the change in biofilm impedance during the transition from turnover to non-turnover. We found that only one element of the biofilm impedance, the interfacial resistance, changed significantly from 900 to 4,200 Ω under turnover and non-turnover conditions, respectively. We ascribed this change to the electron transfer resistance overcome by the biofilm metabolism and estimate this value as 3,300 Ω. Additionally, under non-turnover, the biofilm impedance developed pseudocapacitive behavior indicative of bound redox mediators. Pseudocapacitance of the biofilm was estimated at 740 µF and was unresponsive to rotation of the electrode. The increase in electron transfer resistance and pseudocapacitive behavior under non-turnover could be used as indicators of acetate limitations inside G. sulfurreducens biofilms.

  19. Geobacter strains that use alternate organic compounds, methods of making, and methods of use thereof

    Science.gov (United States)

    Lovley, Derek R; Summers, Zarath Morgan; Haveman, Shelley Annette; Izallalen, Mounir

    2013-12-03

    In preferred embodiments, the present invention provides new isolated strains of Geobacter species that are capable of using a carbon source that is selected from C.sub.3 to C.sub.12 organic compounds selected from pyruvate or metabolic precursors of pyruvate as an electron donor in metabolism and in subsequent energy production. In other aspects, other preferred embodiments of the present invention include methods of making such strains and methods of using such strains. In general, the wild type strain of the microorganisms has been shown to be unable to use these C.sub.3 to C.sub.12 organic compounds as electron donors in metabolic steps such as the reduction of metallic ions. The inventive strains of microorganisms are useful improving bioremediation applications, including in situ bioremediation (including uranium bioremediation and halogenated solvent bioremediation), microbial fuel cells, power generation from small and large-scale waste facilities (e.g., biomass waste from dairy, agriculture, food processing, brewery, or vintner industries, etc.) using microbial fuel cells, and other applications of microbial fuel cells, including, but not limited to, improved electrical power supplies for environmental sensors, electronic sensors, and electric vehicles.

  20. Metabolic efficiency of Geobacter sulfurreducens growing on anodes with different redox potentials.

    Science.gov (United States)

    Bosch, Julian; Lee, Keun-Young; Hong, Siang-Fu; Harnisch, Falk; Schröder, Uwe; Meckenstock, Rainer U

    2014-06-01

    Microorganisms respiring Fe(III) in the environment face a range of redox potentials of the prospective terminal ferric electron acceptors, because Fe(III) can be present in different minerals or organic complexes. We investigated the adaptation of Geobacter sulfurreducens to this range by exposing the bacteria to different redox potentials between the electron donor acetate and solid, extracellular anodes in a microbial fuel-cell set-up. Over a range of anode potentials from -0.105 to +0.645 V versus standard hydrogen electrode, G. sulfurreducens produced identical amounts of biomass per electron respired. This indicated that the organism cannot utilize higher available energies for energy conservation to ATP, and confirmed recent studies. Either the high potentials cannot be used due to physiological limitations, or G. sulfurreducens decreased its metabolic efficiency, and less biomass per unit of energy was produced. In this case, G. sulfurreducens "wasted" energy at high-potential differences, most likely as heat to fuel growth kinetics.

  1. Structure of the Type IVa Major Pilin from the Electrically Conductive Bacterial Nanowires of Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Reardon, Patrick N.; Mueller, Karl T.

    2013-10-11

    Several species of bacteria are capable of reducing insoluble metal oxides as well as other extracellular electron acceptors. These bacteria play a critical role in the cycling of minerals in subsurface environments, sediments, and groundwater. In some species of bacteria, such as Geobacter sulfurreducens, the transport of electrons is facilitated by filamentous fibers that are referred to as bacterial nanowires. These nanowires belong to the type IVa family of pilin proteins and are mainly comprised of one subunit protein, PilA. Here, we report the high resolution solution nuclear magnetic resonance (NMR) structure of the PilA protein from G. sulfurreducens determined in detergent micelles. The protein is over 85% α-helical and exhibits similar architecture to the N-terminal regions of other non-conductive type IVa pilins. The detergent micelle interacts with the first 21 amino acids of the protein, indicating that this region likely associates with the bacterial inner membrane prior to fiber formation. A model of the G. sulfurreducens pilus fiber is proposed based on docking of this structure into the fiber model of the type IVa pilin from Neisseria gonorrhoeae. This model provides insight into the organization of aromatic amino acids that are important for electrical conduction.

  2. Inocula selection in microbial fuel cells based on anodic biofilm abundance of Geobacter sulfurreducens

    Institute of Scientific and Technical Information of China (English)

    Guotao Sun; Diogo de Sacadura Rodrigues; Anders Thygesen; Geoffrey Daniel; Dinesh Fernando; Anne S Meyer

    2016-01-01

    Microbial fuel cells (MFCs) rely on microbial conversion of organic substrates to electricity. The optimal perfor-mance depends on the establishment of a microbial community rich in electrogenic bacteria. Usual y this micro-bial community is established from inoculation of the MFC anode chamber with naturally occurring mixed inocula. In this study, the electrochemical performance of MFCs and microbial community evolution were eval-uated for three inocula including domestic wastewater (DW), lake sediment (LS) and biogas sludge (BS) with varying substrate loading (Lsub) and external resistance (Rext) on the MFC. The electrogenic bacterium Geobacter sulfurreducens was identified in al inocula and its abundance during MFC operation was positively linked to the MFC performance. The LS inoculated MFCs showed highest abundance (18%± 1%) of G. sulfurreducens, maximum current density [Imax=(690 ± 30) mA·m−2] and coulombic efficiency (CE=29%± 1%) with acetate as the substrate. Imax and CE increased to (1780 ± 30) mA·m−2 and 58%± 1%, respectively, after decreasing the Rext from 1000Ωto 200Ω, which also correlated to a higher abundance of G. sulfurreducens (21%± 0.7%) on the MFC anodic biofilm. The data obtained contribute to understanding the microbial community response to Lsub and Rext for optimizing electricity generation in MFCs.

  3. High methylation rates of mercury bound to cysteine by Geobacter sulfurreducens

    Science.gov (United States)

    Schaefer, Jeffra K.; Morel, François M. M.

    2009-02-01

    Methylmercury bioaccumulates in aquatic food chains and is able to cross the blood-brain barrier, making this organometallic compound a much more worrisome pollutant than inorganic mercury. We know that methylation of inorganic mercury is carried out by microbes in the anoxic layers of sediments and water columns, but the factors that control the extent of this methylation are poorly known. Mercury methylation is generally thought to be catalysed accidentally by some methylating enzyme, and it has been suggested that cellular mercury uptake results from passive diffusion of neutral mercury complexes. Here, we show that mercury methylation by the bacterium Geobacter sulfurreducens is greatly enhanced in the presence of low concentrations of the amino acid cysteine. The formation of a mercury-cysteine complex promotes both the uptake of inorganic mercury by the bacteria and the enzymatic formation of methylmercury, which is subsequently released to the external medium. Our results suggest that mercury uptake and methylation by microbes are controlled more tightly by biological mechanisms than previously thought, and that the formation of specific mercury complexes in anoxic waters modulates the efficiency of the microbial methylation of mercury.

  4. Light/electricity conversion by defined cocultures of Chlamydomonas and Geobacter.

    Science.gov (United States)

    Nishio, Koichi; Hashimoto, Kazuhito; Watanabe, Kazuya

    2013-04-01

    Biological energy-conversion systems are attractive in terms of their self-organizing and self-sustaining properties and are expected to be applied towards environmentally friendly bioenergy processes. Recent studies have demonstrated that sustainable light/electricity-conversion systems, termed microbial solar cells (MSCs), can be constructed using naturally occurring microbial communities. To better understand the energy-conversion mechanisms in microbial communities, the present study attempted to construct model MSCs comprised of defined cocultures of a green alga, Chlamydomonas reinhardtii, and an iron-reducing bacterium, Geobacter sulfurreducens, and examined their metabolism and interactions in MSCs. When MSC bioreactors were inoculated with these microbes and irradiated on a 12-h light/dark cycle, periodic current was generated in the dark with energy-conversion efficiencies of 0.1%. Metabolite analyses revealed that G. sulfurreducens generated current by oxidizing formate that was produced by C. reinhardtii in the dark. These results demonstrate that the light/electricity conversion occurs via syntrophic interactions between phototrophs and electricity-generating bacteria. Based on the results and data in literatures, it is estimated that the excretion of organics by the phototroph was the bottleneck step in the syntrophic light/electricity conversion. We also discuss differences between natural-community and defined-coculture MSCs.

  5. Enhancing factors of electricity generation in a microbial fuel cell using Geobacter sulfurreducens.

    Science.gov (United States)

    Kim, Mi-Sun; Cha, Jaehwan; Kim, Dong-Hoon

    2012-10-01

    In this study, we investigated various cultural and operational factors to enhance electricity generation in a microbial fuel cell (MFC) using Geobacter sulfurreducens. The pure culture of G. sulfurreducens was cultivated using various substrates including acetate, malate, succinate, and butyrate, with fumarate as an electron acceptor. Cell growth was observed only in acetate-fed medium, when the cell concentrations increased 4-fold for 3 days. A high acetate concentration suppressed electricity generation. As the acetate concentration was increased from 5 to 20 mM, the power density dropped from 16 to 13 mW/m2, whereas the coulombic efficiency (CE) declined by about half. The immobilization of G. sulfurreducens on the anode considerably reduced the enrichment period from 15 to 7 days. Using argon gas to create an anaerobic condition in the anode chamber led to increased pH, and electricity generation subsequently dropped. When the plain carbon paper cathode was replaced by Pt-coated carbon paper (0.5 mg Pt/cm2), the CE increased greatly from 39% to 83%.

  6. Reduction of palladium and production of nano-catalyst by Geobacter sulfurreducens.

    Science.gov (United States)

    Pat-Espadas, Aurora M; Razo-Flores, Elías; Rangel-Mendez, J Rene; Cervantes, Francisco J

    2013-11-01

    The present study is the first report on the ability of Geobacter sulfurreducens PCA to reduce Pd(II) and produce Pd(0) nano-catalyst, using acetate as electron donor at neutral pH (7.0 ± 0.1) and 30 °C. The microbial production of Pd(0) nanoparticles (NPs) was greatly enhanced by the presence of the redox mediator, anthraquinone-2,6-disulfonate (AQDS) when compared with controls lacking AQDS and cell-free controls. A cell dry weight (CDW) concentration of 800 mg/L provided a larger surface area for Pd(0) NPs deposition than a CDW concentration of 400 mg/L. Sample analysis by transmission electron microscopy revealed the formation of extracellular Pd(0) NPs ranging from 5 to 15 nm and X-ray diffraction confirmed the Pd(0) nature of the nano-catalyst produced. The present findings open the possibility for a new alternative to synthesize Pd(0) nano-catalyst and the potential application for microbial metal recovery from metal-containing waste streams.

  7. Direct and quinone-mediated palladium reduction by Geobacter sulfurreducens: mechanisms and modeling.

    Science.gov (United States)

    Pat-Espadas, Aurora M; Razo-Flores, Elías; Rangel-Mendez, J Rene; Cervantes, Francisco J

    2014-01-01

    Palladium(II) reduction to Pd(0) nanoparticles by Geobacter sulfurreducens was explored under conditions of neutral pH, 30 °C and concentrations of 25, 50, and 100 mg of Pd(II)/L aiming to investigate the effect of solid species of palladium on their microbial reduction. The influence of anthraquinone-2,6-disulfonate was reported to enhance the palladium reaction rate in an average of 1.7-fold and its addition is determining to achieve the reduction of solid species of palladium. Based on the obtained results two mechanisms are proposed: (1) direct, which is fully described considering interactions of amide, sulfur, and phosphoryl groups associated to proteins from bacteria on palladium reduction reaction, and (2) quinone-mediated, which implies multiheme c-type cytochromes participation. Speciation analysis and kinetic results were considered and integrated into a model to fit the experimental data that explain both mechanisms. This work provides elements for a better understanding of direct and quinone-mediated palladium reduction by G. sulfurreducens, which could facilitate metal recovery with concomitant formation of valuable palladium nanoparticles in industrial processes.

  8. Investigating different mechanisms for biogenic selenite transformations: Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica

    Science.gov (United States)

    Pearce, C.I.; Pattrick, R.A.D.; Law, N.; Charnock, J.M.; Coker, V.S.; Fellowes, J.W.; Oremland, R.S.; Lloyd, J.R.

    2009-01-01

    The metal-reducing bacteria Geobacter sulfurreducens, Shewanella oneidensis and Veillonella atypica, use different mechanisms to transform toxic, bioavailable sodium selenite to less toxic, non-mobile elemental selenium and then to selenide in anaerobic environments, offering the potential for in situ and ex situ bioremediation of contaminated soils, sediments, industrial effluents, and agricultural drainage waters. The products of these reductive transformations depend on both the organism involved and the reduction conditions employed, in terms of electron donor and exogenous extracellular redox mediator. The intermediary phase involves the precipitation of elemental selenium nanospheres and the potential role of proteins in the formation of these structures is discussed. The bionanomineral phases produced during these transformations, including both elemental selenium nanospheres and metal selenide nanoparticles, have catalytic, semiconducting and light-emitting properties, which may have unique applications in the realm of nanophotonics. This research offers the potential to combine remediation of contaminants with the development of environmentally friendly manufacturing pathways for novel bionanominerals. ?? 2009 Taylor & Francis.

  9. Structural and biochemical characterization of DHC2, a novel diheme cytochrome c from Geobacter sulfurreducens.

    Science.gov (United States)

    Heitmann, Daniel; Einsle, Oliver

    2005-09-20

    Multiheme cytochromes c constitute a widespread class of proteins with essential functions in electron transfer and enzymatic catalysis. Their functional properties are in part determined by the relative arrangement of multiple heme cofactors, which in many cases have been found to pack in conserved interaction motifs. Understanding the significance of these motifs is crucial for the elucidation of the highly optimized properties of multiheme cytochromes c, but their spectroscopic investigation is often hindered by the large number and efficient coupling of the individual centers and the limited availability of recombinant protein material. We have identified a diheme cytochrome c, DHC2, from the metal-reducing soil bacterium Geobacter sulfurreducens and determined its crystal structure by the method of multiple-wavelength anomalous dispersion (MAD). The two heme groups of DHC2 pack into one of the typical heme interaction motifs observed in larger multiheme cytochromes, but because of the absence of further, interfering cofactors, the properties of this heme packing motif can be conveniently studied in detail. Spectroscopic properties (UV-vis and EPR) of the protein are typical for cytochromes containing low-spin Fe(III) centers with bis-histidinyl coordination. Midpoint potentials for the two heme groups have been determined to be -135 and -289 mV by potentiometric redox titrations. DHC2 has been produced by recombinant expression in Escherichia coli using the accessory plasmid pEC86 and is therefore accessible for systematic mutational studies in further investigating the properties of heme packing interactions in cytochromes c.

  10. Use of a small overpotential approximation to analyze Geobacter sulfurreducens biofilm impedance

    Science.gov (United States)

    Babauta, Jerome T.; Beyenal, Haluk

    2017-07-01

    The electrochemical impedance of Geobacter sulfurreducens biofilms reflects the extracellular electron transfer mechanisms determining the rate of current output. Binned into two characteristic parameters, conductance and capacitance, biofilm impedance has received significant attention. The goal of this study was to evaluate a small overpotential approximation for extracellular electron transfer in G. sulfurreducens biofilms. Our motivation was to determine whether conductance over biofilm growth behaved linearly with respect to limiting current. Biofilm impedance was tracked during growth using electrochemical impedance spectroscopy (EIS) and electrochemical quartz crystal microbalance (eQCM). We showed that normalization of the biofilm impedance is useful for characterizing the changes during growth. When the conductance and capacitance were compared to the biofilm current, we found that: 1) conductance had a linear response and 2) constant phase elements (CPE) had a saturating response that coincided with the limiting current. We provided a framework using a simple iV relationship that predicted the conductance-current slope to be 9.57 V-1. CPEs showed more variability across biofilm replicates than conductance values. Although G. sulfurreducens biofilms were used here, other electrochemically active biofilms exhibiting catalytic waves could be studied using the same methods.

  11. Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens.

    Directory of Open Access Journals (Sweden)

    Daniel Segura

    2008-02-01

    Full Text Available Previous model-based analysis of the metabolic network of Geobacter sulfurreducens suggested the existence of several redundant pathways. Here, we identified eight sets of redundant pathways that included redundancy for the assimilation of acetate, and for the conversion of pyruvate into acetyl-CoA. These equivalent pathways and two other sub-optimal pathways were studied using 5 single-gene deletion mutants in those pathways for the evaluation of the predictive capacity of the model. The growth phenotypes of these mutants were studied under 12 different conditions of electron donor and acceptor availability. The comparison of the model predictions with the resulting experimental phenotypes indicated that pyruvate ferredoxin oxidoreductase is the only activity able to convert pyruvate into acetyl-CoA. However, the results and the modeling showed that the two acetate activation pathways present are not only active, but needed due to the additional role of the acetyl-CoA transferase in the TCA cycle, probably reflecting the adaptation of these bacteria to acetate utilization. In other cases, the data reconciliation suggested additional capacity constraints that were confirmed with biochemical assays. The results demonstrate the need to experimentally verify the activity of key enzymes when developing in silico models of microbial physiology based on sequence-based reconstruction of metabolic networks.

  12. Geobacter sulfurreducens subsp. ethanolicus, subsp. nov., an ethanol-utilizing dissimilatory Fe(III)-reducing bacterium from a lotus field.

    Science.gov (United States)

    Viulu, Samson; Nakamura, Kohei; Kojima, Akihiro; Yoshiyasu, Yuki; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-01-01

    An ethanol-utilizing Fe(III)-reducing bacterial strain, OSK2A(T), was isolated from a lotus field in Aichi, Japan. Phylogenetic analysis of the 16S rRNA gene sequences of OSK2A(T) and related strains placed it within Geobacter sulfurreducens PCA(T). Strain OSK2A(T) was shown to be a Gram-negative, motile, rod-shaped bacterium, strictly anaerobic, 0.76-1.65 µm long and 0.28-0.45 μm wide. Its growth occurred at 20-40℃, pH 6.0-8.1, and it tolerated up to 1% NaCl. The G+C content of the genomic DNA was 61.2 mol% and DNA-DNA hybridization value with Geobacter sulfurreducens PCA(T) was 60.7%. The major respiratory quinone was MK-8. The major fatty acids were 16:1 ω7c, 16:0, 14:0, 15:0 iso, 16:1 ω5c, and 18:1 ω7c. Strain OSK2A(T) could utilize H2, ethanol, acetate, lactate, pyruvate, and formate as substrates with Fe(III)-citrate as electron acceptor. Amorphous Fe(III) hydroxide, Fe(III)-NTA, fumarate, malate, and elemental sulfur were utilized as electron acceptors with either acetate or ethanol as substrates. Results obtained from physiological, DNA-DNA hybridization, and chemotaxonomic tests support genotypic and phenotypic differentiation of strain OSK2A(T) from its closest relative. The isolate is assigned as a novel subspecies with the name Geobacter sulfurreducens subsp. ethanolicus, subsp. nov. (type strain OSK2A(T)=DSMZ 26126(T)=JCM 18752(T)).

  13. Stimulating the In Situ Activity of Geobacter Species to Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, R. T.; Vrionis, Helen A.; Ortiz-Bernad, Irene; Resch, Charles T.; Long, Philip E.; Dayvault, R. D.; Karp, Ken; Marutzky, Sammy J.; Metzler, Donald R.; Peacock, Aaron D.; White, David C.; Lowe, Mary; Lovley, Derek R.

    2003-10-01

    The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 _M in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.

  14. OmcB, a c-Type Polyheme Cytochrome, Involved in Fe(III) Reduction in Geobacter sulfurreducens

    OpenAIRE

    2003-01-01

    Microorganisms in the family Geobacteraceae are the predominant Fe(III)-reducing microorganisms in a variety of subsurface environments in which Fe(III) reduction is an important process, but little is known about the mechanisms for electron transport to Fe(III) in these organisms. The Geobacter sulfurreducens genome was found to contain a 10-kb chromosomal duplication consisting of two tandem three-gene clusters. The last genes of the two clusters, designated omcB and omcC, encode putative o...

  15. A Description of an Acidophilic, Iron Reducer, Geobacter sp. FeAm09 Isolated from Tropical Soils

    Science.gov (United States)

    Healy, O.; Souchek, J.; Heithoff, A.; LaMere, B.; Pan, D.; Hollis, G.; Yang, W. H.; Silver, W. L.; Weber, K. A.

    2014-12-01

    Iron (Fe) is the fourth most abundant element in the Earth's crust and plays a significant role controlling the geochemistry in soils, sediments, and aquatic systems. As part of a study to understand microbially-catalysed iron biogeochemical cycling in tropical soils, an iron reducing isolate, strain FeAm09, was obtained. Strain FeAm09 was isolated from acidic, Fe-rich soils collected from a tropical forest (Luquillo Experimental Forest, Puerto Rico). Strain FeAm09 is a rod-shaped, motile, Gram-negative bacterium. Taxonomic analysis of the near complete 16S rRNA gene sequence revealed that strain FeAm09 is 94.7% similar to Geobacter lovleyi, placing it in the genus Geobacter within the Family Geobacteraceae in the Deltaproteobacteria. Characterization of the optimal growth conditions revealed that strain FeAm09 is a moderate acidophile with an optimal growth pH of 5.0. The optimal growth temperature was 37°C. Growth of FeAm09 was coupled to the reduction of soluble Fe(III), Fe(III)-NTA, with H2, fumarate, ethanol, and various organic acids and sugars serving as the electron donor. Insoluble Fe(III), in the form of synthetic ferrihydrite, was reduced by strain FeAm09 using acetate or H2 as the electron donor. The use of H2 as an electron donor in the presence of CO2 and absence of organic carbon and assimilation of 14C-labelled CO2 into biomass indicate that strain FeAm09 is an autotrophic Fe(III)-reducing bacterium. Together, these data describe the first acidophilic, autotrophic Geobacter species. Iron reducing bacteria were previously shown to be as abundant in tropical soils as in saturated sediments (lake-bottoms) and saturated soils (wetlands) where Fe(III) reduction is more commonly recognized as a dominant mode of microbial respiration. Furthermore, Fe(III) reduction was identified as a primary driver of carbon mineralization in these tropical soils (Dubinsky et al. 2010). In addition to mineralizing organic carbon, Geobacter sp. FeAm09 is likely to also

  16. Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes

    OpenAIRE

    Shi, Liang; Squier, Thomas C.; Zachara, John M.; Fredrickson, James K.

    2007-01-01

    Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram-negative bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c-type cytochromes (c-Cyts). In S. oneidensis MR-1, multihaem c-Cyts CymA and MtrA are believed to transfer ...

  17. U(VI) reduction by diverse outer surface c-type cytochromes of Geobacter sulfurreducens.

    Science.gov (United States)

    Orellana, Roberto; Leavitt, Janet J; Comolli, Luis R; Csencsits, Roseann; Janot, Noemie; Flanagan, Kelly A; Gray, Arianna S; Leang, Ching; Izallalen, Mounir; Mester, Tünde; Lovley, Derek R

    2013-10-01

    Early studies with Geobacter sulfurreducens suggested that outer-surface c-type cytochromes might play a role in U(VI) reduction, but it has recently been suggested that there is substantial U(VI) reduction at the surface of the electrically conductive pili known as microbial nanowires. This phenomenon was further investigated. A strain of G. sulfurreducens, known as Aro-5, which produces pili with substantially reduced conductivity reduced U(VI) nearly as well as the wild type, as did a strain in which the gene for PilA, the structural pilin protein, was deleted. In order to reduce rates of U(VI) reduction to levels less than 20% of the wild-type rates, it was necessary to delete the genes for the five most abundant outer surface c-type cytochromes of G. sulfurreducens. X-ray absorption near-edge structure spectroscopy demonstrated that whereas 83% ± 10% of the uranium associated with wild-type cells correspond to U(IV) after 4 h of incubation, with the quintuple mutant, 89% ± 10% of uranium was U(VI). Transmission electron microscopy and X-ray energy dispersion spectroscopy revealed that wild-type cells did not precipitate uranium along pili as previously reported, but U(IV) was precipitated at the outer cell surface. These findings are consistent with those of previous studies, which have suggested that G. sulfurreducens requires outer-surface c-type cytochromes but not pili for the reduction of soluble extracellular electron acceptors.

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

    Science.gov (United States)

    Smith, Jessica A; Tremblay, Pier-Luc; Shrestha, Pravin Malla; Snoeyenbos-West, Oona L; Franks, Ashley E; Nevin, Kelly P; Lovley, Derek R

    2014-07-01

    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.

  19. Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up.

    Science.gov (United States)

    Muhamadali, Howbeer; Xu, Yun; Ellis, David I; Allwood, J William; Rattray, Nicholas J W; Correa, Elon; Alrabiah, Haitham; Lloyd, Jonathan R; Goodacre, Royston

    2015-05-15

    During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However

  20. Thermodynamic Characterization of a Triheme Cytochrome Family from Geobacter sulfurreducens Reveals Mechanistic and Functional Diversity

    Science.gov (United States)

    Morgado, Leonor; Bruix, Marta; Pessanha, Miguel; Londer, Yuri Y.; Salgueiro, Carlos A.

    2010-01-01

    Abstract A family of five periplasmic triheme cytochromes (PpcA-E) was identified in Geobacter sulfurreducens, where they play a crucial role by driving electron transfer from the cytoplasm to the cell exterior and assisting the reduction of extracellular acceptors. The thermodynamic characterization of PpcA using NMR and visible spectroscopies was previously achieved under experimental conditions identical to those used for the triheme cytochrome c7 from Desulfuromonas acetoxidans. Under such conditions, attempts to obtain NMR data were complicated by the relatively fast intermolecular electron exchange. This work reports the detailed thermodynamic characterization of PpcB, PpcD, and PpcE under optimal experimental conditions. The thermodynamic characterization of PpcA was redone under these new conditions to allow a proper comparison of the redox properties with those of other members of this family. The heme reduction potentials of the four proteins are negative, differ from each other, and cover different functional ranges. These reduction potentials are strongly modulated by heme-heme interactions and by interactions with protonated groups (the redox-Bohr effect) establishing different cooperative networks for each protein, which indicates that they are designed to perform different functions in the cell. PpcA and PpcD appear to be optimized to interact with specific redox partners involving e−/H+ transfer via different mechanisms. Although no evidence of preferential electron transfer pathway or e−/H+ coupling was found for PpcB and PpcE, the difference in their working potential ranges suggests that they may also have different physiological redox partners. This is the first study, to our knowledge, to characterize homologous cytochromes from the same microorganism and provide evidence of their different mechanistic and functional properties. These findings provide an explanation for the coexistence of five periplasmic triheme cytochromes in G

  1. Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation

    Directory of Open Access Journals (Sweden)

    Lovley Derek R

    2010-11-01

    Full Text Available Abstract Background Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen and acceptors (Fe(III, fumarate was investigated via 13C-based metabolic flux analysis. We examined the 13C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with 13C-acetate. Results Using 13C-based metabolic flux analysis, we observed that donor and acceptor variations gave rise to differences in gluconeogenetic initiation, tricarboxylic acid cycle activity, and amino acid biosynthesis pathways. Culturing G. sulfurreducens cells with Fe(III as the electron acceptor and acetate as the electron donor resulted in pyruvate as the primary carbon source for gluconeogenesis. When fumarate was provided as the electron acceptor and acetate as the electron donor, the flux analysis suggested that fumarate served as both an electron acceptor and, in conjunction with acetate, a carbon source. Growth on fumarate and acetate resulted in the initiation of gluconeogenesis by phosphoenolpyruvate carboxykinase and a slightly elevated flux through the oxidative tricarboxylic acid cycle as compared to growth with Fe(III as the electron acceptor. In addition, the direction of net flux between acetyl-CoA and pyruvate was reversed during growth on fumarate relative to Fe(III, while growth in the presence of Fe(III and acetate which provided hydrogen as an electron donor, resulted in decreased flux through the tricarboxylic acid cycle. Conclusions We gained detailed insight into the metabolism of G. sulfurreducens cells under various electron donor/acceptor conditions using 13C-based metabolic flux analysis. Our results can be used for the development of G. sulfurreducens as a chassis for a variety of applications including bioremediation and renewable biofuel production.

  2. Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens

    Science.gov (United States)

    Levar, Caleb E; Hoffman, Colleen L; Dunshee, Aubrey J; Toner, Brandy M; Bond, Daniel R

    2017-01-01

    Geobacter sulfurreducens uses at least two different pathways to transport electrons out of the inner membrane quinone pool before reducing acceptors beyond the outer membrane. When growing on electrodes poised at oxidizing potentials, the CbcL-dependent pathway operates at or below redox potentials of –0.10 V vs the standard hydrogen electrode, whereas the ImcH-dependent pathway operates only above this value. Here, we provide evidence that G. sulfurreducens also requires different electron transfer proteins for reduction of a wide range of Fe(III)- and Mn(IV)-(oxyhydr)oxides, and must transition from a high- to low-potential pathway during reduction of commonly studied soluble and insoluble metal electron acceptors. Freshly precipitated Fe(III)-(oxyhydr)oxides could not be reduced by mutants lacking the high-potential pathway. Aging these minerals by autoclaving did not change their powder X-ray diffraction pattern, but restored reduction by mutants lacking the high-potential pathway. Mutants lacking the low-potential, CbcL-dependent pathway had higher growth yields with both soluble and insoluble Fe(III). Together, these data suggest that the ImcH-dependent pathway exists to harvest additional energy when conditions permit, and CbcL switches on to allow respiration closer to thermodynamic equilibrium conditions. With evidence of multiple pathways within a single organism, the study of extracellular respiration should consider not only the crystal structure or solubility of a mineral electron acceptor, but rather the redox potential, as this variable determines the energetic reward affecting reduction rates, extents, and final microbial growth yields in the environment. PMID:28045456

  3. Promoting interspecies electron transfer with biochar

    DEFF Research Database (Denmark)

    Chen, Shanshan; Rotaru, Amelia-Elena; Shrestha, Pravin Malla;

    2014-01-01

    to that previously reported for granular activated carbon (GAC). Although the biochars investigated were 1000 times less conductive than GAC, they stimulated DIET in co-cultures of Geobacter metallireducens with Geobacter sulfurreducens or Methanosarcina barkeri in which ethanol was the electron donor. Cells were...

  4. Growth advantage in stationary-phase (GASP) phenotype in long-term survival strains of Geobacter sulfurreducens.

    Science.gov (United States)

    Helmus, Ruth A; Liermann, Laura J; Brantley, Susan L; Tien, Ming

    2012-01-01

    Geobacter sulfurreducens exists in the subsurface and has been identified in sites contaminated with radioactive metals, consistent with its ability to reduce metals under anaerobic conditions. The natural state of organisms in the environment is one that lacks access to high concentrations of nutrients, namely electron donors and terminal electron acceptors (TEAs). Most studies have investigated G. sulfurreducens under high-nutrient conditions or have enriched for it in environmental systems via acetate amendments. We replicated the starvation state through long-term batch culture of G. sulfurreducens, where both electron donor and TEA were scarce. The growth curve revealed lag, log, stationary, death, and survival phases using acetate as electron donor and either fumarate or iron(III) citrate as TEA. In survival phase, G. sulfurreducens persisted at a constant cell count for as long as 23 months without replenishment of growth medium. Geobacter sulfurreducens demonstrated an ability to acquire a growth advantage in stationary-phase phenotype (GASP), with strains derived from subpopulations from death- or survival phase being able to out-compete mid-log-phase populations when co-cultured. The molecular basis for GASP was not because of any detectable mutation in the rpoS gene (GSU1525) nor because of a mutation in a putative homolog to Escherichia coli lrp, GSU3370.

  5. Survival during long-term starvation: global proteomics analysis of Geobacter sulfurreducens under prolonged electron-acceptor limitation.

    Science.gov (United States)

    Bansal, Reema; Helmus, Ruth A; Stanley, Bruce A; Zhu, Junjia; Liermann, Laura J; Brantley, Susan L; Tien, Ming

    2013-10-04

    The bioavailability of terminal electron acceptors (TEAs) and other substrates affects the efficiency of subsurface bioremediation. While it is often argued that microorganisms exist under "feast or famine", in the laboratory most organisms are studied under "feast" conditions, whereas they typically encounter "famine" in nature. The work described here aims to understand the survival strategies of the anaerobe Geobacter sulfurreduces under TEA-starvation conditions. Cultures were starved for TEA and at various times sampled to perform global comparative proteomic analysis using iTRAQ to obtain insight into the dynamics of change in proteins/enzymes expression associated with change in nutrient availability/environmental stress. Proteins varying in abundance with a high level of statistical significance (p Geobacter under starvation conditions. The cell shuts down anabolic processes and becomes poised, through changes in its membrane proteins, to sense nutrients in the environment, to transport nutrients into the cell, and to detect or utilize TEAs that are encountered. Under TEA-limiting conditions, the cells turned from translucent white to red in color, indicating higher heme content. The increase in heme content supported proteomics results showing an increase in the number of cytochromes involved in membrane electron transport during the survival phase. The cell is also highly reduced with minimal change in energy charge (ATP to total adenine nucleotide ratio). Nonetheless, these proteomic and biochemical results indicate that even under TEA starvation cells remain poised for bioremediation.

  6. Electronic properties of conductive pili of the metal-reducing bacterium Geobacter sulfurreducens probed by scanning tunneling microscopy

    Science.gov (United States)

    Veazey, Joshua P.; Reguera, Gemma; Tessmer, Stuart H.

    2011-12-01

    The metal-reducing bacterium Geobacter sulfurreducens produces conductive protein appendages known as “pilus nanowires” to transfer electrons to metal oxides and to other cells. These processes can be harnessed for the bioremediation of toxic metals and the generation of electricity in bioelectrochemical cells. Key to these applications is a detailed understanding of how these nanostructures conduct electrons. However, to the best of our knowledge, their mechanism of electron transport is not known. We used the capability of scanning tunneling microscopy (STM) to probe conductive materials with higher spatial resolution than other scanning probe methods to gain insights into the transversal electronic behavior of native, cell-anchored pili. Despite the presence of insulating cellular components, the STM topography resolved electronic molecular substructures with periodicities similar to those reported for the pilus shaft. STM spectroscopy revealed electronic states near the Fermi level, consistent with a conducting material, but did not reveal electronic states expected for cytochromes. Furthermore, the transversal conductance was asymmetric, as previously reported for assemblies of helical peptides. Our results thus indicate that the Geobacter pilus shaft has an intrinsic electronic structure that could play a role in charge transport.

  7. Role of Geobacter sulfurreducens Outer Surface c-Type Cytochromes in Reduction of Soil Humic Acid and Anthraquinone-2,6-Disulfonate▿

    Science.gov (United States)

    Voordeckers, James W.; Kim, Byoung-Chan; Izallalen, Mounir; Lovley, Derek R.

    2010-01-01

    Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones. PMID:20154112

  8. Role of Geobacter sulfurreducens outer surface c-type cytochromes in reduction of soil humic acid and anthraquinone-2,6-disulfonate.

    Science.gov (United States)

    Voordeckers, James W; Kim, Byoung-Chan; Izallalen, Mounir; Lovley, Derek R

    2010-04-01

    Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.

  9. Functional characterization of PccH, a key cytochrome for electron transfer from electrodes to the bacterium Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Tomaz, Diogo M; Morgado, Leonor; Salgueiro, Carlos A

    2013-08-19

    The cytochrome PccH from Geobacter sulfurreducens (Gs) plays a crucial role in current-consuming fumarate-reducing biofilms. Deletion of pccH gene inhibited completely electron transfer from electrodes toward Gs cells. The pccH gene was cloned and the protein heterologously expressed in Escherichia coli. Complementary biophysical techniques including CD, UV-visible and NMR spectroscopy were used to characterize PccH. This cytochrome contains one low-spin c-type heme with His-Met axial coordination and unusual low-reduction potential. This reduction potential is pH-dependent, within the Gs physiological pH range, and is discussed within the context of the electron transfer mechanisms from electrodes to Gs cells.

  10. Anode biofilm transcriptomics reveals outer surface components essential for high density current production in Geobacter sulfurreducens fuel cells.

    Directory of Open Access Journals (Sweden)

    Kelly P Nevin

    Full Text Available The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (>50 microm biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and the genes for two outer c-type membrane cytochromes, OmcB and OmcZ. Down-regulated genes included the genes for the outer-membrane c-type cytochromes, OmcS and OmcT. Results of quantitative RT-PCR of gene transcript levels during biofilm growth were consistent with microarray results. OmcZ and the outer-surface c-type cytochrome, OmcE, were more abundant and OmcS was less abundant in current-harvesting cells. Strains in which pilA, the gene immediately downstream from pilA, omcB, omcS, omcE, or omcZ was deleted demonstrated that only deletion of pilA or omcZ severely inhibited current production and biofilm formation in current-harvesting mode. In contrast, these gene deletions had no impact on biofilm formation on graphite surfaces when fumarate served as the electron acceptor. These results suggest that biofilms grown harvesting current are specifically poised for electron transfer to electrodes and that, in addition to pili, OmcZ is a key component in electron transfer through differentiated G. sulfurreducens biofilms to electrodes.

  11. A trans-outer membrane porin-cytochrome protein complex for extracellular electron transfer by Geobacter sulfurreducens PCA.

    Science.gov (United States)

    Liu, Yimo; Wang, Zheming; Liu, Juan; Levar, Caleb; Edwards, Marcus J; Babauta, Jerome T; Kennedy, David W; Shi, Zhi; Beyenal, Haluk; Bond, Daniel R; Clarke, Thomas A; Butt, Julea N; Richardson, David J; Rosso, Kevin M; Zachara, John M; Fredrickson, James K; Shi, Liang

    2014-12-01

    The multi-heme, outer membrane c-type cytochrome (c-Cyt) OmcB of Geobacter sulfurreducens was previously proposed to mediate electron transfer across the outer membrane. However, the underlying mechanism has remained uncharacterized. In G. sulfurreducens, the omcB gene is part of two tandem four-gene clusters, each is predicted to encode a transcriptional factor (OrfR/OrfS), a porin-like outer membrane protein (OmbB/OmbC), a periplasmic c-type cytochrome (OmaB/OmaC) and an outer membrane c-Cyt (OmcB/OmcC) respectively. Here, we showed that OmbB/OmbC, OmaB/OmaC and OmcB/OmcC of G. sulfurreducens PCA formed the porin-cytochrome (Pcc) protein complexes, which were involved in transferring electrons across the outer membrane. The isolated Pcc protein complexes reconstituted in proteoliposomes transferred electrons from reduced methyl viologen across the lipid bilayer of liposomes to Fe(III)-citrate and ferrihydrite. The pcc clusters were found in all eight sequenced Geobacter and 11 other bacterial genomes from six different phyla, demonstrating a widespread distribution of Pcc protein complexes in phylogenetically diverse bacteria. Deletion of ombB-omaB-omcB-orfS-ombC-omaC-omcC gene clusters had no impact on the growth of G. sulfurreducens PCA with fumarate but diminished the ability of G. sulfurreducens PCA to reduce Fe(III)-citrate and ferrihydrite. Complementation with the ombB-omaB-omcB gene cluster restored the ability of G. sulfurreducens PCA to reduce Fe(III)-citrate and ferrihydrite.

  12. Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination.

    Science.gov (United States)

    Prakash, Om; Gihring, Thomas M; Dalton, Dava D; Chin, Kuk-Jeong; Green, Stefan J; Akob, Denise M; Wanger, Greg; Kostka, Joel E

    2010-03-01

    An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32(T), was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the Geobacteraceae-specific citrate synthase (gltA) mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus Geobacter and shared 92-98 % 16S rRNA gene and 75-81 % rpoB gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Geobacter uraniireducens Rf4(T), according to 16S rRNA gene sequence similarity, strain FRC-32(T) showed a DNA-DNA relatedness value of 21 %. Cells of strain FRC-32(T) were Gram-negative, non-spore-forming, curved rods, 1.0-1.5 microm long and 0.3-0.5 microm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus Geobacter. The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 degrees C and pH 6.7-7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the Geobacter group, strain FRC-32(T) conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32(T) was metabolically versatile and, unlike its closest relative, G. uraniireducens, was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with

  13. Inhibition of Geobacter dechlorinators at elevated trichloroethene concentrations is explained by a reduced activity rather than by an enhanced cell decay.

    Science.gov (United States)

    Philips, Jo; Haest, Pieter Jan; Springael, Dirk; Smolders, Erik

    2013-02-05

    Microbial dechlorination of trichloroethene (TCE) is inhibited at elevated TCE concentrations. A batch experiment and modeling analysis were performed to examine whether this self-inhibition is related to an enhanced cell decay or a reduced dechlorination activity at increasing TCE concentrations. The batch experiment combined four different initial TCE concentrations (1.4-3.0 mM) and three different inoculation densities (4.0 × 10(5) to 4.0 × 10(7)Geobacter cells·mL(-1)). Chlorinated ethene concentrations and Geobacter 16S rRNA gene copy numbers were measured. The time required for complete conversion of TCE to cis-DCE increased with increasing initial TCE concentration and decreasing inoculation density. Both an enhanced decay and a reduced activity model fitted the experimental results well, although the reduced activity model better described the lag phase and microbial decay in some treatments. In addition, the reduced activity model succeeded in predicting the reactivation of the dechlorination reaction in treatments in which the inhibiting TCE concentration was lowered after 80 days. In contrast, the enhanced decay model predicted a Geobacter cell density that was too low to allow recovery for these treatments. Conclusively, our results suggest that TCE self-inhibition is related to a reduced dechlorination activity rather than to an enhanced cell decay at elevated TCE concentrations.

  14. Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells.

    Science.gov (United States)

    Nevin, K P; Richter, H; Covalla, S F; Johnson, J P; Woodard, T L; Orloff, A L; Jia, H; Zhang, M; Lovley, D R

    2008-10-01

    It has been previously noted that mixed communities typically produce more power in microbial fuel cells than pure cultures. If true, this has important implications for the design of microbial fuel cells and for studying the process of electron transfer on anode biofilms. To further evaluate this, Geobacter sulfurreducens was grown with acetate as fuel in a continuous flow 'ministack' system in which the carbon cloth anode and cathode were positioned in close proximity, and the cation-selective membrane surface area was maximized in order to overcome some of the electrochemical limitations that were inherent in fuel cells previously employed for the study of pure cultures. Reducing the size of the anode in order to eliminate cathode limitation resulted in maximum current and power densities per m(2) of anode surface of 4.56 A m(-2) and 1.88 W m(-2) respectively. Electron recovery as current from acetate oxidation was c. 100% when oxygen diffusion into the system was minimized. This performance is comparable to the highest levels previously reported for mixed communities in similar microbial fuel cells and slightly higher than the power output of an anaerobic sludge inoculum in the same ministack system. Minimizing the volume of the anode chamber yielded a volumetric power density of 2.15 kW m(-3), which is the highest power density per volume yet reported for a microbial fuel cell. Geobacter sulfurreducens formed relatively uniform biofilms 3-18 mum thick on the carbon cloth anodes. When graphite sticks served as the anode, the current density (3.10 A m(-2)) was somewhat less than with the carbon cloth anodes, but the biofilms were thicker (c. 50 mum) with a more complex pillar and channel structure. These results suggest that the previously observed disparity in power production in pure and mixed culture microbial fuel cell systems can be attributed more to differences in the fuel cell designs than to any inherent superior capability of mixed cultures to produce

  15. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

    DEFF Research Database (Denmark)

    Nagarajan, Harish; Embree, Mallory; Rotaru, Amelia-Elena

    2013-01-01

    Syntrophic associations are central to microbial communities and thus have a fundamental role in the global carbon cycle. Despite biochemical approaches describing the physiological activity of these communities, there has been a lack of a mechanistic understanding of the relationship between...... metallireducens and Geobacter sulfurreducens. Genome-scale modelling of direct interspecies electron transfer reveals insights into the energetics of electron transfer mechanisms. While G. sulfurreducens adapts to rapid syntrophic growth by changes at the genomic and transcriptomic level, G. metallireducens...

  16. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell.

    Science.gov (United States)

    Bourdakos, Nicholas; Marsili, Enrico; Mahadevan, Radhakrishnan

    2014-04-01

    Wastewater-fed microbial fuel cells (MFCs) are a promising technology to treat low-organic carbon wastewater and recover part of the chemical energy in wastewater as electrical power. However, the interactions between electrochemically active and fermentative microorganisms cannot be easily studied in wastewater-fed MFCs because of their complex microbial communities. Defined co-culture MFCs provide a detailed understanding of such interactions. In this study, we characterize the extracellular metabolites in laboratory-scale membrane-less MFCs inoculated with Geobacter sulfurreducens and Escherichia coli co-culture and compare them with pure culture MFCs. G. sulfurreducens MFCs are sparged to maintain anaerobic conditions, while co-culture MFCs rely on E. coli for oxygen removal. G. sulfurreducens MFCs have a power output of 128 mW m(-2) , compared to 63 mW m(-2) from the co-culture MFCs. Analysis of metabolites shows that succinate production in co-culture MFCs decreases current production by G. sulfurreducens and that the removal of succinate is responsible for the increased current density in the late co-culture MFCs. Interestingly, pH adjustment is not required for co-culture MFCs but a base addition is necessary for E. coli MFCs and cultures in vials. Our results show that defined co-culture MFCs provide clear insights into metabolic interactions among bacteria while maintaining a low operational complexity.

  17. Reduction of low potential electron acceptors requires the CbcL inner membrane cytochrome of Geobacter sulfurreducens.

    Science.gov (United States)

    Zacharoff, Lori; Chan, Chi Ho; Bond, Daniel R

    2016-02-01

    The respiration of metals by the bacterium Geobacter sulfurreducens requires electrons generated by metabolism to pass from the interior of the cell to electron acceptors beyond the cell membranes. The G. sulfurreducens inner membrane multiheme c-type cytochrome ImcH is required for respiration to extracellular electron acceptors with redox potentials greater than -0.1 V vs. SHE, but ImcH is not essential for electron transfer to lower potential acceptors. In contrast, deletion of cbcL, encoding an inner membrane protein consisting of b-type and multiheme c-type cytochrome domains, severely affected reduction of low potential electron acceptors such as Fe(III)-oxides and electrodes poised at -0.1 V vs. SHE. Catalytic cyclic voltammetry of a ΔcbcL strain growing on poised electrodes revealed a 50 mV positive shift in driving force required for electron transfer out of the cell. In non-catalytic conditions, low-potential peaks present in wild type biofilms were absent in ∆cbcL mutants. Expression of cbcL in trans increased growth at low redox potential and restored features to cyclic voltammetry. This evidence supports a model where CbcL is a component of a second electron transfer pathway out of the G. sulfurreducens inner membrane that dominates when redox potential is at or below -0.1 V vs. SHE.

  18. Fate of Cd during microbial Fe(III) mineral reduction by a novel and Cd-tolerant Geobacter species.

    Science.gov (United States)

    Muehe, E Marie; Obst, Martin; Hitchcock, Adam; Tyliszczak, Tolek; Behrens, Sebastian; Schröder, Christian; Byrne, James M; Michel, F Marc; Krämer, Ute; Kappler, Andreas

    2013-12-17

    Fe(III) (oxyhydr)oxides affect the mobility of contaminants in the environment by providing reactive surfaces for sorption. This includes the toxic metal cadmium (Cd), which prevails in agricultural soils and is taken up by crops. Fe(III)-reducing bacteria can mobilize such contaminants by Fe(III) mineral dissolution or immobilize them by sorption to or coprecipitation with secondary Fe minerals. To date, not much is known about the fate of Fe(III) mineral-associated Cd during microbial Fe(III) reduction. Here, we describe the isolation of a new Geobacter sp. strain Cd1 from a Cd-contaminated field site, where the strain accounts for 10(4) cells g(-1) dry soil. Strain Cd1 reduces the poorly crystalline Fe(III) oxyhydroxide ferrihydrite in the presence of at least up to 112 mg Cd L(-1). During initial microbial reduction of Cd-loaded ferrihydrite, sorbed Cd was mobilized. However, during continuous microbial Fe(III) reduction, Cd was immobilized by sorption to and/or coprecipitation within newly formed secondary minerals that contained Ca, Fe, and carbonate, implying the formation of an otavite-siderite-calcite (CdCO3-FeCO3-CaCO3) mixed mineral phase. Our data shows that microbially mediated turnover of Fe minerals affects the mobility of Cd in soils, potentially altering the dynamics of Cd uptake into food or phyto-remediating plants.

  19. Enhanced dechlorination of carbon tetrachloride by Geobacter sulfurreducens in the presence of naturally occurring quinones and ferrihydrite.

    Science.gov (United States)

    Doong, Ruey-an; Lee, Chun-chi; Lien, Chia-min

    2014-02-01

    The effect of naturally occurring quinones including lawsone (LQ), ubiquinone (UQ), juglone (JQ), and 1,4-naphthoquinone (NQ) on the biotransformation of carbon tetrachloride (CT) in the presence of Geobacter sulfurreducens and ferrihydrite was investigated. AQDS was used as the model compound for comparison. The reductive dissolution of ferrihydrite by G. sulfurreducens was enhanced by AQDS, NQ, and LQ. However, addition of UQ and JQ had little enhancement effect on Fe(II) production. The bioreduction efficiency and rate of ferrihydrite was highly dependent on the natural property and concentration of quinone compounds and the addition of low concentrations of LQ and NQ significantly accelerated the biotransformation rate of CT. The pseudo-first-order rate constants for CT dechlorination (kobsCT) in AQDS-, LQ- and NQ-amended batches were 5.4-5.8, 4.6-7.4 and 2.4-5.8 times, respectively, higher than those in the absence of quinone. A good relationship between kobsCT for CT dechlorination and bioreduction ratio of ferrihydrite was observed, indicating the important role of biogenic Fe(II) in dechlorination of CT under iron-reducing conditions. Spectroscopic analysis showed that AQDS and NQ could be reduced to semiquinones and hydroquinones, while only hydroquinones were generated in LQ-amended batches.

  20. Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens.

    Science.gov (United States)

    Morgado, Leonor; Bruix, Marta; Pokkuluri, P Raj; Salgueiro, Carlos A; Turner, David L

    2017-01-15

    The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e(-)/H(+) coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e(-)/H(+) coupling molecular mechanisms driven by PpcA in G. sulfurreducens. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  1. pH, redox potential and local biofilm potential microenvironments within Geobacter sulfurreducens biofilms and their roles in electron transfer.

    Science.gov (United States)

    Babauta, Jerome T; Nguyen, Hung Duc; Harrington, Timothy D; Renslow, Ryan; Beyenal, Haluk

    2012-10-01

    The limitation of pH inside electrode-respiring biofilms is a well-known concept. However, little is known about how pH and redox potential are affected by increasing current inside biofilms respiring on electrodes. Quantifying the variations in pH and redox potential with increasing current is needed to determine how electron transfer is tied to proton transfer within the biofilm. In this research, we quantified pH and redox potential variations in electrode-respiring Geobacter sulfurreducens biofilms as a function of respiration rates, measured as current. We also characterized pH and redox potential at the counter electrode. We concluded that (1) pH continued to decrease in the biofilm through different growth phases, showing that the pH is not always a limiting factor in a biofilm and (2) decreasing pH and increasing redox potential at the biofilm electrode were associated only with the biofilm, demonstrating that G. sulfurreducens biofilms respire in a unique internal environment. Redox potential inside the biofilm was also compared to the local biofilm potential measured by a graphite microelectrode, where the tip of the microelectrode was allowed to acclimatize inside the biofilm. Copyright © 2012 Wiley Periodicals, Inc.

  2. Respiration of metal (hydr)oxides by Shewanella and Geobacter: a key role for multihaem c-type cytochromes.

    Science.gov (United States)

    Shi, Liang; Squier, Thomas C; Zachara, John M; Fredrickson, James K

    2007-07-01

    Dissimilatory reduction of metal (e.g. Fe, Mn) (hydr)oxides represents a challenge for microorganisms, as their cell envelopes are impermeable to metal (hydr)oxides that are poorly soluble in water. To overcome this physical barrier, the Gram-negative bacteria Shewanella oneidensis MR-1 and Geobacter sulfurreducens have developed electron transfer (ET) strategies that require multihaem c-type cytochromes (c-Cyts). In S. oneidensis MR-1, multihaem c-Cyts CymA and MtrA are believed to transfer electrons from the inner membrane quinone/quinol pool through the periplasm to the outer membrane. The type II secretion system of S. oneidensis MR-1 has been implicated in the reduction of metal (hydr)oxides, most likely by translocating decahaem c-Cyts MtrC and OmcA across outer membrane to the surface of bacterial cells where they form a protein complex. The extracellular MtrC and OmcA can directly reduce solid metal (hydr)oxides. Likewise, outer membrane multihaem c-Cyts OmcE and OmcS of G. sulfurreducens are suggested to transfer electrons from outer membrane to type IV pili that are hypothesized to relay the electrons to solid metal (hydr)oxides. Thus, multihaem c-Cyts play critical roles in S. oneidensis MR-1- and G. sulfurreducens-mediated dissimilatory reduction of solid metal (hydr)oxides by facilitating ET across the bacterial cell envelope.

  3. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture.

    Science.gov (United States)

    Galushko, A S; Schink, B

    2000-11-01

    Geobacter sulfurreducens strain PCA oxidized acetate to CO2 via citric acid cycle reactions during growth with acetate plus fumarate in pure culture, and with acetate plus nitrate in coculture with Wolinella succinogenes. Acetate was activated by succinyl-CoA:acetate CoA-transferase and also via acetate kinase plus phosphotransacetylase. Citrate was formed by citrate synthase. Soluble isocitrate and malate dehydrogenases NADP+ and NAD+, respectively. Oxidation of 2-oxoglutarate was measured as benzyl viologen reduction and strictly CoA-dependent; a low activity was also observed with NADP+. Succinate dehydrogenase and fumarate ductase both were membrane-bound. Succinate oxidation was coupled to NADP+ reduction whereas fumarate reduction was coupled to NADPH and NADH Coupling of succinate oxidation to NADP+ or cytochrome(s) reduction required an ATP-dependent reversed electron transport. Net ATP synthesis proceeded exclusively through electron transport phosphorylation. During fumarate reduction, both NADPH and NADH delivered reducing equivalents into the electron transport chain, which contained a menaquinone. Overall, acetate oxidation with fumarate proceeded through an open loop of citric acid cycle reactions, excluding succinate dehydrogenase, with fumarate reductase as the key reaction for electron delivery, whereas acetate oxidation in the syntrophic coculture required the complete citric acid cycle.

  4. Quantifying Temporal Autocorrelations for the Expression of Geobacter species mRNA Gene Transcripts at Variable Ammonium Levels during in situ U(VI) Bioremediation

    Science.gov (United States)

    Mouser, P. J.

    2010-12-01

    In order to develop decision-making tools for the prediction and optimization of subsurface bioremediation strategies, we must be able to link the molecular-scale activity of microorganisms involved in remediation processes with biogeochemical processes observed at the field-scale. This requires the ability to quantify changes in the in situ metabolic condition of dominant microbes and associate these changes to fluctuations in nutrient levels throughout the bioremediation process. It also necessitates a need to understand the spatiotemporal variability of the molecular-scale information to develop meaningful parameters and constraint ranges in complex bio-physio-chemical models. The expression of three Geobacter species genes (ammonium transporter (amtB), nitrogen fixation (nifD), and a housekeeping gene (recA)) were tracked at two monitoring locations that differed significantly in ammonium (NH4+) concentrations during a field-scale experiment where acetate was injected into the subsurface to simulate Geobacteraceae in a uranium-contaminated aquifer. Analysis of amtB and nifD mRNA transcript levels indicated that NH4+ was the primary form of fixed nitrogen during bioremediation. Overall expression levels of amtB were on average 8-fold higher at NH4+ concentrations of 300 μM or more than at lower NH4+ levels (average 60 μM). The degree of temporal correlation in Geobacter species mRNA expression levels was calculated at both locations using autocorrelation methods that describe the relationship between sample semi-variance and time lag. At the monitoring location with lower NH4+, a temporal correlation lag of 8 days was observed for both amtB and nifD transcript patterns. At the location where higher NH4+ levels were observed, no discernable temporal correlation lag above the sampling frequency (approximately every 2 days) was observed for amtB or nifD transcript fluctuations. Autocorrelation trends in recA expression levels at both locations indicated that

  5. OmcF, a Putative c-Type Monoheme Outer Membrane Cytochrome Required for the Expression of Other Outer Membrane Cytochromes in Geobacter sulfurreducens

    OpenAIRE

    2005-01-01

    Outer membrane cytochromes are often proposed as likely agents for electron transfer to extracellular electron acceptors, such as Fe(III). The omcF gene in the dissimilatory Fe(III)-reducing microorganism Geobacter sulfurreducens is predicted to code for a small outer membrane monoheme c-type cytochrome. An OmcF-deficient strain was constructed, and its ability to reduce and grow on Fe(III) citrate was found to be impaired. Following a prolonged lag phase (150 h), the OmcF-deficient strain de...

  6. Genome Scale Mutational Analysis of Geobacter sulfurreducens Reveals Distinct Molecular Mechanisms for Respiration and Sensing of Poised Electrodes versus Fe(III) Oxides.

    Science.gov (United States)

    Chan, Chi Ho; Levar, Caleb E; Jiménez-Otero, Fernanda; Bond, Daniel R

    2017-10-01

    Geobacter sulfurreducens generates electrical current by coupling intracellular oxidation of organic acids to the reduction of proteins on the cell surface that are able to interface with electrodes. This ability is attributed to the bacterium's capacity to respire other extracellular electron acceptors that require contact, such as insoluble metal oxides. To directly investigate the genetic basis of electrode-based respiration, we constructed Geobacter sulfurreducens transposon-insertion sequencing (Tn-Seq) libraries for growth, with soluble fumarate or an electrode as the electron acceptor. Libraries with >33,000 unique insertions and an average of 9 insertions/kb allowed an assessment of each gene's fitness in a single experiment. Mutations in 1,214 different genomic features impaired growth with fumarate, and the significance of 270 genes unresolved by annotation due to the presence of one or more functional homologs was determined. Tn-Seq analysis of -0.1 V versus standard hydrogen electrode (SHE) electrode-grown cells identified mutations in a subset of genes encoding cytochromes, processing systems for proline-rich proteins, sensory networks, extracellular structures, polysaccharides, and metabolic enzymes that caused at least a 50% reduction in apparent growth rate. Scarless deletion mutants of select genes identified via Tn-Seq revealed a new putative porin-cytochrome conduit complex (extABCD) crucial for growth with electrodes, which was not required for Fe(III) oxide reduction. In addition, four mutants lacking components of a putative methyl-accepting chemotaxis-cyclic dinucleotide sensing network (esnABCD) were defective in electrode colonization but grew normally with Fe(III) oxides. These results suggest that G. sulfurreducens possesses distinct mechanisms for recognition, colonization, and reduction of electrodes compared to Fe(III) oxides.IMPORTANCE Since metal oxide electron acceptors are insoluble, one hypothesis is that cells sense and reduce

  7. Structural characterization of a family of cytochromes c(7) involved in Fe(III) respiration by Geobacter sulfurreducens.

    Science.gov (United States)

    Pokkuluri, P R; Londer, Y Y; Yang, X; Duke, N E C; Erickson, J; Orshonsky, V; Johnson, G; Schiffer, M

    2010-02-01

    Periplasmic cytochromes c(7) are important in electron transfer pathway(s) in Fe(III) respiration by Geobacter sulfurreducens. The genome of G. sulfurreducens encodes a family of five 10-kDa, three-heme cytochromes c(7). The sequence identity between the five proteins (designated PpcA, PpcB, PpcC, PpcD, and PpcE) varies between 45% and 77%. Here, we report the high-resolution structures of PpcC, PpcD, and PpcE determined by X-ray diffraction. This new information made it possible to compare the sequences and structures of the entire family. The triheme cores are largely conserved but are not identical. We observed changes, due to different crystal packing, in the relative positions of the hemes between two molecules in the crystal. The overall protein fold of the cytochromes is similar. The structure of PpcD differs most from that of the other homologs, which is not obvious from the sequence comparisons of the family. Interestingly, PpcD is the only cytochrome c(7) within the family that has higher abundance when G. sulfurreducens is grown on insoluble Fe(III) oxide compared to ferric citrate. The structures have the highest degree of conservation around "heme IV"; the protein surface around this heme is positively charged in all of the proteins, and therefore all cytochromes c(7) could interact with similar molecules involving this region. The structures and surface characteristics of the proteins near the other two hemes, "heme I" and "heme III", differ within the family. The above observations suggest that each of the five cytochromes c(7) could interact with its own redox partner via an interface involving the regions of heme I and/or heme III; this provides a possible rationalization for the existence of five similar proteins in G. sulfurreducens. 2009 Elsevier B.V. All rights reserved.

  8. Unveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Simões, Telma; Morgado, Leonor; Caciones, Clara; Fernandes, Ana P; Silva, Marta A; Bruix, Marta; Pokkuluri, P Raj; Salgueiro, Carlos A

    2016-10-06

    A family of triheme cytochromes from Geobacter sulfurreducens plays an important role in extracellular electron transfer. In addition to their role in electron transfer pathways, two members of this family (PpcA and PpcD) were also found to be able to couple e(-)/H(+) transfer through the redox Bohr effect observed in the physiological pH range, a feature not observed for cytochromes PpcB and PpcE. In attempting to understand the molecular control of the redox Bohr effect in this family of cytochromes, which is highly homologous both in amino acid sequence and structures, it was observed that residue 6 is a conserved leucine in PpcA and PpcD, whereas in the other two characterized members (PpcB and PpcE) the equivalent residue is a phenylalanine. To determine the role of this residue located close to the redox Bohr center, we replaced Leu(6) in PpcA with Phe and determined the redox properties of the mutant, as well as its solution structure in the fully reduced state. In contrast with the native form, the mutant PpcAL6F is not able to couple the e(-)/H(+) pathway. We carried out the reverse mutation in PpcB and PpcE (i.e., replacing Phe(6) in these two proteins by leucine) and the mutated proteins showed an increased redox Bohr effect. The results clearly establish the role of residue 6 in the control of the redox Bohr effect in this family of cytochromes, a feature that could enable the rational design of G. sulfurreducens strains that carry mutant cytochromes with an optimal redox Bohr effect that would be suitable for various biotechnological applications.

  9. Reduction Kinetics of Manganese Dioxide by Geobacter Sulfurreducens and Associated Biofilm Morphology in a Flow-Through Reactor

    Science.gov (United States)

    Berns, E.; Werth, C. J.; Valocchi, A. J.; Sanford, R. A.

    2015-12-01

    Biogeochemical interactions have been investigated extensively to characterize natural nutrient cycling and predict contaminant transport in surface and groundwater. Dissimilatory metal reducing bacteria, many of which form biofilms, play an important role in reducing a variety of metals in these systems. It has been shown that biofilm morphology is impacted by flow conditions, but there has been little work that explores how reduction kinetics change as a result of these different morphologies. Different flow rates may affect physical properties of the biofilm that influence the rate of substrate reduction. We introduce an approach to calculate changes in Monod kinetic parameters while simultaneously evaluating biofilm morphologies under different flow rates. A vertical, cylindrical flow cell with removable glass slide sections coated in manganese dioxide (electron acceptor) was used to grow a biofilm of Geobacter sulfurreducens with acetate as the electron donor under both high (50 mL/hr) and low (5 mL/h) flow rates. The removable sections allowed for visualization of the biofilm at different time points with a confocal microscope, and quantification of the biomass on the surface using a combination of a protein assay and image analysis. Data collected from the experiments was used to determine yield and specific growth rate at the different flow rates, and a simple numerical model was used to estimate the half saturation constant of manganese dioxide at both flow rates. A smaller half saturation constant was estimated at the higher flow rate, indicating that the biofilm was more efficient in the high flow system, but a strong correlation between morphology and the faster reduction rate was not observed. Monod kinetic parameters are important for the development of accurate nutrient cycling and contaminant transport models in natural environments, and understanding how they are impacted by flow will be important for the development of new, improved models.

  10. Analysis of enhanced current-generating mechanism of Geobacter sulfurreducens strain via model-driven metabolism simulation.

    Science.gov (United States)

    Meng, Jing; Xu, Zixiang; Guo, Jing; Yue, Yunxia; Sun, Xiao

    2013-01-01

    Microbial fuel cells (MFCs) are a class of ideal technologies that function via anaerobic respiration of electricigens, which bring current generation and environmental restoration together. An in-depth understanding of microbial metabolism is of great importance in engineering microbes to further improve their respiration. We employed flux balance analysis and selected Fe(iii) as a substitute for the electrode to simulate current-generating metabolism of Geobacter sulfurreducens PCA with a fixed acetate uptake rate. Simulation results indicated the fluxes of reactions directing acetate towards dissimilation to generate electrons increased under the suboptimal growth condition, resulting in an increase in the respiration rate and a decrease in the growth rate. The results revealed the competitive relationship between oxidative respiration and cell growth during the metabolism of microbe current generation. The results helped us quantitatively understand why microbes growing slowly have the potential to make good use of fuel in MFCs. At the same time, slow growth does not necessarily result in speedy respiration. Alternative respirations may exist under the same growth state due to redundant pathways in the metabolic network. The big difference between the maximum and minimum respiration mainly results from the total formate secretion. With iterative flux variability analysis, a relatively ideal model of variant of G. sulfurreducens PCA was reconstructed by deleting several enzymes in the wild model, which could reach simultaneous suboptimal growth and maximum respiration. Under this ideal condition, flux towards extracellular electron transfer rather than for biosynthesis is beneficial for the conversion of organic matter to electricity without large accumulations of biomass and electricigens may maximize utilization of limited fuel. Our simulations will provide an insight into the enhanced current-generating mechanism and identify theoretical range of respiration

  11. Analysis of enhanced current-generating mechanism of Geobacter sulfurreducens strain via model-driven metabolism simulation.

    Directory of Open Access Journals (Sweden)

    Jing Meng

    Full Text Available Microbial fuel cells (MFCs are a class of ideal technologies that function via anaerobic respiration of electricigens, which bring current generation and environmental restoration together. An in-depth understanding of microbial metabolism is of great importance in engineering microbes to further improve their respiration. We employed flux balance analysis and selected Fe(iii as a substitute for the electrode to simulate current-generating metabolism of Geobacter sulfurreducens PCA with a fixed acetate uptake rate. Simulation results indicated the fluxes of reactions directing acetate towards dissimilation to generate electrons increased under the suboptimal growth condition, resulting in an increase in the respiration rate and a decrease in the growth rate. The results revealed the competitive relationship between oxidative respiration and cell growth during the metabolism of microbe current generation. The results helped us quantitatively understand why microbes growing slowly have the potential to make good use of fuel in MFCs. At the same time, slow growth does not necessarily result in speedy respiration. Alternative respirations may exist under the same growth state due to redundant pathways in the metabolic network. The big difference between the maximum and minimum respiration mainly results from the total formate secretion. With iterative flux variability analysis, a relatively ideal model of variant of G. sulfurreducens PCA was reconstructed by deleting several enzymes in the wild model, which could reach simultaneous suboptimal growth and maximum respiration. Under this ideal condition, flux towards extracellular electron transfer rather than for biosynthesis is beneficial for the conversion of organic matter to electricity without large accumulations of biomass and electricigens may maximize utilization of limited fuel. Our simulations will provide an insight into the enhanced current-generating mechanism and identify theoretical

  12. On the road to improve the bioremediation and electricity-harvesting skills of Geobacter sulfurreducens: functional and structural characterization of multihaem cytochromes.

    Science.gov (United States)

    Morgado, Leonor; Fernandes, Ana P; Dantas, Joana M; Silva, Marta A; Salgueiro, Carlos A

    2012-12-01

    Extracellular electron transfer is one of the physiological hallmarks of Geobacter sulfurreducens, allowing these bacteria to reduce toxic and/or radioactive metals and grow on electrode surfaces. Aiming to functionally optimize the respiratory electron-transfer chains, such properties can be explored through genetically engineered strains. Geobacter species comprise a large number of different multihaem c-type cytochromes involved in the extracellular electron-transfer pathways. The functional characterization of multihaem proteins is particularly complex because of the coexistence of several microstates in solution, connecting the fully reduced and oxidized states. NMR spectroscopy has been used to monitor the stepwise oxidation of each individual haem and thus to obtain information on each microstate. For the structural study of these proteins, a cost-effective isotopic labelling of the protein polypeptide chains was combined with the comparative analysis of 1H-13C HSQC (heteronuclear single-quantum correlation) NMR spectra obtained for labelled and unlabelled samples. These new methodological approaches allowed us to study G. sulfurreducens haem proteins functionally and structurally, revealing functional mechanisms and key residues involved in their electron-transfer capabilities. Such advances can now be applied to the design of engineered haem proteins to improve the bioremediation and electricity-harvesting skills of G. sulfurreducens.

  13. Two ATP phosphoribosyltransferase isozymes of Geobacter sulfurreducens contribute to growth in the presence or absence of histidine and under nitrogen fixation conditions.

    Science.gov (United States)

    Aklujkar, Muktak

    2011-07-01

    Bacteria of the Geobacter clade possess two distinct ATP phosphoribosyltransferases encoded by hisG(L) and hisG(S)+hisZ to catalyze the first reaction of histidine biosynthesis. This very unusual redundancy was investigated by mutational analysis. The hisG(L), hisG(S), and hisZ genes of Geobacter sulfurreducens were deleted, effects on growth and histidine biosynthesis gene expression were evaluated, and deficiencies were complemented with plasmid-borne genes. Both hisG(L) and hisG(S)+hisZ encode functional ATP phosphoribosyltransferases. However, deletion of hisG(L) resulted in no growth defect, whereas deletion of hisG(S) delayed growth when histidine was not provided. Both deletions increased hisZ transcript abundance, and both ΔhisG(S) and ΔhisZ mutations increased hisG(L) transcript abundance. Growth with HisG(L) alone (due to deletion of either hisG(S) or hisZ) was better under nitrogen fixation conditions than when ammonium was provided. Deletion of hisZ caused growth defects under all conditions tested, with or without exogenous sources of histidine, with different patterns of histidine biosynthesis gene expression under each condition. Taken together, the data indicate that G. sulfurreducens depends primarily on the HisG(S)Z isozyme as an ATP phosphoribosyltransferase in histidine biosynthesis, and for other functions when histidine is available; however, HisG(L) also functions as ATP phosphoribosyltransferase, particularly during nitrogen fixation.

  14. A Geobacter sulfurreducens strain expressing pseudomonas aeruginosa type IV pili localizes OmcS on pili but is deficient in Fe(III) oxide reduction and current production.

    Science.gov (United States)

    Liu, Xing; Tremblay, Pier-Luc; Malvankar, Nikhil S; Nevin, Kelly P; Lovley, Derek R; Vargas, Madeline

    2014-02-01

    The conductive pili of Geobacter species play an important role in electron transfer to Fe(III) oxides, in long-range electron transport through current-producing biofilms, and in direct interspecies electron transfer. Although multiple lines of evidence have indicated that the pili of Geobacter sulfurreducens have a metal-like conductivity, independent of the presence of c-type cytochromes, this claim is still controversial. In order to further investigate this phenomenon, a strain of G. sulfurreducens, designated strain PA, was constructed in which the gene for the native PilA, the structural pilin protein, was replaced with the PilA gene of Pseudomonas aeruginosa PAO1. Strain PA expressed and properly assembled P. aeruginosa PilA subunits into pili and exhibited a profile of outer surface c-type cytochromes similar to that of a control strain expressing the G. sulfurreducens PilA. Surprisingly, the strain PA pili were decorated with the c-type cytochrome OmcS in a manner similar to the control strain. However, the strain PA pili were 14-fold less conductive than the pili of the control strain, and strain PA was severely impaired in Fe(III) oxide reduction and current production. These results demonstrate that the presence of OmcS on pili is not sufficient to confer conductivity to pili and suggest that there are unique structural features of the G. sulfurreducens PilA that are necessary for conductivity.

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

    Science.gov (United States)

    Speers, Allison M.; Schindler, Bryan D.; Hwang, Jihwan; Genc, Aycin; Reguera, Gemma

    2016-01-01

    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. PMID:27799920

  16. Genetic identification of a PilT motor in Geobacter sulfurreducens reveals a role for pilus retraction in extracellular electron transfer

    Directory of Open Access Journals (Sweden)

    Allison Speers

    2016-10-01

    Full Text Available 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 paralogue 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.

  17. Comparative genomic analysis of Geobacter sulfurreducens KN400, a strain with enhanced capacity for extracellular electron transfer and electricity production

    Directory of Open Access Journals (Sweden)

    Butler Jessica E

    2012-09-01

    Full Text Available Abstract Background A new strain of Geobacter sulfurreducens, strain KN400, produces more electrical current in microbial fuel cells and reduces insoluble Fe(III oxides much faster than the wildtype strain, PCA. The genome of KN400 was compared to wildtype with the goal of discovering how the network for extracellular electron transfer has changed and how these two strains evolved. Results Both genomes were re-annotated, resulting in 14 fewer genes (net in the PCA genome; 28 fewer (net in the KN400 genome; and ca. 400 gene start and stop sites moved. 96% of genes in KN400 had clear orthologs with conserved synteny in PCA. Most of the remaining genes were in regions of genomic mobility and were strain-specific or conserved in other Geobacteraceae, indicating that the changes occurred post-divergence. There were 27,270 single nucleotide polymorphisms (SNP between the genomes. There was significant enrichment for SNP locations in non-coding or synonymous amino acid sites, indicating significant selective pressure since the divergence. 25% of orthologs had sequence differences, and this set was enriched in phosphorylation and ATP-dependent enzymes. Substantial sequence differences (at least 12 non-synonymous SNP/kb were found in 3.6% of the orthologs, and this set was enriched in cytochromes and integral membrane proteins. Genes known to be involved in electron transport, those used in the metabolic cell model, and those that exhibit changes in expression during growth in microbial fuel cells were examined in detail. Conclusions The improvement in external electron transfer in the KN400 strain does not appear to be due to novel gene acquisition, but rather to changes in the common metabolic network. The increase in electron transfer rate and yield in KN400 may be due to changes in carbon flux towards oxidation pathways and to changes in ATP metabolism, both of which indicate that the overall energy state of the cell may be different. The

  18. Selection of a variant of Geobacter sulfurreducens with enhanced capacity for current production in microbial fuel cells.

    Science.gov (United States)

    Yi, Hana; Nevin, Kelly P; Kim, Byoung-Chan; Franks, Ashely E; Klimes, Anna; Tender, Leonard M; Lovley, Derek R

    2009-08-15

    Geobacter sulfurreducens produces current densities in microbial fuel cells that are among the highest known for pure cultures. The possibility of adapting this organism to produce even higher current densities was evaluated. A system in which a graphite anode was poised at -400 mV (versus Ag/AgCl) was inoculated with the wild-type strain of G. sulfurreducens, strain DL-1. An isolate, designated strain KN400, was recovered from the biofilm after 5 months of growth on the electrode. KN400 was much more effective in current production than strain DL-1. This was apparent with anodes poised at -400 mV, as well as in systems run in true fuel cell mode. KN400 had current (7.6A/m(2)) and power (3.9 W/m(2)) densities that respectively were substantially higher than those of DL1 (1.4A/m(2) and 0.5 W/m(2)). On a per cell basis KN400 was more effective in current production than DL1, requiring thinner biofilms to make equivalent current. The enhanced capacity for current production in KN400 was associated with a greater abundance of electrically conductive microbial nanowires than DL1 and lower internal resistance (0.015 versus 0.130 Omega/m(2)) and mass transfer limitation in KN400 fuel cells. KN400 produced flagella, whereas DL1 does not. Surprisingly, KN400 had much less outer-surface c-type cytochromes than DL1. KN400 also had a greater propensity to form biofilms on glass or graphite than DL1, even when growing with the soluble electron acceptor, fumarate. These results demonstrate that it is possible to enhance the ability of microorganisms to electrochemically interact with electrodes with the appropriate selective pressure and that improved current production is associated with clear differences in the properties of the outer surface of the cell that may provide insights into the mechanisms for microbe-electrode interactions.

  19. Fe(III) reduction-mediated phosphate removal as vivianite (Fe3(PO4)2⋅8H2O) in septic system wastewater.

    Science.gov (United States)

    Azam, Hossain M; Finneran, Kevin T

    2014-02-01

    Phosphate is a water contaminant from fertilizers, soaps, and detergents that enters municipal and onsite wastewater from households, businesses, and other commercial operations. Phosphate is a limiting nutrient for algae, and is one of the molecules that promotes eutrophication of water bodies. Phosphate is especially problematic in onsite wastewater because there are few removal mechanisms under normal operating conditions; a system must be amended specifically with compounds to bond to or adsorb phosphate in the septic tank or within the leach field. Vivianite (Fe3(PO4)2⋅8H2O) is a stable mineral formed from ferrous iron and phosphate, often as the result of Fe(III) reducing microbial activity. What was unknown was the concentration of phosphate that could be removed by this process, and whether it was relevant to mixed microbial systems like septic tank wastewater. Data presented here demonstrate that significant concentrations of phosphate (12-14mM) were removed as vivianite in growing cultures of Geobacter metallireducens strain GS-15. Vivianite precipitates were identified on the cell surfaces and within multi cell clusters using TEM-EDX; the mineral phases were directly characterized using XRD. Phosphate was also removed in dilute and raw (undiluted) septic wastewater amended with different forms of Fe(III) including solid phase and soluble Fe(III). Vivianite precipitates were recovered and identified using XRD, along with siderite (ferrous carbonate), which was expected given that the systems were likely bicarbonate buffered. These data demonstrate that ferric iron amendments in septic wastewater increase phosphate removal as the mineral vivianite, and this may be a good strategy for phosphate attenuation in the septic tank portion of onsite wastewater systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Thermodynamic and kinetic characterization of two methyl-accepting chemotaxis heme sensors from Geobacter sulfurreducens reveals the structural origin of their functional difference.

    Science.gov (United States)

    Silva, Marta A; Valente, Raquel C; Pokkuluri, P Raj; Turner, David L; Salgueiro, Carlos A; Catarino, Teresa

    2014-06-01

    The periplasmic sensor domains GSU582 and GSU935 are part of methyl-accepting chemotaxis proteins of the bacterium Geobacter sulfurreducens containing one c-type heme and a PAS-like fold. Their spectroscopic properties were shown previously to share similar spectral features. In both sensors, the heme group is in the high-spin form in the oxidized state and low-spin after reduction and binding of a methionine residue. Therefore, it was proposed that this redox-linked ligand switch might be related to the signal transduction mechanism. We now report the thermodynamic and kinetic characterization of the sensors GSU582 and GSU935 by visible spectroscopy and stopped-flow techniques, at several pH and ionic strength values. Despite their similar spectroscopic features, the midpoint reduction potentials and the rate constants for reduction by dithionite are considerably different in the two sensors. The reduction potentials of both sensors are negative and well framed within the typical anoxic subsurface environments in which Geobacter species predominate. The midpoint reduction potentials of sensor GSU935 are lower than those of GSU582 at all pH and ionic strength values and the same was observed for the reduction rate constants. The origin of the different functional properties of these closely related sensors is rationalized in the terms of the structures. The results suggest that the sensors are designed to function in different working potential ranges, allowing the bacteria to trigger an adequate cellular response in different anoxic subsurface environments. These findings provide an explanation for the co-existence of two similar methyl-accepting chemotaxis proteins in G. sulfurreducens.

  1. Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator.

    Science.gov (United States)

    Summers, Zarath M; Ueki, Toshiyuki; Ismail, Wael; Haveman, Shelley A; Lovley, Derek R

    2012-05-01

    The addition of organic compounds to groundwater in order to promote bioremediation may represent a new selective pressure on subsurface microorganisms. The ability of Geobacter sulfurreducens, which serves as a model for the Geobacter species that are important in various types of anaerobic groundwater bioremediation, to adapt for rapid metabolism of lactate, a common bioremediation amendment, was evaluated. Serial transfer of five parallel cultures in a medium with lactate as the sole electron donor yielded five strains that could metabolize lactate faster than the wild-type strain. Genome sequencing revealed that all five strains had non-synonymous single-nucleotide polymorphisms in the same gene, GSU0514, a putative transcriptional regulator. Introducing the single-base-pair mutation from one of the five strains into the wild-type strain conferred rapid growth on lactate. This strain and the five adaptively evolved strains had four to eight-fold higher transcript abundance than wild-type cells for genes for the two subunits of succinyl-CoA synthase, an enzyme required for growth on lactate. DNA-binding assays demonstrated that the protein encoded by GSU0514 bound to the putative promoter of the succinyl-CoA synthase operon. The binding sequence was not apparent elsewhere in the genome. These results demonstrate that a single-base-pair mutation in a transcriptional regulator can have a significant impact on the capacity for substrate utilization and suggest that adaptive evolution should be considered as a potential response of microorganisms to environmental change(s) imposed during bioremediation.

  2. A novel Geobacteraceae-specific outer membrane protein J (OmpJ is essential for electron transport to Fe (III and Mn (IV oxides in Geobacter sulfurreducens

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    Schiffer Marianne

    2005-07-01

    Full Text Available Abstract Background Metal reduction is thought to take place at or near the bacterial outer membrane and, thus, outer membrane proteins in the model dissimilatory metal-reducing organism Geobacter sulfurreducens are of interest to understand the mechanisms of Fe(III reduction in the Geobacter species that are the predominant Fe(III reducers in many environments. Previous studies have implicated periplasmic and outer membrane cytochromes in electron transfer to metals. Here we show that the most abundant outer membrane protein of G. sulfurreducens, OmpJ, is not a cytochrome yet it is required for metal respiration. Results When outer membrane proteins of G. sulfurreducens were separated via SDS-PAGE, one protein, designated OmpJ (outer membrane protein J, was particularly abundant. The encoding gene, which was identified from mass spectrometry analysis of peptide fragments, is present in other Geobacteraceae, but not in organisms outside this family. The predicted localization and structure of the OmpJ protein suggested that it was a porin. Deletion of the ompJ gene in G. sulfurreducens produced a strain that grew as well as the wild-type strain with fumarate as the electron acceptor but could not grow with metals, such as soluble or insoluble Fe (III and insoluble Mn (IV oxide, as the electron acceptor. The heme c content in the mutant strain was ca. 50% of the wild-type and there was a widespread loss of multiple cytochromes from soluble and membrane fractions. Transmission electron microscopy analyses of mutant cells revealed an unusually enlarged periplasm, which is likely to trigger extracytoplasmic stress response mechanisms leading to the degradation of periplasmic and/or outer membrane proteins, such as cytochromes, required for metal reduction. Thus, the loss of the capacity for extracellular electron transport in the mutant could be due to the missing c-type cytochromes, or some more direct, but as yet unknown, role of OmpJ in metal

  3. A novel Geobacteraceae-specific outer membrane protein J (OmpJ) is essential for electron transport to Fe (III) and Mn (IV) oxides in Geobacter sulfurreducens

    Science.gov (United States)

    Afkar, Eman; Reguera, Gemma; Schiffer, Marianne; Lovley, Derek R

    2005-01-01

    Background Metal reduction is thought to take place at or near the bacterial outer membrane and, thus, outer membrane proteins in the model dissimilatory metal-reducing organism Geobacter sulfurreducens are of interest to understand the mechanisms of Fe(III) reduction in the Geobacter species that are the predominant Fe(III) reducers in many environments. Previous studies have implicated periplasmic and outer membrane cytochromes in electron transfer to metals. Here we show that the most abundant outer membrane protein of G. sulfurreducens, OmpJ, is not a cytochrome yet it is required for metal respiration. Results When outer membrane proteins of G. sulfurreducens were separated via SDS-PAGE, one protein, designated OmpJ (outer membrane protein J), was particularly abundant. The encoding gene, which was identified from mass spectrometry analysis of peptide fragments, is present in other Geobacteraceae, but not in organisms outside this family. The predicted localization and structure of the OmpJ protein suggested that it was a porin. Deletion of the ompJ gene in G. sulfurreducens produced a strain that grew as well as the wild-type strain with fumarate as the electron acceptor but could not grow with metals, such as soluble or insoluble Fe (III) and insoluble Mn (IV) oxide, as the electron acceptor. The heme c content in the mutant strain was ca. 50% of the wild-type and there was a widespread loss of multiple cytochromes from soluble and membrane fractions. Transmission electron microscopy analyses of mutant cells revealed an unusually enlarged periplasm, which is likely to trigger extracytoplasmic stress response mechanisms leading to the degradation of periplasmic and/or outer membrane proteins, such as cytochromes, required for metal reduction. Thus, the loss of the capacity for extracellular electron transport in the mutant could be due to the missing c-type cytochromes, or some more direct, but as yet unknown, role of OmpJ in metal reduction. Conclusion Omp

  4. The structure of PccH from Geobacter sulfurreducens: A novel low reduction potential monoheme cytochrome essential for accepting electrons from an electrode

    Energy Technology Data Exchange (ETDEWEB)

    Dantas, Joana M; Campelo, Luisa; Duke, Norma E. C.; Salgueiro, Carlos A; Pokkuluri, P. Raj

    2015-06-01

    The structure of cytochrome-c (GSU3274) designated as PccH from Geobacter sulfurreducens was determined at 2.0 Å resolution. PccH is a small (15 kDa) cytochrome containing one c-type heme, found to be essential for growth of G. sulfurreducens accepting electrons from graphite electrodes poised at -300 mV versus SHE with fumarate as the terminal electron acceptor. The structure of PccH is unique among the monoheme cytochromes described to date. The structural fold of PccH can be described as forming two lobes with the heme sandwiched in a cleft between the two lobes. In addition, PccH has a low reduction potential of -24 mV at pH 7, which is unusual for monoheme cytochromes. Based on difference in structure together with sequence phylogenetic analysis we propose that PccH can be regarded as a first characterized example of a new subclass of class I monoheme cytochromes. The low reduction potential of PccH may enable the protein to be redox active at the typically negative potential ranges encountered by this bacterium. Because PccH is predicted to be located in the periplasm of G. sulfurreducens, it could not be involved in the first step of accepting electrons from the electrode but very likely involved in the downstream electron transport events in the periplasm.

  5. HisE11 and HisF8 provide bis-histidyl heme hexa-coordination in the globin domain of Geobacter sulfurreducens globin-coupled sensor.

    Science.gov (United States)

    Pesce, Alessandra; Thijs, Liesbet; Nardini, Marco; Desmet, Filip; Sisinni, Lorenza; Gourlay, Louise; Bolli, Alessandro; Coletta, Massimiliano; Van Doorslaer, Sabine; Wan, Xuehua; Alam, Maqsudul; Ascenzi, Paolo; Moens, Luc; Bolognesi, Martino; Dewilde, Sylvia

    2009-02-13

    Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS(162)) is reported. A combination of X-ray crystallography (crystal structure at 1.5 A resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS(162) as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS(162) is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS(162) is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS(162) is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.

  6. Abundance of the multiheme c-type cytochrome OmcB increases in outer biofilm layers of electrode-grown Geobacter sulfurreducens.

    Directory of Open Access Journals (Sweden)

    Camille S Stephen

    Full Text Available When Geobacter sulfurreducens utilizes an electrode as its electron acceptor, cells embed themselves in a conductive biofilm tens of microns thick. While environmental conditions such as pH or redox potential have been shown to change close to the electrode, less is known about the response of G. sulfurreducens to growth in this biofilm environment. To investigate whether respiratory protein abundance varies with distance from the electrode, antibodies against an outer membrane multiheme cytochrome (OmcB and cytoplasmic acetate kinase (AckA were used to determine protein localization in slices spanning ∼25 µm-thick G. sulfurreducens biofilms growing on polished electrodes poised at +0.24 V (vs. Standard Hydrogen Electrode. Slices were immunogold labeled post-fixing, imaged via transmission electron microscopy, and digitally reassembled to create continuous images allowing subcellular location and abundance per cell to be quantified across an entire biofilm. OmcB was predominantly localized on cell membranes, and 3.6-fold more OmcB was detected on cells 10-20 µm distant from the electrode surface compared to inner layers (0-10 µm. In contrast, acetate kinase remained constant throughout the biofilm, and was always associated with the cell interior. This method for detecting proteins in intact conductive biofilms supports a model where the utilization of redox proteins changes with depth.

  7. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.

    Science.gov (United States)

    Cabezas, Angela; Pommerenke, Bianca; Boon, Nico; Friedrich, Michael W

    2015-06-01

    Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.

  8. The structure of PccH from Geobacter sulfurreducens - a novel low reduction potential monoheme cytochrome essential for accepting electrons from an electrode.

    Science.gov (United States)

    Dantas, Joana M; Campelo, Luísa M; Duke, Norma E C; Salgueiro, Carlos A; Pokkuluri, P Raj

    2015-06-01

    The structure of cytochrome c (GSU3274) designated as PccH from Geobacter sulfurreducens was determined at a resolution of 2.0 Å. PccH is a small (15 kDa) cytochrome containing one c-type heme, found to be essential for the growth of G. sulfurreducens with respect to accepting electrons from graphite electrodes poised at -300 mV versus standard hydrogen electrode. with fumarate as the terminal electron acceptor. The structure of PccH is unique among the monoheme cytochromes described to date. The structural fold of PccH can be described as forming two lobes with the heme sandwiched in a cleft between the two lobes. In addition, PccH has a low reduction potential of -24 mV at pH 7, which is unusual for monoheme cytochromes. Based on difference in structure, together with sequence phylogenetic analysis, we propose that PccH can be regarded as a first characterized example of a new subclass of class I monoheme cytochromes. The low reduction potential of PccH may enable the protein to be redox active at the typically negative potential ranges encountered by G. sulfurreducens. Because PccH is predicted to be located in the periplasm of this bacterium, it could not be involved in the first step of accepting electrons from the electrode but is very likely involved in the downstream electron transport events in the periplasm.

  9. Changes in phosphorylation of adenosine phosphate and redox state of nicotinamide-adenine dinucleotide (phosphate) in Geobacter sulfurreducens in response to electron acceptor and anode potential variation.

    Science.gov (United States)

    Rose, Nicholas D; Regan, John M

    2015-12-01

    Geobacter sulfurreducens is one of the dominant bacterial species found in biofilms growing on anodes in bioelectrochemical systems. The intracellular concentrations of reduced and oxidized forms of nicotinamide-adenine dinucleotide (NADH and NAD(+), respectively) and nicotinamide-adenine dinucleotide phosphate (NADPH and NADP(+), respectively) as well as adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) were measured in G. sulfurreducens using fumarate, Fe(III)-citrate, or anodes poised at different potentials (110, 10, -90, and -190 mV (vs. SHE)) as the electron acceptor. The ratios of CNADH/CNAD+ (0.088±0.022) and CNADPH/CNADP+ (0.268±0.098) were similar under all anode potentials tested and with Fe(III)-citrate (reduced extracellularly). Both ratios significantly increased with fumarate as the electron acceptor (0.331±0.094 for NAD and 1.96±0.37 for NADP). The adenylate energy charge (the fraction of phosphorylation in intracellular adenosine phosphates) was maintained near 0.47 under almost all conditions. Anode-growing biofilms demonstrated a significantly higher molar ratio of ATP/ADP relative to suspended cultures grown on fumarate or Fe(III)-citrate. These results provide evidence that the cellular location of reduction and not the redox potential of the electron acceptor controls the intracellular redox potential in G. sulfurreducens and that biofilm growth alters adenylate phosphorylation.

  10. Reduction of ferrihydrite with adsorbed and coprecipitated organic matter: microbial reduction by Geobacter bremensis vs. abiotic reduction by Na-dithionite

    Science.gov (United States)

    Eusterhues, K.; Hädrich, A.; Neidhardt, J.; Küsel, K.; Keller, T. F.; Jandt, K. D.; Totsche, K. U.

    2014-09-01

    Ferrihydrite is a widespread poorly crystalline Fe oxide which becomes easily coated by natural organic matter in the environment. This mineral-bound organic matter entirely changes the mineral surface properties and therefore the reactivity of the original mineral. Here, we investigated 2-line ferrihydrite, ferrihydrite with adsorbed organic matter, and ferrihydrite coprecipitated with organic matter for microbial and abiotic reduction of Fe(III). Ferrihydrite-organic matter associations with different organic matter loadings were reduced either by Geobacter bremensis or abiotically by Na-dithionite. Both types of experiments showed decreasing initial Fe-reduction rates and decreasing degrees of reduction with increasing amounts of mineral-bound organic matter. At similar organic matter loadings, coprecipitated ferrihydrites were more reactive than ferrihydrites with adsorbed organic matter. The difference can be explained by the smaller crystal size and poor crystallinity of such coprecipitates. At small organic matter loadings the poor crystallinity of coprecipitates led to even faster Fe-reduction rates than found for pure ferrihydrite. The amount of mineral-bound organic matter also affected the formation of secondary minerals: goethite was only found after reduction of organic matter-free ferrihydrite and siderite was only detected when ferrihydrites with relatively low amounts of mineral-bound organic matter were reduced. We conclude that direct contact of G. bremensis to the Fe oxide mineral surface was inhibited by attached organic matter. Consequently, mineral-bound organic matter shall be taken into account as a factor in slowing down reductive dissolution.

  11. Role of Met58 in the regulation of electron/proton transfer in trihaem cytochrome PpcA from Geobacter sulfurreducens

    Science.gov (United States)

    Morgado, Leonor; Dantas, Joana M.; Simões, Telma; Londer, Yuri Y.; Pokkuluri, P. Raj; Salgueiro, Carlos A.

    2012-01-01

    The bacterium Gs (Geobacter sulfurreducens) is capable of oxidizing a large variety of compounds relaying electrons out of the cytoplasm and across the membranes in a process designated as extracellular electron transfer. The trihaem cytochrome PpcA is highly abundant in Gs and is most probably the reservoir of electrons destined for the outer surface. In addition to its role in electron transfer pathways, we have previously shown that this protein could perform e−/H+ energy transduction. This mechanism is achieved by selecting the specific redox states that the protein can access during the redox cycle and might be related to the formation of proton electrochemical potential gradient across the periplasmic membrane. The regulatory role of haem III in the functional mechanism of PpcA was probed by replacing Met58, a residue that controls the solvent accessibility of haem III, with serine, aspartic acid, asparagine or lysine. The data obtained from the mutants showed that the preferred e−/H+ transfer pathway observed for PpcA is strongly dependent on the reduction potential of haem III. It is striking to note that one residue can fine tune the redox states that can be accessed by the trihaem cytochrome enough to alter the functional pathways. PMID:23030844

  12. Outer-membrane cytochrome-c, OmcF, from Geobacter sulfurreducens : high structural similarity to an algal cytochrone c{sub 6}.

    Energy Technology Data Exchange (ETDEWEB)

    Pokkuluri, P. R.; Londer, Y. Y.; Wood, S. J.; Duke, N. E. C.; Morgado, L.; Salgueiro, C. A.; Schiffer, M.; Biosciences Division; Univ. Nova de Lisboa, Campus Caparica

    2009-01-01

    Putative outer membrane c-type cytochromes have been implicated in metal ion reducing properties of Geobacter sulfurreducens. OmcF (GSU2432), OmcB (GSU2731), and OmcC are three such proteins that have predicted lipid anchors. MmcF is a monoheme cytochrome, whereas OmcB and OmcC are multiheme cytochromes. Deletion of OmcF was reported to affect the expression of OmcB and OmcC in G. sulfurreducens. The OmcF deficient strain was impaired in its ability to both reduce and grow on Fe(III) citrate probably because the expression fo OmcB, which is crucial for iron reduction, is low in this strain. U(VI) reduction activity of this bacterium is also lower on deletion of OmcB or OmcF. The U(VI) reduction activity is affected more by the deletion of OmcF than by the deletion of OmcB.

  13. Changes in phosphorylation of adenosine phosphate and redox state of nicotinamide-adenine dinucleotide (phosphate) in Geobacter sulfurreducens in response to electron acceptor and anode potential variation

    KAUST Repository

    Rose, Nicholas D.

    2015-12-01

    © 2015 Elsevier B.V. Geobacter sulfurreducens is one of the dominant bacterial species found in biofilms growing on anodes in bioelectrochemical systems. The intracellular concentrations of reduced and oxidized forms of nicotinamide-adenine dinucleotide (NADH and NAD+, respectively) and nicotinamide-adenine dinucleotide phosphate (NADPH and NADP+, respectively) as well as adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) were measured in G. sulfurreducens using fumarate, Fe(III)-citrate, or anodes poised at different potentials (110, 10, -90, and -190mV (vs. SHE)) as the electron acceptor. The ratios of CNADH/CNAD+ (0.088±0.022) and CNADPH/CNADP+ (0.268±0.098) were similar under all anode potentials tested and with Fe(III)-citrate (reduced extracellularly). Both ratios significantly increased with fumarate as the electron acceptor (0.331±0.094 for NAD and 1.96±0.37 for NADP). The adenylate energy charge (the fraction of phosphorylation in intracellular adenosine phosphates) was maintained near 0.47 under almost all conditions. Anode-growing biofilms demonstrated a significantly higher molar ratio of ATP/ADP relative to suspended cultures grown on fumarate or Fe(III)-citrate. These results provide evidence that the cellular location of reduction and not the redox potential of the electron acceptor controls the intracellular redox potential in G. sulfurreducens and that biofilm growth alters adenylate phosphorylation.

  14. Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET in Defined Co-Cultures

    Directory of Open Access Journals (Sweden)

    Li-YIng eWang

    2016-03-01

    Full Text Available Direct interspecies electron transfer (DIET has been recognized as an alternative to interspecies H2 transfer as a mechanism for syntrophic growth, but previous studies on DIET with defined co-cultures have only documented DIET with ethanol as the electron donor in the absence of conductive materials. Co-cultures of Geobacter metallireducens and Geobacter sulfurreducens metabolized propanol, butanol, propionate, and butyrate with the reduction of fumarate to succinate. G. metallireducens utilized each of these substrates whereas only electrons available from DIET supported G. sulfurreducens respiration. A co-culture of G. metallireducens and a strain of G. sulfurreducens that could not metabolize acetate oxidized acetate with fumarate as the electron acceptor, demonstrating that acetate can also be syntrophically metabolized via DIET. A co-culture of G. metallireducens and Methanosaeta harundinacea previously shown to syntrophically convert ethanol to methane via DIET metabolized propanol or butanol as the sole electron donor, but not propionate or butyrate. The stoichiometric accumulation of propionate or butyrate in the propanol- or butanol-fed cultures demonstrated that M. harundinaceae could conserve energy to support growth solely from electrons derived from DIET. Co-cultures of G. metallireducens and Methanosarcina barkeri could also incompletely metabolize propanol and butanol and did not metabolize propionate or butyrate as sole electron donors. These results expand the range of substrates that are known to be syntrophically metabolized through DIET, but suggest that claims of propionate and butyrate metabolism via DIET in mixed microbial communities warrant further validation.

  15. Spectroscopic Studies of Abiotic and Biological Nanomaterials: Silver Nanoparticles, Rhodamine 6G Adsorbed on Graphene, and c-Type Cytochromes and Type IV Pili in Geobacter sulfurreducens

    Science.gov (United States)

    Thrall, Elizabeth S.

    This thesis describes spectroscopic studies of three different systems: silver nanoparticles, the dye molecule rhodamine 6G adsorbed on graphene, and the type IV pili and c-type cytochromes produced by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens. Although these systems are quite different in some ways, they can all be considered examples of nanomaterials. A nanomaterial is generally defined as having at least one dimension below 100 nm in size. Silver nanoparticles, with sub-100 nm size in all dimensions, are examples of zero-dimensional nanomaterials. Graphene, a single atomic layer of carbon atoms, is the paradigmatic two-dimensional nanomaterial. And although bacterial cells are on the order of 1 μm in size, the type IV pili and multiheme c-type cytochromes produced by G. sulfurreducens can be considered to be one- and zero-dimensional nanomaterials respectively. A further connection between these systems is their strong interaction with visible light, allowing us to study them using similar spectroscopic tools. The first chapter of this thesis describes research on the plasmon-mediated photochemistry of silver nanoparticles. Silver nanoparticles support coherent electron oscillations, known as localized surface plasmons, at resonance frequencies that depend on the particle size and shape and the local dielectric environment. Nanoparticle absorption and scattering cross-sections are maximized at surface plasmon resonance frequencies, and the electromagnetic field is amplified near the particle surface. Plasmonic effects can enhance the photochemistry of silver particles alone or in conjunction with semiconductors according to several mechanisms. We study the photooxidation of citrate by silver nanoparticles in a photoelectrochemical cell, focusing on the wavelength-dependence of the reaction rate and the role of the semiconductor substrate. We find that the citrate photooxidation rate does not track the plasmon resonance of the silver

  16. Unveiling the Structural Basis That Regulates the Energy Transduction Properties within a Family of Triheme Cytochromes from Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Dantas, Joana M.; Simões, Telma; Morgado, Leonor; Caciones, Clara; Fernandes, Ana P.; Silva, Marta A.; Bruix, Marta; Pokkuluri, P. Raj; Salgueiro, Carlos A.

    2016-10-06

    A family of triheme cytochromes from Geobacter sulfurreducens plays an important role in extracellular electron transfer. In addition to their role in electron transfer pathways, two members of this family (PpcA and PpcD) were also found to be able to couple e(-)/H+ transfer through the redox Bohr effect observed in the physiological pH range, a feature not observed for cytochromes PpcB and PpcE. In attempting to understand the molecular control of the redox Bohr effect in this family of cytochromes, which is highly homologous both in amino acid sequence and structures, it was observed that residue 6 is a conserved leucine in PpcA and PpcD, whereas in the other two characterized members (PpcB and PpcE) the equivalent residue is a phenylalanine. To determine the role of this residue located close to the redox Bohr center, we replaced Leu(6) in PpcA with Phe and determined the redox properties of the mutant, as well as its solution structure in the fully reduced state. In contrast with the native form, the mutant PpcAL6F is not able to couple the e(-)/H+ pathway. We carried out the reverse mutation in PpcB and PpcE (i.e., replacing Phe(6) in these two proteins by leucine) and the mutated proteins showed an increased redox Bohr effect. The results clearly establish the role of residue 6 in the control of the redox Bohr effect in this family of cytochromes, a feature that could enable the rational design of G. sulfurreducens strains that carry mutant cytochromes with an optimal redox Bohr effect that would be suitable for various biotechnological applications.

  17. Structures and solution properties of two novel periplasmic sensor domains with c-type heme from chemotaxis proteins of Geobacter sulfurreducens : implications for signal transduction.

    Energy Technology Data Exchange (ETDEWEB)

    Pokkuluri, P. R.; Pessanha, M.; Londer, Y. Y.; Wood, S. J.; Duke, N. E. C.; Wilton, R.; Catarino, T.; Salgueiro, C. A.; Schiffer, M.; Biosciences Division; Univ.Nova de Lisboa; Insti. de Tecnologia Quimica e Biologica

    2008-04-11

    Periplasmic sensor domains from two methyl-accepting chemotaxis proteins from Geobacter sulfurreducens (encoded by genes GSU0935 and GSU0582) were expressed in Escherichia coli. The sensor domains were isolated, purified, characterized in solution, and their crystal structures were determined. In the crystal, both sensor domains form swapped dimers and show a PAS-type fold. The swapped segment consists of two helices of about 45 residues at the N terminus with the hemes located between the two monomers. In the case of the GSU0582 sensor, the dimer contains a crystallographic 2-fold symmetry and the heme is coordinated by an axial His and a water molecule. In the case of the GSU0935 sensor, the crystals contain a non-crystallographic dimer, and surprisingly, the coordination of the heme in each monomer is different; monomer A heme has His-Met ligation and monomer B heme has His-water ligation as found in the GSU0582 sensor. The structures of these sensor domains are the first structures of PAS domains containing covalently bound heme. Optical absorption, electron paramagnetic resonance and NMR spectroscopy have revealed that the heme groups of both sensor domains are high-spin and low-spin in the oxidized and reduced forms, respectively, and that the spin-state interconversion involves a heme axial ligand replacement. Both sensor domains bind NO in their ferric and ferrous forms but bind CO only in the reduced form. The binding of both NO and CO occurs via an axial ligand exchange process, and is fully reversible. The reduction potentials of the sensor domains differ by 95 mV (-156 mV and -251 mV for sensors GSU0582 and GSU0935, respectively). The swapped dimerization of these sensor domains and redox-linked ligand switch might be related to the mechanism of signal transduction by these chemotaxis proteins.

  18. Reduction of ferrihydrite with adsorbed and coprecipitated organic matter: microbial reduction by Geobacter bremensis vs. abiotic reduction by Na-dithionite

    Directory of Open Access Journals (Sweden)

    K. Eusterhues

    2014-04-01

    Full Text Available Ferrihydrite (Fh is a widespread poorly crystalline Fe oxide which becomes easily coated by natural organic matter (OM in the environment. This mineral-bound OM entirely changes the mineral surface properties and therefore the reactivity of the original mineral. Here, we investigated the reactivity of 2-line Fh, Fh with adsorbed OM and Fh coprecipitated with OM towards microbial and abiotic reduction of Fe(III. As a surrogate for dissolved soil OM we used a water extract of a Podzol forest floor. Fh-OM associations with different OM-loadings were reduced either by Geobacter bremensis or abiotically by Na-dithionite. Both types of experiments showed decreasing initial Fe reduction rates and decreasing degrees of reduction with increasing amounts of mineral-bound OM. At similar OM-loadings, coprecipitated Fhs were more reactive than Fhs with adsorbed OM. The difference can be explained by the smaller crystal size and poor crystallinity of such coprecipitates. At small OM loadings this led to even faster Fe reduction rates than found for pure Fh. The amount of mineral-bound OM also affected the formation of secondary minerals: goethite was only found after reduction of OM-free Fh and siderite was only detected when Fhs with relatively low amounts of mineral-bound OM were reduced. We conclude that direct contact of G. bremensis to the Fe oxide mineral surface was inhibited when blocked by OM. Consequently, mineral-bound OM shall be taken into account besides Fe(II accumulation as a further widespread mechanism to slow down reductive dissolution.

  19. Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c-Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens▿ †

    Science.gov (United States)

    Inoue, Kengo; Qian, Xinlei; Morgado, Leonor; Kim, Byoung-Chan; Mester, Tünde; Izallalen, Mounir; Salgueiro, Carlos A.; Lovley, Derek R.

    2010-01-01

    Previous studies have demonstrated that Geobacter sulfurreducens requires the c-type cytochrome OmcZ, which is present in large (OmcZL; 50-kDa) and small (OmcZS; 30-kDa) forms, for optimal current production in microbial fuel cells. This protein was further characterized to aid in understanding its role in current production. Subcellular-localization studies suggested that OmcZS was the predominant extracellular form of OmcZ. N- and C-terminal amino acid sequence analysis of purified OmcZS and molecular weight measurements indicated that OmcZS is a cleaved product of OmcZL retaining all 8 hemes, including 1 heme with the unusual c-type heme-binding motif CX14CH. The purified OmcZS was remarkably thermally stable (thermal-denaturing temperature, 94.2°C). Redox titration analysis revealed that the midpoint reduction potential of OmcZS is approximately −220 mV (versus the standard hydrogen electrode [SHE]) with nonequivalent heme groups that cover a large reduction potential range (−420 to −60 mV). OmcZS transferred electrons in vitro to a diversity of potential extracellular electron acceptors, such as Fe(III) citrate, U(VI), Cr(VI), Au(III), Mn(IV) oxide, and the humic substance analogue anthraquinone-2,6-disulfonate, but not Fe(III) oxide. The biochemical properties and extracellular localization of OmcZ suggest that it is well suited for promoting electron transfer in current-producing biofilms of G. sulfurreducens. PMID:20400562

  20. De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.

    Directory of Open Access Journals (Sweden)

    Harish Nagarajan

    Full Text Available State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated.We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454 to assemble a complete microbial genome de novo. We applied this approach to completely assemble the 3.7 Mb genome of a rare Geobacter variant (KN400 that is capable of unprecedented current production at an electrode. Two key components of our strategy enabled us to achieve this result. First, we integrated the two data types early in the process to maximally leverage their complementary characteristics. And second, we used the output of different short read assembly programs in such a way so as to leverage the complementary nature of their different underlying algorithms or of their different implementations of the same underlying algorithm.The significance of our result is that it demonstrates a general approach for maximizing the efficiency and success of genome assembly projects as new sequencing technologies and new assembly algorithms are introduced. The general approach is a meta strategy, wherein sequencing data are integrated as early as possible and in particular ways and wherein multiple assembly algorithms are judiciously applied such that the deficiencies in one are complemented by another.

  1. Insights into genes involved in electricity generation in Geobacter sulfurreducens via whole genome microarray analysis of the OmcF-deficient mutant.

    Science.gov (United States)

    Kim, Byoung-Chan; Postier, Bradley L; Didonato, Raymond J; Chaudhuri, Swades K; Nevin, Kelly P; Lovley, Derek R

    2008-06-01

    Geobacter sulfurreducens effectively produces electricity in microbial fuel cells by oxidizing acetate with an electrode serving as the sole electron acceptor. Deletion of the gene encoding OmcF, a monoheme outer membrane c-type cytochrome, substantially decreased current production. Previous studies demonstrated that inhibition of Fe(III) reduction in the OmcF-deficient mutant could be attributed to poor transcription of the gene for OmcB, an outer membrane c-type cytochrome that is required for Fe(III) reduction. However, a mutant in which omcB was deleted produced electricity as well as wild type. Microarray analysis of the OmcF-deficient mutant versus the wild type revealed that many of the genes with the greatest decreases in transcript levels were genes whose expression was previously reported to be upregulated in cells grown with an electrode as the sole electron acceptor. These included genes with putative functions related to metal efflux and/or type I secretion and two hypothetical proteins. The outer membrane cytochromes, OmcS and OmcE, which previous studies have demonstrated are required for optimal current generation, were not detected on the outer surface of the OmcF-deficient mutant even though the omcS and omcE genes were still transcribed, suggesting that the putative secretion system could be involved in the export of outer membrane proteins necessary for electron transfer to the fuel cell anode. These results suggest that the requirement for OmcF for optimal current production is not because OmcF is directly involved in extracellular electron transfer but because OmcF is required for the appropriate transcription of other genes either directly or indirectly involved in electricity production.

  2. Bidirectional Photoinduced Electron Transfer in Ruthenium(II)-tris-Bipyridyl Modified PpcA, a Multi-Heme c-type Cytochrome from Geobacter sulfurreducens

    Energy Technology Data Exchange (ETDEWEB)

    Kokhan, Oleksandr; Ponomarenko, Nina S.; Pokkuluri, Phani R.; Schiffer, Marianne; Mulfort, Karen L.; Tiede, David M.

    2015-06-18

    PpcA, a tri-heme cytochrome c7 from Geobacter sulfurreducens was investigated as a model for photosensitizer-initiated electron transfer within a multi-heme "molecular wire" protein architecture. E. coli expression of PpcA was found to be tolerant of cysteine site-directed mutagenesis, demonstrated by the successful expression of natively folded proteins bearing cysteine mutations at a series of sites selected to vary characteristically with respect to the three -CXXCH- heme binding domains. A preliminary survey of 5 selected mutants found that the introduced cysteines can be readily covalently linked to a Ru(II)-(2,2'-bpy)2(4-bromomethyl-4’-methyl-2,2'-bpy) photosensitizer (where bpy = bipyridine), and that the linked constructs support both photo-oxidative and photo-reductive quenching of the photosensitizer excited-state, depending upon the initial heme redox state. For photo-oxidative electron transfer, apparent heme reduction risetimes were found to vary from 7 x 10-12 s to 5 x 10-8 s, depending upon the site of photosensitizer linking. The excited-state electron transfers are about 103-fold faster than any previously reported photosensitizer-redox protein covalently linked construct. Preliminary conformational analysis using molecular dynamics simulations shows that rates for electron transfer track both the distance and pathways for electron transfer. Two mutants with the fastest charge transfer rates, A23C and K29C, showed a significant role of specific paths for electron transfer. While K29C labeled mutant was expected to have approximately 0.8Å greater donor-acceptor distance, it showed 20-fold faster charge separation rate. Clear evidence for inter-heme electron transfer within the multi-heme protein is not detected within the lifetimes of the charge separated states. These results demonstrate an opportunity to develop multi-heme c-cytochromes for investigation of electron transfer in protein "molecular wires" and to serve as frameworks for

  3. Outer-membrane cytochrome-c, OmcF from Geobacter sulfurreducens: high structural similarity to an algal cytochrome c6.

    Energy Technology Data Exchange (ETDEWEB)

    Pokkuluri, P. R.; Londer, Y. Y.; Wood, S. J.; Duke, N. E. C.; Morgado, L.; Salgueiro, C. A.; Schiffer, M.; Biosciences Division; Univ. Nova de Lisboa

    2009-01-01

    Putative outer membrane c-type cytochromes have been implicated in metal ion reducing properties of Geobacter sulfurreducens. OmcF (GSU2432), OmcB (GSU2731), and OmcC (GSU2737) are three such proteins that have predicted lipid anchors. OmcF is a monoheme cytochrome, whereas OmcB and OmcC are multiheme cytochromes. Deletion of OmcF was reported to affect the expression of OmcB and OmcC in G. sulfurreducens. The OmcF deficient strain was impaired in its ability to both reduce and grow on Fe(III) citrate probably because the expression of OmcB, which is crucial for iron reduction, is low in this strain. U(VI) reduction activity of this bacterium is also lower on deletion of OmcB or OmcF. The U(VI) reduction activity is affected more by the deletion of OmcF than by the deletion of OmcB. The soluble part of OmcF (residues 20-104, referred to as OmcF{sub S} hereafter) has sequence similarity to soluble cytochromes c{sub 6} of photosynthetic algae and cyanobacteria. The cytochrome c{sub 6} proteins in algae and cyanobacteria are electron transport proteins that mediate the transfer of electrons from cytochrome b{sub 6}f to photosystem I and have high reduction potentials of about +350 mV and low pI. The structures of seven cytochromes c{sub 6} have been previously determined. Further, a c{sub 6}-like cytochrome (PetJ2) of unknown function was recently identified in Synechoccus sp. PCC 7002 with a reduction potential of +148 mV and high pI. Here, we report the structure of OmcF{sub S} and its remarkable structural similarity to that of cytochrome c{sub 6} from the green alga, Monoraphidium braunii. To our knowledge, OmcF{sub S} is the first example of a cytochrome c{sub 6}-like structure from a nonphotosynthetic organism.

  4. Direct Involvement of ombB, omaB and omcB Genes in Extracellular Reduction of Fe(III by Geobacter sulfurreducens PCA

    Directory of Open Access Journals (Sweden)

    Yimo eLiu

    2015-10-01

    Full Text Available The tandem gene clusters orfR-ombB-omaB-omcB and orfS-ombC-omaC-omcC of the metal-reducing bacterium Geobacter sulfurreducens PCA are responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III-citrate and ferrihydrite [a poorly crystalline Fe(III oxide]. Each gene cluster encodes a putative transcriptional factor (OrfR/OrfS, a porin-like outer-membrane protein (OmbB/OmbC, a periplasmic c-type cytochrome (c-Cyt, OmaB/OmaC and an outer-membrane c-Cyt (OmcB/OmcC. The individual roles of OmbB, OmaB and OmcB in extracellular reduction of Fe(III, however, have remained either uninvestigated or controversial. Here, we showed that replacements of ombB, omaB, omcB and ombB-omaB with an antibiotic gene in the presence of ombC-omaC-omcC had no impact on reduction of Fe(III-citrate by G. sulfurreducens PCA. Disruption of ombB, omaB, omcB and ombB-omaB in the absence of ombC-omaC-omcC, however, severely impaired the bacterial ability to reduce Fe(III-citrate as well as ferrihydrite. These results unequivocally demonstrate an overlapping role of ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III reduction by G. sulfurreducens PCA. Involvement of both ombB-omaB-omcB and ombC-omaC-omcC in extracellular Fe(III reduction reflects the importance of these trans-outer membrane protein complexes in the physiology of this bacterium. Moreover, the kinetics of Fe(III-citrate and ferrihydrite reduction by these mutants in the absence of ombC-omaC-omcC were nearly identical, which suggests that absence of any protein subunit eliminates function of OmaB/OmbB/OmcB protein complex. Finally, orfS was found to have a negative impact on the extracellular reduction of Fe(III-citrate and ferrihydrite in G. sulfurreducens PCA probably by serving as a transcriptional repressor.

  5. Promoting direct interspecies electron transfer with activated carbon

    DEFF Research Database (Denmark)

    Liu, Fanghua; Rotaru, Amelia-Elena; Shrestha, Pravin M.

    2012-01-01

    of methanogenesis might be to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens. Metabolism was substantially accelerated when GAC was added to co-cultures of Geobacter metallireducens and Geobacter sulfurreducens grown under conditions previously shown to require DIET. Cells...... were attached to GAC, but did not aggregate as they do when making biological electrical connections between cells. Studies with a series of gene deletion mutants eliminated the possibility that GAC promoted electron exchange via interspecies hydrogen or formate transfer and demonstrated that DIET...

  6. The Role of Shewanella oneidensis MR-1 Outer Surface Structures in Extracellular Electron Transfer

    Science.gov (United States)

    2010-01-01

    bacteria such as Shewanella putrefaciens sp200, Geobacter metallireducens, and G. sulfurreducens [14 – 17]. In several of these bacteria, target- ing of c...Full Paper The Role of Shewanella oneidensis MR-1 Outer Surface Structures in Extracellular Electron Transfer Rachida A. Bouhenni,a, f Gary J. Vora,b...metal reducer Shewanella oneidensis MR-1 to generate electricity in microbial fuel cells (MFCs) depends on the activity of a predicted type IV prepilin

  7. Annual progress Report on research related to our research project “Stabilization of Plutonium in Subsurface Environments via Microbial Reduction and Biofilm Formation” funded by the Environmental Remediation Sciences Division (ERSD)

    Energy Technology Data Exchange (ETDEWEB)

    New, Mary

    2006-06-01

    The overarching goal of this research project is to investigate and optimize the mechanisms for in situ immobilization of Pu species by naturally-occurring bacteria. Specific research objectives are: (a) investigate the mechanism of bacterial accumulation and immobilization of plutonium species by biofilm formation under aerobic conditions and (b) to demonstrate the direct and indirect stabilization of Pu via dissimilatory reduction by Geobacter metallireducens.

  8. 纯培养条件下不同氧化铁的微生物还原能力%MICROBIAL REDUCTION ABILITY OF VARIOUS IRON OXIDES IN PURE CULTURE EXPERIMENT

    Institute of Scientific and Technical Information of China (English)

    曲东; Sylvia; Schnell

    2001-01-01

    @@ 在自然湿地及含水沉积物中铁的还原是纯化学过程还是生物学过程,这一问题直到80年代末才有了比较明确的认识.过去认为,厌氧环境中低氧化还原电位的发生是氧的微生物消耗的结果,具有还原性的代谢物的产生能引起Fe(Ⅲ)自发地向Fe(Ⅱ)的非生物转化.然而,对这一假设的直接评价[1]已经表明:低氧化还原电位不是引起Fe(Ⅲ)还原的充分条件,而需要具有酶学还原Fe(Ⅲ)能力的微生物存在.只有当沉积物环境中保持一定的酶学活性时,才有显著的Fe(Ⅲ)还原作用发生.因此,现在的观点是:具有还原Fe(Ⅲ)能力的细菌及铁还原酶才是厌氧沉积物环境中含铁氧化物还原的真正动力[2~4].自从1987年分离得到Geobacter metallireducens GS-15[5]金属还原菌以来,采用纯培养的方法已获得了大量的微生物还原Fe(Ⅲ)的证据,对Fe(Ⅲ)的微生物还原机理也有了较为深入的认识,即铁还原菌由Fe(Ⅲ)还原为Fe(Ⅱ)的过程中获取能量,有机物的氧化将提供电子给Fe(Ⅲ).土壤中全铁的含量约为4%,除无定形氧化铁以外,晶体结构存在的氧化铁占到75%以上,其中包括纤铁矿、赤铁矿、针铁矿及其铝取代物.在厌氧条件下,不同的氧化铁晶体能否被还原或还原程度如何,目前并不十分清楚.本文采用纯培养的实验方法,通过接种Fe(Ⅲ)还原菌GS-15,以便探讨不同氧化铁的微生物还原能力,其结果将有助于对淹水土壤中Fe(Ⅲ)还原特征的认识.

  9. Evidence for interaction between the triheme cytochrome PpcA from Geobacter sulfurreducens and anthrahydroquinone-2,6-disulfonate, an analog of the redox active components of humic substances.

    Science.gov (United States)

    Dantas, Joana M; Morgado, Leonor; Catarino, Teresa; Kokhan, Oleksandr; Pokkuluri, P Raj; Salgueiro, Carlos A

    2014-06-01

    The bacterium Geobacter sulfurreducens displays an extraordinary respiratory versatility underpinning the diversity of electron donors and acceptors that can be used to sustain anaerobic growth. Remarkably, G. sulfurreducens can also use as electron donors the reduced forms of some acceptors, such as the humic substance analog anthraquinone-2,6-disulfonate (AQDS), a feature that confers environmentally competitive advantages to the organism. Using UV-visible and stopped-flow kinetic measurements we demonstrate that there is electron exchange between the triheme cytochrome PpcA from Gs and AQDS. 2D-(1)H-(15)N HSQC NMR spectra were recorded for (15)N-enriched PpcA samples, in the absence and presence of AQDS. Chemical shift perturbation measurements, at increasing concentration of AQDS, were used to probe the interaction region and to measure the binding affinity of the PpcA-AQDS complex. The perturbations on the NMR signals corresponding to the PpcA backbone NH and heme substituents showed that the region around heme IV interacts with AQDS through the formation of a complex with a definite life time in the NMR time scale. The comparison of the NMR data obtained for PpcA in the presence and absence of AQDS showed that the interaction is reversible. Overall, this study provides for the first time a clear illustration of the formation of an electron transfer complex between AQDS and a G. sulfurreducens triheme cytochrome, shedding light on the electron transfer pathways underlying the microbial oxidation of humics.

  10. Dissimilatory Fe(III) Reduction by the Marine Microorganism Desulfuromonas acetoxidans

    OpenAIRE

    Roden, Eric E.; Lovley, Derek R.

    1993-01-01

    The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c-type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)-citrate and Mn(IV)-oxalate, as well as by two electron acceptors...

  11. Promoting Interspecies Electron Transfer with Biochar

    Science.gov (United States)

    Chen, Shanshan; Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Malvankar, Nikhil S.; Liu, Fanghua; Fan, Wei; Nevin, Kelly P.; Lovley, Derek R.

    2014-01-01

    Biochar, a charcoal-like product of the incomplete combustion of organic materials, is an increasingly popular soil amendment designed to improve soil fertility. We investigated the possibility that biochar could promote direct interspecies electron transfer (DIET) in a manner similar to that previously reported for granular activated carbon (GAC). Although the biochars investigated were 1000 times less conductive than GAC, they stimulated DIET in co-cultures of Geobacter metallireducens with Geobacter sulfurreducens or Methanosarcina barkeri in which ethanol was the electron donor. Cells were attached to the biochar, yet not in close contact, suggesting that electrons were likely conducted through the biochar, rather than biological electrical connections. The finding that biochar can stimulate DIET may be an important consideration when amending soils with biochar and can help explain why biochar may enhance methane production from organic wastes under anaerobic conditions. PMID:24846283

  12. Promoting interspecies electron transfer with biochar

    DEFF Research Database (Denmark)

    Chen, Shanshan; Rotaru, Amelia-Elena; Shrestha, Pravin Malla

    2014-01-01

    Biochar, a charcoal-like product of the incomplete combustion of organic materials, is an increasingly popular soil amendment designed to improve soil fertility. We investigated the possibility that biochar could promote direct interspecies electron transfer (DIET) in a manner similar...... to that previously reported for granular activated carbon (GAC). Although the biochars investigated were 1000 times less conductive than GAC, they stimulated DIET in co-cultures of Geobacter metallireducens with Geobacter sulfurreducens or Methanosarcina barkeri in which ethanol was the electron donor. Cells were...... attached to the biochar, yet not in close contact, suggesting that electrons were likely conducted through the biochar, rather than biological electrical connections. The finding that biochar can stimulate DIET may be an important consideration when amending soils with biochar and can help explain why...

  13. Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

    KAUST Repository

    Kiely, Patrick D.

    2011-01-01

    Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H2 gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current. © 2010 Elsevier Ltd.

  14. Syntrophic Growth via Quinone-Mediated Interspecies Electron Transfer

    Directory of Open Access Journals (Sweden)

    Jessica A Smith

    2015-02-01

    Full Text Available The mechanisms by which microbial species exchange electrons are of interest because interspecies electron transfer can expand the metabolic capabilities of microbial communities. Previous studies with the humic substance analog anthraquinone-2,6-disulfonate (AQDS suggested that quinone-mediated interspecies electron transfer (QUIET is feasible, but it was not determined if sufficient energy is available from QUIET to support the growth of both species. Furthermore, there have been no previous studies on the mechanisms for the oxidation of anthrahydroquinone-2,6-disulfonate (AHQDS. A co-culture of Geobacter metallireducens and Geobacter sulfurreducens metabolized ethanol with the reduction of fumarate much faster in the presence of AQDS, and there was an increase in cell protein. G. sulfurreducens was more abundant, consistent with G. sulfurreducens obtaining electrons from acetate that G. metallireducens produced from ethanol, as well as from AHQDS. Cocultures initiated with a citrate synthase-deficient strain of G. sulfurreducens that was unable to use acetate as an electron donor also metabolized ethanol with the reduction of fumarate and cell growth, but acetate accumulated over time. G. sulfurreducens and G. metallireducens were equally abundant in these co-cultures reflecting the inability of the citrate synthase-deficient strain of G. sulfurreducens to metabolize acetate. Evaluation of the mechanisms by which G. sulfurreducens accepts electrons from AHQDS demonstrated that a strain deficient in outer-surface c-type cytochromes that are required for AQDS reduction was as effective at QUIET as the wild-type strain. Deletion of additional genes previously implicated in extracellular electron transfer also had no impact on QUIET. These results demonstrate that QUIET can yield sufficient energy to support the growth of both syntrophic partners, but that the mechanisms by which electrons are derived from extracellular hydroquinones require

  15. Microbial Reduction of Chromate in the presence of Nitrate by Three Nitrate Respiring Organisms.

    Directory of Open Access Journals (Sweden)

    Peter eChovanec

    2012-12-01

    Full Text Available A major challenge for the bioremediation of toxic metals is the co-occurrence of nitrate, as it can inhibit metal transformation. Geobacter metallireducens, Desulfovibrio desulfuricans, and Sulfurospirillum barnesii are three soil bacteria that can reduce chromate (Cr(VI and nitrate, and may be beneficial for developing bioremediation strategies. All three organisms respire through dissimilatory nitrate reduction to ammonia (DNRA, employing different nitrate reductases but similar nitrite reductase (Nrf. G. metallireducens reduces nitrate to nitrite via the membrane bound nitrate reductase (Nar, while S. barnesii and D. desulfuricans strain 27774 have slightly different forms of periplasmic nitrate reductase (Nap. We investigated the effect of DNRA growth in the presence of Cr(VI in these three organisms and the ability of each to reduce Cr(VI to Cr(III, and each organisms responded differently. Growth of G. metallireducens on nitrate was completely inhibited by Cr(VI. Cultures of D. desulfuricans on nitrate media was initially delayed (48 h in the presence of Cr(VI, but ultimately reached comparable cell yields to the non-treated control. This prolonged lag phase accompanied the transformation of Cr(VI to Cr(III. Viable G. metallireducens cells could reduce Cr(VI, whereas Cr(VI reduction by D. desulfuricans during growth, was mediated by a filterable and heat stable extracellular metabolite. S. barnesii growth on nitrate was not affected by Cr(VI, and Cr(VI was reduced to Cr(III. However, Cr(VI reduction activity in S. barnesii, was detected in both the cell free spent medium and cells, indicating both extracellular and cell associated mechanisms. Taken together, these results have demonstrated that Cr(VI affects DNRA in the three organisms differently, and that each have a unique mechanism for Cr(VI reduction.

  16. Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange

    DEFF Research Database (Denmark)

    Shrestha, Pravin Malla; Rotaru, Amelia-Elena; Aklujkar, Muktak

    2013-01-01

    Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy...... dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration....... to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G. sulfurreducens via DIET, were established with a citrate synthase-deficient G. sulfurreducens strain that can receive electrons for respiration through DIET only...

  17. Syntrophic growth with direct interspecies electron transfer as the primary mechanism for energy exchange.

    Science.gov (United States)

    Shrestha, Pravin Malla; Rotaru, Amelia-Elena; Aklujkar, Muktak; Liu, Fanghua; Shrestha, Minita; Summers, Zarath M; Malvankar, Nikhil; Flores, Dan Carlo; Lovley, Derek R

    2013-12-01

    Direct interspecies electron transfer (DIET) through biological electrical connections is an alternative to interspecies H2 transfer as a mechanism for electron exchange in syntrophic cultures. However, it has not previously been determined whether electrons received via DIET yield energy to support cell growth. In order to investigate this, co-cultures of Geobacter metallireducens, which can transfer electrons to wild-type G. sulfurreducens via DIET, were established with a citrate synthase-deficient G. sulfurreducens strain that can receive electrons for respiration through DIET only. In a medium with ethanol as the electron donor and fumarate as the electron acceptor, co-cultures with the citrate synthase-deficient G. sulfurreducens strain metabolized ethanol as fast as co-cultures with wild-type, but the acetate that G. metallireducens generated from ethanol oxidation accumulated. The lack of acetate metabolism resulted in less fumarate reduction and lower cell abundance of G. sulfurreducens. RNAseq analysis of transcript abundance was consistent with a lack of acetate metabolism in G. sulfurreducens and revealed gene expression levels for the uptake hydrogenase, formate dehydrogenase, the pilus-associated c-type cytochrome OmcS and pili consistent with electron transfer via DIET. These results suggest that electrons transferred via DIET can serve as the sole energy source to support anaerobic respiration. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  18. Constraint-based modeling analysis of the metabolism of two Pelobacter species

    Directory of Open Access Journals (Sweden)

    Bui Olivia

    2010-12-01

    Full Text Available Abstract Background Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. Results In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. Conclusions We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community.

  19. Promoting direct interspecies electron transfer with activated carbon

    DEFF Research Database (Denmark)

    Liu, Fanghua; Rotaru, Amelia-Elena; Shrestha, Pravin M.

    2012-01-01

    Granular activated carbon (GAC) is added to methanogenic digesters to enhance conversion of wastes to methane, but the mechanism(s) for GAC’s stimulatory effect are poorly understood. GAC has high electrical conductivity and thus it was hypothesized that one mechanism for GAC stimulation of metha......Granular activated carbon (GAC) is added to methanogenic digesters to enhance conversion of wastes to methane, but the mechanism(s) for GAC’s stimulatory effect are poorly understood. GAC has high electrical conductivity and thus it was hypothesized that one mechanism for GAC stimulation...... of methanogenesis might be to facilitate direct interspecies electron transfer (DIET) between bacteria and methanogens. Metabolism was substantially accelerated when GAC was added to co-cultures of Geobacter metallireducens and Geobacter sulfurreducens grown under conditions previously shown to require DIET. Cells...... were attached to GAC, but did not aggregate as they do when making biological electrical connections between cells. Studies with a series of gene deletion mutants eliminated the possibility that GAC promoted electron exchange via interspecies hydrogen or formate transfer and demonstrated that DIET...

  20. Characterization of proton production and consumption associated with microbial metabolism

    Directory of Open Access Journals (Sweden)

    Mahadevan Radhakrishnan

    2010-01-01

    Full Text Available Abstract Background Production or consumption of protons in growth medium during microbial metabolism plays an important role in determining the pH of the environment. Such pH changes resulting from microbial metabolism may influence the geochemical speciation of many elements in subsurface environments. Protons produced or consumed during microbial growth were measured by determining the amount of acid or base added in a 5 L batch bioreactor equipped with pH control for different species including Escherichia coli, Geobacter sulfurreducens, and Geobacter metallireducens. Results An in silico model was used to predict the proton secretion or consumption rates and the results were compared with the data. The data was found to confirm predictions of proton consumption during aerobic growth of E. coli with acetate as the carbon source. However, in contrast to proton consumption observed during aerobic growth of E. coli with acetate, proton secretion was observed during growth of Geobacter species with acetate as the donor and Fe(III as the extracellular electron acceptor. Conclusions In this study, we have also shown that the final pH of the medium can be either acidic or basic depending on the choice of the electron acceptor for the same electron donor. In all cases, the in silico model could predict qualitatively the proton production/consumption rates obtained from the experimental data. Therefore, measurements of pH equivalents generated or consumed during growth can help characterize the microbial physiology further and can be valuable for optimizing practical applications such as microbial fuel cells, where growth associated pH changes can limit current generation rates.

  1. Humic substances as a mediator for microbially catalyzed metal reduction

    Science.gov (United States)

    Lovley, D.R.; Fraga, J.L.; Blunt-Harris, E. L.; Hayes, L.A.; Phillips, E.J.P.; Coates, J.D.

    1998-01-01

    The potential for humic substances to serve as a terminal electron acceptor in microbial respiration and to function as an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides was investigated. The Fe(III)-reducing microorganism Geobacter metallireducens conserved energy to support growth from electron transport to humics as evidenced by continued oxidation of acetate to carbon dioxide after as many as nine transfers in a medium with acetate as the electron donor and soil humic acids as the electron acceptor. Growth of G. metallireducens with poorly crystalline Fe(III) oxide as the electron acceptor was greatly stimulated by the addition of as little as 100 ??M of the humics analog, anthraquinone-2,6-disulfonate. Other quinones investigated, including lawsone, menadione, and anthraquinone-2-sulfonate, also stimulated Fe(III) oxide reduction. A wide phylogenetic diversity of microorganisms capable of Fe(III) reduction were also able to transfer electrons to humics. Microorganisms which can not reduce Fe(III) could not reduce humics. Humics stimulated the reduction of structural Fe(III) in clay and the crystalline Fe(III) forms, goethite and hematite. These results demonstrate that electron shuttling between Fe(III)-reducing microorganisms and Fe(III) via humics not only accelerates the microbial reduction of poorly crystalline Fe(III) oxide, but also can facilitate the reduction of Fe(III) forms that are not typically reduced by microorganisms in the absence of humics. Addition of humic substances to enhance electron shuttling between Fe(III)-reducing microorganisms and Fe(III) oxides may be a useful strategy to stimulate the remediation of soils and sediments contaminated with organic or metal pollutants.

  2. Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans

    Science.gov (United States)

    Roden, E.E.; Lovley, D.R.

    1993-01-01

    The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c-type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)- citrate and Mn(IV)-oxalate, as well as by two electron acceptors known to support growth, colloidal sulfur and malate. D. acetoxidans grew in defined anoxic, bicarbonate-buffered medium with acetate as the sole electron donor and poorly crystalline Fe(III) or Mn(IV) as the sole electron acceptor. Magnetite (Fe3O4) and siderite (FeCO3) were the major end products of Fe(III) reduction, whereas rhodochrosite (MnCO3) was the end product of Mn(IV) reduction. Ethanol, propanol, pyruvate, and butanol also served as electron donors for Fe(III) reduction. In contrast to D. acetoxidans, G. metallireducens could only grow in freshwater medium and it did not conserve energy to support growth from colloidal S0 reduction. D. acetoxidans is the first marine microorganism shown to conserve energy to support growth by coupling the complete oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). Thus, D. acetoxidans provides a model enzymatic mechanism for Fe(III) or Mn(IV) oxidation of organic compounds in marine and estuarine sediments. These findings demonstrate that 16S rRNA phylogenetic analyses can suggest previously unrecognized metabolic capabilities of microorganisms.

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

    Science.gov (United States)

    Fortney, N W; He, S; Converse, B J; Beard, B L; Johnson, C M; Boyd, E S; Roden, E E

    2016-05-01

    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

  4. Final Report Systems Level Analysis of the Function and Adaptive Responses of Methanogenic Consortia

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R. [Univ. of Massachusetts, Amherst, MA (United States)

    2015-03-09

    The purpose of this research was to determine whether the syntrophic microbial associations that are central to the functioning of methane-producing terrestrial wetlands can be predictively modeled with coupled multi-species genome-scale metabolic models. Such models are important because methane is an important greenhouse gas and there is a need to predictively model how the methane-producing microbial communities will respond to environmental perturbations, such as global climate change. The research discovered that the most prodigious methane-producing microorganisms on earth participate in a previously unrecognized form of energy exchange. The methane-producers Methanosaeta and Methanosarcina forge biological electrical connections with other microbes in order to obtain electrons to reduce carbon dioxide to methane. This direct interspecies electron transfer (DIET) was demonstrated in complex microbial communities as well as in defined co-cultures. For example, metatranscriptomic analysis of gene expression in both natural communities and defined co-cultures demonstrated that Methanosaeta species highly expressed genes for the enzymes for the reduction of carbon dioxide to methane. Furthermore, Methanosaeta’s electron-donating partners highly expressed genes for the biological electrical connections known as microbial nanowires. A series of studies involving transcriptomics, genome resequencing, and analysis of the metabolism of a series of strains with targeted gene deletions, further elucidated the mechanisms and energetics of DIET in methane-producing co-cultures, as well as in a co-culture of Geobacter metallireducens and Geobacter sulfurreducens, which provided a system for studying DIET with two genetically tractable partners. Genome-scale modeling of DIET in the G. metallireducens/G. sulfurreducens co-culture suggested that DIET provides more energy to the electron-donating partner that electron exchange via interspecies hydrogen transfer, but that the

  5. A method for high throughput bioelectrochemical research based on small scale microbial electrolysis cells

    KAUST Repository

    Call, Douglas F.

    2011-07-01

    There is great interest in studying exoelectrogenic microorganisms, but existing methods can require expensive electrochemical equipment and specialized reactors. We developed a simple system for conducting high throughput bioelectrochemical research using multiple inexpensive microbial electrolysis cells (MECs) built with commercially available materials and operated using a single power source. MECs were small crimp top serum bottles (5mL) with a graphite plate anode (92m 2/m 3) and a cathode of stainless steel (SS) mesh (86m 2/m 3), graphite plate, SS wire, or platinum wire. The highest volumetric current density (240A/m 3, applied potential of 0.7V) was obtained using a SS mesh cathode and a wastewater inoculum (acetate electron donor). Parallel operated MECs (single power source) did not lead to differences in performance compared to non-parallel operated MECs, which can allow for high throughput reactor operation (>1000 reactors) using a single power supply. The utility of this method for cultivating exoelectrogenic microorganisms was demonstrated through comparison of buffer effects on pure (Geobacter sulfurreducens and Geobacter metallireducens) and mixed cultures. Mixed cultures produced current densities equal to or higher than pure cultures in the different media, and current densities for all cultures were higher using a 50mM phosphate buffer than a 30mM bicarbonate buffer. Only the mixed culture was capable of sustained current generation with a 200mM phosphate buffer. These results demonstrate the usefulness of this inexpensive method for conducting in-depth examinations of pure and mixed exoelectrogenic cultures. © 2011 Elsevier B.V.

  6. Integrated Ecogenomics Study for Bioremediation of Cr(VI) at Hanford 100H Area

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Chakraborty, Romy

    2008-08-12

    Hexavalent chromium is a widespread contaminant found in groundwater. In order to stimulate microbially mediated Cr(VI)-reduction, a poly-lactate compound was injected into Cr(VI)-contaminated aquifers at site 100H at Hanford. Investigation of bacterial community composition using high-density DNA microarray analysis of 16S rRNA gene products revealed a stimulation of Pseudomonas, Desulfovibrio and Geobacter species amongst others. Enrichment of these organisms coincided with continued Cr(VI) depletion. Functional gene-array analysis of DNA from monitoring well indicated high abundance of genes involved in nitrate-reduction, sulfate-reduction, iron-reduction, methanogenesis, chromium tolerance/reduction. Clone-library data revealed Psedomonas was the dominant genus in these samples. Based on above results, we conducted lab investigations to study the dominant anaerobic culturable microbial populations present at this site and their role in Cr(VI)-reduction. Enrichments using defined anaerobic media resulted in isolation of an iron-reducing, a sulfate-reducing and a nitrate-reducing isolate among several others. Preliminary 16S rDNA sequence analysis identified the isolates as Geobacter metallireducens, Pseudomonas stutzeri and Desulfovibrio vulgaris species respectively. The Pseudomonas isolate utilized acetate, lactate, glycerol and pyruvate as alternative carbon sources, and reduced Cr(VI). Anaerobic washed cell suspension of strain HLN reduced almost 95?M Cr(VI) within 4 hr. Further, with 100?M Cr(VI) as sole electron-acceptor, cells grew to 4.05 x 107 /ml over 24 h after an initial lag, demonstrating direct enzymatic Cr(VI) reduction coupled to growth. These results demonstrate that Cr(VI)-immobilization at Hanford 100H site could be mediated by direct microbial metabolism in addition to indirect chemical reduction of Cr(VI) by end-products of microbial activity.

  7. Nonproteinogenic D-amino acids at millimolar concentrations are a toxin for anaerobic microorganisms relevant to early Earth and other anoxic planets.

    Science.gov (United States)

    Nixon, Sophie L; Cockell, Charles S

    2015-03-01

    The delivery of extraterrestrial organics to early Earth provided a potentially important source of carbon and energy for microbial life. Optically active organic compounds of extraterrestrial origin exist in racemic form, yet life on Earth has almost exclusively selected for L- over D-enantiomers of amino acids. Although D-enantiomers of proteinogenic amino acids are known to inhibit aerobic microorganisms, the role of concentrated nonproteinogenic meteoritic D-amino acids on anaerobic metabolisms relevant to early Earth and other anoxic planets such as Mars is unknown. Here, we test the inhibitory effect of D-enantiomers of two nonproteinogenic amino acids common to carbonaceous chondrites, norvaline and α-aminobutyric acid, on microbial iron reduction. Three pure strains (Geobacter bemidjiensis, Geobacter metallireducens, Geopsychrobacter electrodiphilus) and an iron-reducing enrichment culture were grown in the presence of 10 mM D-enantiomers of both amino acids. Further tests were conducted to assess the inhibitory effect of these D-amino acids at 1 and 0.1 mM. The presence of 10 mM D-norvaline and D-α-aminobutyric acid inhibited microbial iron reduction by all pure strains and the enrichment. G. bemidjiensis was not inhibited by either amino acid at 0.1 mM, but D-α-aminobutyric acid still inhibited at 1 mM. Calculations using published meteorite accumulation rates to the martian surface indicate D-α-aminobutyric acid may have reached inhibitory concentrations in little over 1000 years during peak infall. These data show that, on a young anoxic planet, the use of one enantiomer over another may render the nonbiological enantiomer an environmental toxin. Processes that generate racemic amino acids in the environment, such as meteoritic infall or impact synthesis, would have been toxic processes and could have been a selection pressure for the evolution of early racemases.

  8. Salt removal using multiple microbial desalination cells under continuous flow conditions

    KAUST Repository

    Qu, Youpeng

    2013-05-01

    Four microbial desalination cells (MDCs) were hydraulically connected and operated under continuous flow conditions. The anode solution from the first MDC flowed into the cathode, and then on to the anode of the next reactor, which avoided pH imbalances that inhibit bacterial metabolism. The salt solution also moved through each desalination chamber in series. Increasing the hydraulic retention times (HRTs) of the salt solution from 1 to 2. days increased total NaCl removal from 76 ± 1% to 97 ± 1%, but coulombic efficiencies decreased from 49 ± 4% to 35 ± 1%. Total COD removals were similar at both HRTs (60 ± 2%, 2. days; 59 ± 2%, 1. day). Community analysis of the anode biofilms showed that bacteria most similar to the xylose fermenting bacterium Klebsiella ornithinolytica predominated in the anode communities, and sequences most similar to Geobacter metallireducens were identified in all MDCs except the first one. These results demonstrated successful operation of a series of hydraulically connected MDCs and good desalination rates. © 2013 Elsevier B.V..

  9. Iron and manganese in anaerobic respiration: environmental significance, physiology, and regulation

    Science.gov (United States)

    Nealson, K. H.; Saffarini, D.

    1994-01-01

    Dissimilatory iron and/or manganese reduction is known to occur in several organisms, including anaerobic sulfur-reducing organisms such as Geobacter metallireducens or Desulfuromonas acetoxidans, and facultative aerobes such as Shewanella putrefaciens. These bacteria couple both carbon oxidation and growth to the reduction of these metals, and inhibitor and competition experiments suggest that Mn(IV) and Fe(III) are efficient electron acceptors similar to nitrate in redox abilities and capable of out-competing electron acceptors of lower potential, such as sulfate (sulfate reduction) or CO2 (methanogenesis). Field studies of iron and/or manganese reduction suggest that organisms with such metabolic abilities play important roles in coupling the oxidation of organic carbon to metal reduction under anaerobic conditions. Because both iron and manganese oxides are solids or colloids, they tend to settle downward in aquatic environments, providing a physical mechanism for the movement of oxidizing potential into anoxic zones. The resulting biogeochemical metal cycles have a strong impact on many other elements including carbon, sulfur, phosphorous, and trace metals.

  10. Genome-Scale Metabolic Modeling in the Simulation of Field-Scale Uranium Bioremediation

    Science.gov (United States)

    Yabusaki, S.; Wilkins, M.; Fang, Y.; Williams, K. H.; Waichler, S.; Long, P. E.

    2015-12-01

    Coupled variably saturated flow and biogeochemical reactive transport modeling is used to improve understanding of the processes, properties, and conditions controlling uranium bio-immobilization in a field experiment where uranium-contaminated groundwater was amended with acetate and bicarbonate. The acetate stimulates indigenous microorganisms that catalyze metal reduction, including the conversion of aqueous U(VI) to solid-phase U(IV), which effectively removes uranium from solution. The initiation of the bicarbonate amendment prior to biostimulation was designed to promote U(VI) desorption that would increase the aqueous U(VI) available for bioreduction. The three-dimensional simulations were able to largely reproduce the timing and magnitude of the physical, chemical and biological responses to the acetate and bicarbonate amendment in the context of changing water table elevation and gradient. A time series of groundwater proteomic samples exhibited correlations between the most abundant Geobacter metallireducens proteins and the genome-scale metabolic model-predicted fluxes of intra-cellular reactions associated with each of those proteins. The desorption of U(VI) induced by the bicarbonate amendment led to initially higher rates of bioreduction compared to locations with minimal bicarbonate exposure. After bicarbonate amendment ceased, bioreduction continued at these locations whereas U(VI) sorption was the dominant removal mechanism at the bicarbonate-impacted sites.

  11. Mechanisms for chelator stimulation of microbial Fe(III) -oxide reduction

    Science.gov (United States)

    Lovley, D.R.; Woodward, J.C.

    1996-01-01

    The mechanisms by which nitrilotriacetic acid (NTA) stimulated Fe(III) reduction in sediments from a petroleum-contaminated aquifer were investigated in order to gain insight into how added Fe(III) chelators stimulate the activity of hydrocarbon-degrading, Fe(III)-reducing microorganisms in these sediments, and how naturally occurring Fe(III) chelators might promote Fe(III) reduction in aquatic sediments. NTA solubilized Fe(III) from the aquifer sediments. NTA stimulation of microbial Fe(III) reduction did not appear to be the result of making calcium, magnesium, potassium, or trace metals more available to the microorganisms. Stimulation of Fe(III) reduction could not be attributed to NTA serving as a source of carbon or fixed nitrogen for Fe(III)-reducing bacteria as NTA was not degraded in the sediments. Studies with the Fe(III)-reducing microorganism, Geobacter metallireducens, and pure Fe(III)-oxide forms, demonstrated that NTA stimulated the reduction of a variety of Fe(III) forms, including highly crystalline Fe(III)-oxides such as goethite and hematite. The results suggest that NTA solubilization of insoluble Fe(III)-oxide is an important mechanism for the stimulation of Fe(III) reduction by NTA in aquifer sediments.

  12. Functional genomic study of the environmentally important Desulfovibrio /Methanococcus syntrophic co-culture.

    Science.gov (United States)

    Mukhopadhyay, A.

    2008-12-01

    The use of microbe-oriented bioremediation for ameliorating extensive environmental pollution has fostered fundamental and applied studies of environmentally relevant microorganisms such as Desulfovibrio vulgaris, Shewanella oneidensis and Geobacter metallireducens.. Concurrently, there has been an increasing appreciation that the physiology of these organisms in pure culture is not necessarily representative of its activities in the environment. To enable a better understanding of microbial physiology under more environmentally relevant conditions, the syntrophic growth between the sulfate reducing bacterium, D. vulgaris and the hydrogenotrophic methanogen, Methanococcus maripaludis serves as an ideal system for laboratory studies. Cell wide analyses using transcript, proteomics and metabolite analysis have been widely used to understand cellular activity at a molecular level. Using D. vulgaris and M. maripaludis arrays, and the iTRAQ proteomics method, we studied the physiology of the D. vulgaris / M. maripaludis syntrophic co- cultures. The results from this study allowed us to identify differences in cellular response in mono-culture vs. co-culture growth for both D. vulgaris and M. maripaludis.

  13. Mercury reduction and cell-surface adsorption by Geobacter sulfurreducens PCA

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Haiyan [ORNL; Lin, Hui [ORNL; Zheng, Wang [ORNL; Feng, Xinbin [ORNL; Liang, Liyuan [ORNL; Elias, Dwayne A [ORNL; Gu, Baohua [ORNL

    2013-01-01

    Both reduction and surface adsorption of mercuric mercury [Hg(II)] are found to occur simultaneously on G. sulfurreducens PCA cells under dark, anaerobic conditions. Reduction of Hg(II) to elemental Hg(0) initially follows a pseudo-first order kinetics with a half-life of < 2 h in the presence of 50 nM Hg(II) and 1011 cells L-1 in a phosphate buffer (pH 7.4). Multiple gene deletions of the outer membrane cytochromes in this organism resulted in decrease in reduction rate from ~ 0.3 to 0.05 h-1, and reduction was nearly absent with heat-killed cells or in the cell filtrate. Adsorption of Hg(II) by cells is found to compete with, and thus inhibit, Hg(II) reduction. Depending on the Hg to cell ratio, maximum Hg(II) reduction was observed at about 5 10-19 mol Hg cell-1, but reduction terminated at a low Hg to cell ratio (< 10-20 mol Hg cell-1). This inhibitory effect is attributed to strong binding between Hg(II) and the thiol ( SH) functional groups on cells and validated by experiments in which the sorbed Hg(II) was readily exchanged by thiols (e.g., glutathione) but not by carboxylic ligands such as ethylenediaminetetraacetate (EDTA). We suggest that coupled Hg(II)-cell interactions, i.e., reduction and surface binding, could be important in controlling Hg species transformation and bioavailability and should therefore be considered in microbial Hg(II) uptake and methylation studies.

  14. Mercury reduction and cell-surface adsorption by Geobacter sulfurreducens PCA.

    Science.gov (United States)

    Hu, Haiyan; Lin, Hui; Zheng, Wang; Rao, Balaji; Feng, Xinbin; Liang, Liyuan; Elias, Dwayne A; Gu, Baohua

    2013-10-01

    Both reduction and surface adsorption of mercuric mercury [Hg(II)] are found to occur simultaneously on G. sulfurreducens PCA cells under dark, anaerobic conditions. Reduction of Hg(II) to elemental Hg(0) initially follows a pseudo-first order kinetics with a half-life of Hg(II) and 10(11) cells L(-1) in a phosphate buffer (pH 7.4). Multiple gene deletions of the outer membrane cytochromes in this organism resulted in a decrease in reduction rate from ∼0.3 to 0.05 h(-1), and reduction was nearly absent with heat-killed cells or in the cell filtrate. Adsorption of Hg(II) by cells is found to compete with, and thus inhibit, Hg(II) reduction. Depending on the Hg to cell ratio, maximum Hg(II) reduction was observed at about 5 × 10(-19) mol Hg cell(-1), but reduction terminated at a low Hg to cell ratio (Hg cell(-1)). This inhibitory effect is attributed to bonding between Hg(II) and the thiol (-SH) functional groups on cells and validated by experiments in which the sorbed Hg(II) was readily exchanged by thiols (e.g., glutathione) but not by carboxylate compounds such as ethylenediamine-tetraacetate (EDTA). We suggest that coupled Hg(II)-cell interactions, i.e., reduction and surface binding, could be important in controlling Hg species transformation and bioavailability and should therefore be considered in microbial Hg(II) uptake and methylation studies.

  15. Coupled mercury-cell sorption, reduction, and oxidation on methylmercury production by Geobacter sulfurreducens PCA.

    Science.gov (United States)

    Lin, Hui; Morrell-Falvey, Jennifer L; Rao, Balaji; Liang, Liyuan; Gu, Baohua

    2014-10-21

    G. sulfurreducens PCA cells have been shown to reduce, sorb, and methylate Hg(II) species, but it is unclear whether this organism can oxidize and methylate dissolved elemental Hg(0) as shown for Desulfovibrio desulfuricans ND132. Using Hg(II) and Hg(0) separately as Hg sources in washed cell assays in phosphate buffered saline (pH 7.4), we report how cell-mediated Hg reduction and oxidation compete or synergize with sorption, thus affecting the production of toxic methylmercury by PCA cells. Methylation is found to be positively correlated to Hg sorption (r = 0.73) but negatively correlated to Hg reduction (r = -0.62). These reactions depend on the Hg and cell concentrations or the ratio of Hg to cellular thiols (-SH). Oxidation and methylation of Hg(0) are favored at relatively low Hg to cell-SH molar ratios (e.g., <1). Increasing Hg to cell ratios from 0.25 × 10(-19) to 25 × 10(-19) moles-Hg/cell (equivalent to Hg/cell-SH of 0.71 to 71) shifts the major reaction from oxidation to reduction. In the absence of five outer membrane c-type cytochromes, mutant ΔomcBESTZ also shows decreases in Hg reduction and increases in methylation. However, the presence of competing thiol-binding ions such as Zn(2+) leads to increased Hg reduction and decreased methylation. These results suggest that the coupled cell-Hg sorption and redox transformations are important in controlling the rates of Hg uptake and methylation by G. sulfurreducens PCA in anoxic environments.

  16. Selective enrichment of Geobacter sulfurreducens from anaerobic granular sludge with quinones as terminal electron acceptors

    NARCIS (Netherlands)

    Cervantes-Carillo, F.J.; Duong Dac, T.; Ivanova, A.E.; Roest, de K.; Akkermans, A.D.L.; Lettinga, G.; Field, J.A.

    2003-01-01

    A quinone-respiring, enrichment culture derived from methanogenic granular sludge was phylogenetically characterized by using a combined cloning-denaturing gradient gel electrophoresis (DGGE) method, which revealed that the consortium developed was dominated by a single microorganism: 97% related, i

  17. Relationship between kinetics of growth and production of exo-electrons: Case study with Geobacter toluenoxydans.

    Science.gov (United States)

    Szöllősi, Attila; Narr, László; Kovács, Attila G; Styevkó, Gabriella

    2015-09-01

    Kinetics of growth and product formation of G. toluenoxydans DSMZ 19350 strain were investigated using sodium-acetate as substrate and Fe(3+)-ions and fumarate as electron acceptor. Response surface method was adapted for evaluation of growth of bacteria. Results showed that maximum growth was detected in the case of 2.2 g/L substrate concentration. Application of higher substrate concentration (>2.5 g/L sodium acetate) significantly inhibits the bacterial growth. Luong's model was found to be the most suitable to determine kinetic parameters (μ(max) = 0.033 1/h, KS = 0.205 g/L) of growth of G.toluenoxydans strain, and the growth was completely inhibited at substrate concentration higher than 3.1 g/L. In the case of product formation the Haldane model was used and kinetic parameters are μ(Pmax) = 0.123 mg/h, K(PS)= 0.184 g/L. Correlation between microbial growth and product formation was observed using the Luedeking-Piret empirical method. Both factors (growth and number of cells) affected significantly iron(III)-reduction, thus the product formation. These results are important and open the possibility to design a continuous MFC setting operating with G. toluenoxydans as biocatalyst.

  18. Long-range Electron Transport in Geobacter sulfurreducens Biofilms is Redox Gradient-Driven

    Science.gov (United States)

    2012-01-01

    anodes of electrochemical reactors , result- ing in electrical current coupled to metabolic organic matter oxidation (18). When grown using an anode as...cells and microbial electrolysis cells. It may also provide valuable insights into the mechanism of long-range biological electron transport in...from industrial and agricultural waste- water . Trends Biotechnol 22:477–485. 55. Rozendal RA, Hamelers HVM, Rabaey K, Keller J, Buisman CJN (2008

  19. Bacteriophage Infection of Model Metal Reducing Bacteria

    Science.gov (United States)

    Weber, K. A.; Bender, K. S.; Gandhi, K.; Coates, J. D.

    2008-12-01

    Microbially-mediated metal reduction plays a significant role controlling contaminant mobility in aqueous, soil, and sedimentary environments. From among environmentally relevant microorganisms mediating metal reduction, Geobacter spp. have been identified as predominant metal-reducing bacteria under acetate- oxidizing conditions. Due to the significance of these bacteria in environmental systems, it is necessary to understand factors influencing their metabolic physiology. Examination of the annotated finished genome sequence of G. sulfurreducens PCA, G. uraniumreducens Rf4, G. metallireduceans GS-15 as well as a draft genome sequence of Geobacter sp. FRC-32 have identified gene sequences of putative bacteriophage origin. Presence of these sequences indicates that these bacteria are susceptible to phage infection. Polymerase chain reaction (PCR) primer sets designed tested for the presence of 12 of 25 annotated phage-like sequences in G. sulfurreducens PCA and 9 of 17 phage-like sequences in FRC- 32. The following genes were successfully amplified in G. sulfurreducens PCA: prophage type transcription regulator, phage-induced endonuclease, phage tail sheath, 2 phage tail proteins, phage protein D, phage base plate protein, phage-related DNA polymerase, integrase, phage transcriptional regulator, and Cro-like transcription regulator. Nine of the following sequences were present in FRC-32: 4 separate phage- related proteins, phage-related tail component, viron core protein, phage Mu protein, phage base plate, and phage tail sheath. In addition to the bioinformatics evidence, incubation of G. sulfurreducens PCA with 1 μg mL-1 mytomycin C (mutagen stimulating prophage induction) during mid-log phase resulted in significant cell lysis relative to cultures that remained unamended. Cell lysis was concurrent with an increase in viral like particles enumerated using epifluorescent microscopy. In addition, samples collected following this lytic event (~44hours) were

  20. In-Situ Survival Mechanisms of U and Tc Reducing Bacteria in Contaminated Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Krumholz, Lee R.

    2005-06-01

    periplasmic space and outer membrane associated proteins. Through blast search analysis, we also showed that 81 out of 94 proteins shown to be important in sediment survival have homologs in D. vulgaris, 70 have homologs in Geobacter metallireducens, and 69 have homologs in Geobacter sulfurreducens PCA. Some interesting proteins include ribonucleotide reductase and chemotaxis related proteins. Ribonucleotide reductase catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides, providing the precursors necessary for DNA synthesis. Two ribonucleotide reductase genes (nrdE, nrdD) were found to be essential for G20 survival in the sediment, but not essential for growth in the lactate-sulfate medium. Bacterial methyl-accepting chemotaxis proteins (MCP) respond to changes in the concentration of attractants and repellents in the environment.

  1. Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture.

    Science.gov (United States)

    Abu Laban, Nidal; Selesi, Draženka; Rattei, Thomas; Tischler, Patrick; Meckenstock, Rainer U

    2010-10-01

    Anaerobic benzene degradation was studied with a highly enriched iron-reducing culture (BF) composed of mainly Peptococcaceae-related Gram-positive microorganisms. The proteomes of benzene-, phenol- and benzoate-grown cells of culture BF were compared by SDS-PAGE. A specific benzene-expressed protein band of 60 kDa, which could not be observed during growth on phenol or benzoate, was subjected to N-terminal sequence analysis. The first 31 amino acids revealed that the protein was encoded by ORF 138 in the shotgun sequenced metagenome of culture BF. ORF 138 showed 43% sequence identity to phenylphosphate carboxylase subunit PpcA of Aromatoleum aromaticum strain EbN1. A LC/ESI-MS/MS-based shotgun proteomic analysis revealed other specifically benzene-expressed proteins with encoding genes located adjacent to ORF 138 on the metagenome. The protein products of ORF 137, ORF 139 and ORF 140 showed sequence identities of 37% to phenylphosphate carboxylase PpcD of A. aromaticum strain EbN1, 56% to benzoate-CoA ligase (BamY) of Geobacter metallireducens and 67% to 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX) of A. aromaticum strain EbN1 respectively. These genes are proposed as constituents of a putative benzene degradation gene cluster (∼ 17 kb) composed of carboxylase-related genes. The identified gene sequences suggest that the initial activation reaction in anaerobic benzene degradation is probably a direct carboxylation of benzene to benzoate catalysed by putative anaerobic benzene carboxylase (Abc). The putative Abc probably consists of several subunits, two of which are encoded by ORFs 137 and 138, and belongs to a family of carboxylases including phenylphosphate carboxylase (Ppc) and 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX).

  2. Microbially-mediated transformation and mobilization of soil Fe-organic associations

    Science.gov (United States)

    Poggenburg, Christine; Mikutta, Robert; Schippers, Axel; Dohrmann, Reiner; Kaufhold, Stephan; Guggenberger, Georg

    2014-05-01

    Soil organic matter (OM) has been proposed to be stabilized in the long term via sorption to iron((oxy)hydr)oxides under aerobic conditions. However, in an anaerobic environment, Fe-organic associations may be subject to microbial reduction and mobilization, which counteract the suggested stabilizing effect of Fe compounds. Desorption of OM can result in its microbial decomposition causing the emission of greenhouse gases (CO2, CH4, N2O) or release of associated contaminants into the soil solution and groundwater. While the reductive dissolution of pure iron((oxy)hydr)oxides by dissimilatory FeIII reducing bacteria is well established, little is known about the influence of natural OM on microbially mediated mobilization of Fe-organic associations. Therefore, this study aims to elucidate the effect of adsorbed OM on microbial FeIII reduction of Fe-organic associations with regard to (i) the composition of OM, (ii) the carbon loading, and (iii) surface coverage and/or pore blockage by adsorbed OM. Mineral-organic associations with varying carbon contents were synthesized using several iron((oxy)hydr)oxides (Goethite, Lepidocrocite, Ferrihydrite, Hematite, Magnetite) and OM of different origin (dissolved OM extracted from the Oa horizon of a Podzol and Oi horizon of a Cambisol, extracellular polymeric substance extracted from Bacillus subtilis). Incubation experiments under anaerobic conditions were conducted for 16 days using two different strains of dissimilatory FeIII reducing bacteria (Shewanella putrefaciens, Geobacter metallireducens). At five sampling points in time the solution phase was analyzed for pH, Fetotal, and FeII. The initial mineral-organic associations and post-incubation phase were characterized by N2 gas adsorption, FTIR, XRD, and XPS. The results indicate that the composition of OM and carbon loading significantly influence the rate and extend of microbial reduction of Fe-organic associations depending on the type of microbial strain and iron

  3. Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells

    Science.gov (United States)

    Kouzuma, Atsushi; Kasai, Takuya; Nakagawa, Gen; Yamamuro, Ayaka; Abe, Takashi; Watanabe, Kazuya

    2013-01-01

    In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors. PMID:24223712

  4. Geochemical control of microbial Fe(III) reduction potential in wetlands: Comparison of the rhizosphere to non-rhizosphere soil

    Science.gov (United States)

    Weiss, J.V.; Emerson, D.; Megonigal, J.P.

    2004-01-01

    We compared the reactivity and microbial reduction potential of Fe(III) minerals in the rhizosphere and non-rhizosphere soil to test the hypothesis that rapid Fe(III) reduction rates in wetland soils are explained by rhizosphere processes. The rhizosphere was defined as the area immediately adjacent to a root encrusted with Fe(III)-oxides or Fe plaque, and non-rhizosphere soil was 0.5 cm from the root surface. The rhizosphere had a significantly higher percentage of poorly crystalline Fe (66??7%) than non-rhizosphere soil (23??7%); conversely, non-rhizosphere soil had a significantly higher proportion of crystalline Fe (50??7%) than the rhizosphere (18??7%, Psoil Fe(III)-oxide pool. Similarly, microbial reduction consumed 75-80% of the rhizosphere pool in 10 days compared to 30-40% of the non-rhizosphere soil pool. Differences between the two pools persisted when samples were amended with an electron-shuttling compound (AQDS), an Fe(III)-reducing bacterium (Geobacter metallireducens), and organic carbon. Thus, Fe(III)-oxide mineralogy contributed strongly to differences in the Fe(III) reduction potential of the two pools. Higher amounts of poorly crystalline Fe(III) and possibly humic substances, and a higher Fe(III) reduction potential in the rhizosphere compared to the non-rhizosphere soil, suggested the rhizosphere is a site of unusually active microbial Fe cycling. The results were consistent with previous speculation that rapid Fe cycling in wetlands is due to the activity of wetland plant roots. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

  5. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron(III-reducing enrichment culture

    Directory of Open Access Journals (Sweden)

    Shiling eZheng

    2015-09-01

    Full Text Available Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.

  6. Microbial community changes during sustained Cr(VI) reduction at the 100H site in Hanford, WA

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Romy; Brodie, Eoin L; Faybishenko, Boris; Piceno, Yvette M; Tom, Lauren; Choudhuri, Swati; Beller, Harry R; Liu, Jenny; Torok, Tamas; Joyner, Dominique C; Joachimiak, Marcin P; Zhou, Aifen; Van Nostrand, Joy D; Zhou, Joe; Long, Phil E; Newcomer, Darrell R; Andersen, Gary L; Hazen, Terry C.

    2010-05-17

    Hexavalent Chromium is a widespread contaminant found in soil, sediment, and groundwater. In order to stimulate microbially-mediated reduction of Cr(VI), a poly-lactate compound (HRC) was injected into the Chromium-contaminated aquifer at the Hanford (WA) 100H site in 2004. Cr(VI) concentrations rapidly declined to below the detection limit and remained so for more than three years after injection. Based on the results of the bacterial community composition using high-density DNA 16S rRNA gene microarrays, we observed the community to transition through denitrifying, ironreducing and sulfate-reducing populations. As a result, we specifically focused isolation efforts on three bacterial species that were significant components of the community. Positive enrichments in defined anaerobic media resulted in the isolation of an iron-reducing Geobacter metallireducens-like isolate, a sulfate-reducing Desulfovibrio vukgaris-like strain and a nitrate-reducing Pseudomonas stutzeri-like isolate among several others. All of these isolates were capable of reducing Cr(VI) anoxically and have been submitted for genome sequencing to JGI. To further characterize the microbial, and geochemical mechanisms associated with in situ Cr(VI) reduction at the site, additional HRC was injected in 2008. The goal was to restimulate the indigenous microbial community and to regenerate the reducing conditions necessary for continued Cr(VI) bio-immobilization in the groundwater. Analysis of the microbial populations post-injection revealed that they recovered to a similar density as after the first injection in 2004. In this study, we present the results from our investigation into microbially-mediated Cr(VI) reduction at Hanford, and a comparison of the microbial community development following two HRC injections four years apart.

  7. Determination of the sediment oxidation capacity by column and field experiments with reactive tracers

    Energy Technology Data Exchange (ETDEWEB)

    Dethlefsen, F.; Bliss, F.; Wachter, T.; Dahmke, A. [Kiel Univ. (Germany). Inst. fuer Geowissenschaften; Meckenstock, R. [Tuebingen Univ. (Germany). Zentrum fuer Angewandte Geowissenschaften

    2003-07-01

    The oxidation capacity of ferric iron in column studies was determined by phosphate tracer tests and validated by biodegradation experiments with toluene as a carbon source and the iron(III)-oxide reducing bacterium Geobacter metallireducens as well as with wet chemical extraction. Toluene mass balance, Fe(II) production and tracer test results showed that about 1/3 of the total Fe(III) mass had been reduced during the biodegradation experiment. The redox reactive tracer sulfide is supposed to be more practicable for field purposes, because a sulfide mass or electron balance enables evaluation of the tracer test. In this way, consideration of mineral specific sorption parameters and long residence periods of a sorptive reactive tracer can be avoided. Laboratory column experiments were performed with an artificially composed sediment (quartz sand and ferrihydrite) as well as with natural sediments from the margin of the benzene contaminated RETZINA test site in Zeitz (Germany). Fast reaction kinetics of sulfide with iron(III) minerals allowed the observation of a successive fixation of black iron sulfides in all the glas columns. Depending on the mineral iron content, the sedimentary oxidation capacity of the column material was used up in few days to weeks. Mass of sulfide reacted in the tracer test and sulfide mass recovered by sediment extraction after the experiment were in very good agreement. Evaluation of the column experiments confirmed the calculated ratio that 3 molar equivalents sulfide were used to reduce and fix 2 molar equivalents of Fe(III). Mean Fe(III) content of natural sediment samples (drilling SafZz 28/02 in Zeitz) was 0.35 mg/g sediment determined by laboratory sulfide tracer test and 5 M HCl extractions. Finally, a single well push-pull test was performed at the RETZINA test site Zeitz to test the applicability of the sulfide tracer in a field-scale experiment. (orig.)

  8. Complete reduction of TNT and other (poly)nitroaromatic compounds under iron-reducing subsurface conditions

    Energy Technology Data Exchange (ETDEWEB)

    Hofstetter, T.B.; Haderlein, S.B.; Schwarzenbach, R.P. [Swiss Federal Inst. for Environmental Science and Technology, Duebendorf (Switzerland); Heijman, C.G.; Holliger, C. [Swiss Federal Inst. for Tech., Duebendorf (Switzerland)

    1999-05-01

    Contamination of soils and aquifers with (poly)nitroaromatic compounds ((P)NACs) is a widespread problem. This work demonstrates that (P)NACs such as the explosive 2,4,6-trinitrotoluene (TNT) can be completely reduced to the corresponding aromatic polyamines by Fe(II) present at the surface of Fe(III)(hydr)oxides or, less efficiently, by hydroquinone moieties of (natural) organic matter in the presence of H{sub 2}S. The reduction kinetics of (P)NACs were investigated in sterile batch systems as well as in columns containing either FeOOH-coated sand and a pure culture of the iron-reducing bacterium Geobacter metallireducens or ferrogenic consortia in aquifer sediments. The relative reactivities as well as the competition behavior of (P)NACs in batch and column systems, respectively, correlated well with their one-electron reduction potentials, E{sub h}{sup 1}{prime}, which the authors determined for TNT and its aminonitrotoluene transformation products. A similar reactivity pattern of (P)NACs was found irrespective of the processes that (re)generated the surface-bound Fe(II), i.e., adsorption of Fe(II) from aqueous solution or microbial reduction of Fe(III)(hydr)oxides. The apparent stability of the toxic arylamine products under ferrogenic conditions may compromise intrinsic attenuation as an acceptable remediation option for (P)NAC contaminated anoxic aquifers. Iron-reducing conditions would, however, be favorable as a first step in a two-stage anaerobic/aerobic treatment of PNAC contaminated sediments since aromatic polyamines are biodegradable and/or bind irreversibly to the solid matrix under oxic conditions.

  9. Biological Recovery of Platinum Complexes from Diluted Aqueous Streams by Axenic Cultures

    Science.gov (United States)

    Maes, Synthia; Props, Ruben; Fitts, Jeffrey P.; De Smet, Rebecca; Vanhaecke, Frank; Boon, Nico; Hennebel, Tom

    2017-01-01

    The widespread use of platinum in high-tech and catalytic applications has led to the production of diverse Pt loaded wastewaters. Effective recovery strategies are needed for the treatment of low concentrated waste streams to prevent pollution and to stimulate recovery of this precious resource. The biological recovery of five common environmental Pt-complexes was studied under acidic conditions; the chloro-complexes PtCl42- and PtCl62-, the amine-complex Pt(NH3)4Cl2 and the pharmaceutical complexes cisplatin and carboplatin. Five bacterial species were screened on their platinum recovery potential; the Gram-negative species Shewanella oneidensis MR-1, Cupriavidus metallidurans CH34, Geobacter metallireducens, and Pseudomonas stutzeri, and the Gram-positive species Bacillus toyonensis. Overall, PtCl42- and PtCl62- were completely recovered by all bacterial species while only S. oneidensis and C. metallidurans were able to recover cisplatin quantitatively (99%), all in the presence of H2 as electron donor at pH 2. Carboplatin was only partly recovered (max. 25% at pH 7), whereas no recovery was observed in the case of the Pt-tetraamine complex. Transmission electron microscopy (TEM) revealed the presence of both intra- and extracellular platinum particles. Flow cytometry based microbial viability assessment demonstrated the decrease in number of intact bacterial cells during platinum reduction and indicated C. metallidurans to be the most resistant species. This study showed the effective and complete biological recovery of three common Pt-complexes, and estimated the fate and transport of the Pt-complexes in wastewater treatment plants and the natural environment. PMID:28046131

  10. Comparative metagenomics of anode-associated microbiomes developed in rice paddy-field microbial fuel cells.

    Science.gov (United States)

    Kouzuma, Atsushi; Kasai, Takuya; Nakagawa, Gen; Yamamuro, Ayaka; Abe, Takashi; Watanabe, Kazuya

    2013-01-01

    In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

  11. Comparative metagenomics of anode-associated microbiomes developed in rice paddy-field microbial fuel cells.

    Directory of Open Access Journals (Sweden)

    Atsushi Kouzuma

    Full Text Available In sediment-type microbial fuel cells (sMFCs operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate- and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

  12. Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Shrestha, Pravin M; Liu, Fanghua

    2012-01-01

    was comparable in cocultures with that for the formate dehydrogenase mutant of G. sulfurreducens or the wild type, suggesting that H(2) was the primary electron carrier in the wild-type cocultures. Cocultures were also initiated with strains of G. sulfurreducens that could not produce pili or OmcS, two essential...

  13. Mössbauer hyperfine parameters of iron species in the course of Geobacter-mediated magnetite mineralization

    Science.gov (United States)

    Li, Yi-Liang; Zhu, San-Yuan; Deng, Kun

    2011-10-01

    Amorphous ferric iron species (ferrihydrite or akaganeite of <5 nm in size) is the only known solid ferric iron oxide that can be reductively transformed by dissimilatory iron-reducing bacteria to magnetite completely. The lepidocrocite crystallite can be transformed into magnetite in the presence of abiotic Fe(II) at elevated pH or biogenic Fe(II) with particular growth conditions. The reduction of lepidocrocite by dissimilatory iron-reducing bacteria has been widely investigated showing varying results. Vali et al. (Proc Natl Acad Sci USA 101:16121-16126, 2004) captured a unique biologically mediated mineralization pathway where the amorphous hydrous ferric oxide transformed to lepidocrocite was followed by the complete reduction of lepidocrocite to single-domain magnetite. Here, we report the 57Fe Mössbauer hyperfine parameters of the time-course samples reported in Vali et al. (Proc Natl Acad Sci USA 101:16121-16126, 2004). Both the quadrupole splittings and linewidths of Fe(III) ions decrease consistently with the change of aqueous Fe(II) and transformations of mineral phases, showing the Fe(II)-mediated gradual regulation of the distorted coordination polyhedrons of Fe3+ during the biomineralization process. The aqueous Fe(II) catalyzes the transformations of Fe(III) minerals but does not enter the mineral structures until the mineralization of magnetite. The simulated abiotic reaction between Fe(II) and lepidocrocite in pH-buffered, anaerobic media shows the simultaneous formation of green rust and its gradual transformation to magnetite plus a small fraction of goethite. We suggested that the dynamics of Fe(II) supply is a critical factor for the mineral transformation in the dissimilatory iron-reducing cultures.

  14. Inocula selection in microbial fuel cells based on anodic biofilm abundance of Geobacter sulfurreducens

    DEFF Research Database (Denmark)

    Sun, Guotao; Rodrigues, Diogo De Sacadura; Thygesen, Anders

    2016-01-01

    Microbial fuel cells (MFCs) rely on microbial conversion of organic substrates to electricity. The optimal performance depends on the establishment of a microbial community rich in electrogenic bacteria. Usually this microbial community is established from inoculation of the MFC anode chamber....... The data obtained contribute to understanding the microbial community response to Lsub and Rext for optimizing electricity generation in MFCs....

  15. STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin; Martin Keller; Joseph W. Stucki

    2011-06-15

    (comprising 50% to 100% of rRNA detected). (2) We demonstrated for the first time that the function of microbial communities can be quantified in subsurface sediments using messenger RNA assays (molecular proxies) under in situ conditions. (3) Active Geobacteraceae were identified and phylogenetically characterized from the cDNA of messenger RNA extracted from ORFRC subsurface sediment cores. Multiple clone sequences were retrieved from G. uraniireducens, G. daltonii, and G. metallireducens. (4) Results show that Geobacter strain FRC-32 is capable of growth on benzoate, toluene and benzene as the electron donor, thereby providing evidence that this strain is physiologically distinct from other described members of the subsurface Geobacter clade. (5) Fe(III)-reducing bacteria transform structural Fe in clay minerals from their layer edges rather than from their basal surfaces.

  16. 5 CFR 2636.303 - Definitions.

    Science.gov (United States)

    2010-01-01

    ... above GS-15. Example 2. An employee of the Environmental Protection Agency who has been a career GS-15... in the management of the partnership, his share of the partnership income is neither “outside earned... hotel expenses paid by the university to permit him to attend quarterly meetings of the Board are...

  17. Targeted Metagenomic Survey of the Fe-Cycling Microbial Community at Chocolate Pots Hot Springs, Yellowstone National Park

    Science.gov (United States)

    Fortney, N. W.; He, S.; Kulkarni, A.; Friedrich, M. W.; Boyd, E. S.; Roden, E. E.

    2016-12-01

    Chocolate Pots hot springs (CP) is a circumneutral pH, Fe-rich geothermal feature located in Yellowstone National Park. Fe-based metabolic processes are deeply rooted in the tree of life and studying environments like CP are important for us to study to gain insight into ancient Earth ecosystems. Recently identified features on Mars are indicative of near-surface hydrothermal environments and studies of modern Earth systems like CP allow us a glimpse into how life may have potentially arisen on other rocky worlds. Previous enrichment culture studies of the microbial community present at CP identified close relatives of dissimilatory Fe-reducing bacteria (DIRB), including Geobacter metallireducens and Melioribacter roseus. However, the question still remains as to the composition and activity of the microbial community in situ. Here we used 13C stable isotope probing to gain an understanding of the Fe cycling microbial community at CP. Fe-Si oxide sediments collected from near the hot spring vent were incubated under in situ conditions and amended with 13C-acetate or -bicarbonate to target DIRB and Fe-oxidizing bacteria, respectively. 16S rRNA gene amplicon libraries along with shotgun metagenomic libraries were obtained from both sets of incubations. Differential read coverage mapping of metagenomic reads identified a set of taxonomic bins that showed a response to the incubation treatments. We searched the Fe-reducing incubation bins for homologues of genes involved in known extracellular electron transfer (EET) systems such as Pcc and MtrAB, as well as putative porins proximal to multiheme cytochrome c genes. We also searched bins from the Fe-oxidizing incubations for these EET systems in addition to homologues of the outer membrane cytochrome c Cyc2. The Fe-oxidizing bins were also examined for genes encoding RuBisCo to identify potential chemolithoautotrophs. Our targeted metagenomic analysis will identify which organisms are likely to be part of an active Fe

  18. Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

    Science.gov (United States)

    Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

    2014-12-01

    Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a

  19. Genome sequence of the deltaproteobacterial strain NaphS2 and analysis of differential gene expression during anaerobic growth on naphthalene.

    Directory of Open Access Journals (Sweden)

    Raymond J DiDonato

    Full Text Available BACKGROUND: Anaerobic polycyclic hydrocarbon (PAH degradation coupled to sulfate reduction may be an important mechanism for in situ remediation of contaminated sediments. Steps involved in the anaerobic degradation of 2-methylnaphthalene have been described in the sulfate reducing strains NaphS3, NaphS6 and N47. Evidence from N47 suggests that naphthalene degradation involves 2-methylnaphthalene as an intermediate, whereas evidence in NaphS2, NaphS3 and NaphS6 suggests a mechanism for naphthalene degradation that does not involve 2-methylnaphthalene. To further characterize pathways involved in naphthalene degradation in NaphS2, the draft genome was sequenced, and gene and protein expression examined. RESULTS: Draft genome sequencing, gene expression analysis, and proteomic analysis revealed that NaphS2 degrades naphthoyl-CoA in a manner analogous to benzoyl-CoA degradation. Genes including the previously characterized NmsA, thought to encode an enzyme necessary for 2-methylnaphthalene metabolism, were not upregulated during growth of NaphS2 on naphthalene, nor were the corresponding protein products. NaphS2 may possess a non-classical dearomatizing enzyme for benzoate degradation, similar to one previously characterized in Geobacter metallireducens. Identification of genes involved in toluene degradation in NaphS2 led us to determine that NaphS2 degrades toluene, a previously unreported capacity. The genome sequence also suggests that NaphS2 may degrade other monoaromatic compounds. CONCLUSION: This study demonstrates that steps leading to the degradation of 2-naphthoyl-CoA are conserved between NaphS2 and N47, however while NaphS2 possesses the capacity to degrade 2-methylnaphthalene, naphthalene degradation likely does not proceed via 2-methylnaphthalene. Instead, carboxylation or another form of activation may serve as the first step in naphthalene degradation. Degradation of toluene and 2-methylnaphthalene, and the presence of at least one

  20. Bacterial putative metacaspase structure from Geobacter sulfureducens as a template for homology modeling of type II Triticum aestivum metacaspase (TaeMCAII).

    Science.gov (United States)

    Dudkiewicz, Malgorzata Z; Piszczek, Ewa

    2012-01-01

    Metacaspases, cysteine proteases belonging to the peptidase C14 family, are suspected of being involved in the programmed cell death of plants, although their sequences and substrate specificity differ from those of animal caspases. At present, the knowledge on the metacaspase reaction mechanism is based only on biochemical data and homology models constructed on caspase templates. Here we propose a novel template for metacaspase modeling and demonstrate important advantages in comparison to the conventionally used caspase templates. We also point out the connection between plant and bacterial metacaspases, underlining the prokaryotic roots of Programmed Cell Death (PCD).

  1. A C-Type Cytochrome and a Transcriptional Regulator Responsible for Enhanced Extracellular Electron Transfer in Geobacter Sulfurreducens Revealed by Adaptive Evolution

    Science.gov (United States)

    2010-01-01

    ducens fuel cells. Appl Environ Microbiol 72: 7345–7348. Sambrook, J., Fritsch, E.F., and Maniatis , T. (1989) Molecular Cloning : A Laboratory Manual... Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA. 3Department of Bioengineering, University of California, San Diego, La...ORGANIZATION NAME(S) AND ADDRESS(ES) Naval Research Laboratory,Center for Bio/ Molecular Science and Engineering,Washington,DC,20375 8. PERFORMING

  2. Nitrate Enhanced Microbial Cr(VI) Reduction-Final Report

    Energy Technology Data Exchange (ETDEWEB)

    John F. Stolz

    2011-06-15

    A major challenge for the bioremediation of radionuclides (i.e., uranium, technetium) and metals (i.e., Cr(VI), Hg) is the co-occurrence of nitrate as it can inhibit metal transformation. Denitrification (nitrate reduction to dinitrogen gas) is considered the most important ecological process. For many metal and metalloid reducing bacteria, however, ammonia is the end product through respiratory nitrate reduction (RNRA). The focus of this work was to determine how RNRA impacts Cr(VI) transformation. The goal was to elucidate the specific mechanism(s) that limits Cr(VI) reduction in the presence of nitrate and to use this information to develop strategies that enhance Cr(VI) reduction (and thus detoxification). Our central hypothesis is that nitrate impacts the biotransformation of metals and metalloids in three ways 1) as a competitive alternative electron acceptor (inhibiting transformation), 2) as a co-metabolite (i.e., concomitant reduction, stimulating transformation), and 3) as an inducer of specific proteins and pathways involved in oxidation/reduction reactions (stimulating transformation). We have identified three model organisms, Geobacter metallireducens (mechanism 1), Sulfurospirillum barnesii, (mechasism 2), and Desulfovibrio desulfuricans (mechanisms 3). Our specific aims were to 1) investigate the role of Cr(VI) concentration on the kinetics of both growth and reduction of nitrate, nitrite, and Cr(VI) in these three organisms; 2) develop a profile of bacterial enzymes involved in nitrate transformation (e.g., oxidoreductases) using a proteomic approach; 3) investigate the function of periplasmic nitrite reductase (Nrf) as a chromate reductase; and 4) develop a strategy to maximize microbial chromium reduction in the presence of nitrate. We found that growth on nitrate by G. metallireducens was inhibited by Cr(VI). Over 240 proteins were identified by LC/MS-MS. Redox active proteins, outer membrane heavy metal efflux proteins, and chemotaxis sensory

  3. Characterization of phenols biodegradation by compound specific stable isotope analysis

    Science.gov (United States)

    Wei, Xi; Gilevska, Tetyana; Wenzig, Felix; Hans, Richnow; Vogt, Carsten

    2015-04-01

    Biodegradation of phenol and alkylphenols has been described under both oxic and anoxic conditions. In the absence of molecular oxygen, the degradation of phenolic compounds is initiated by microorganisms through carboxylation, fumarate addition to the methyl moiety or anoxic hydroxylation of the methyl moiety. Comparatively, under aerobic condition, the initiation mechanisms are revealed to be monoxygenation or dihydroxylation for phenol and ring hydroxylation or methyl group oxidation for cresols. While several studies biochemically characterized the enzymes and reaction mechanisms in the relevant degradation pathways, isotope fractionation patterns were rarely reported possibly due to constraints in current analytical methods. In this study, the carbon isotope fractionation patterns upon the degradation of phenol and cresols by several strains were analyzed by using isotope ratio mass spectrometry connected with liquid chromatography (LC-IRMS). The corresponding enrichment factors for carbon (ƐC) have been obtained. Cresols degradation by various strains showed generally moderate carbon isotope fractionation patterns with notable differences. For p-cresol degradation, five strains were examined. The aerobic strain Acinetobacter calcoaceticus NCIMB8250 exploits ring hydroxylation by molecular oxygen as initial reaction, and a ƐC value of -1.4±0.2‰ was obtained. Pseudomonas pseudoalcaligenes NCIMB 9867, an aerobic strain initiating cresols degradation via oxygen-dependent side chain hydroxylation, yielded a ƐC value of -2.3±0.2‰. Under nitrate-reducing conditions, Geobacter metallireducens DSM 7210 and Azoarcus buckelii DSM 14744 attacks p-cresol at the side chain by monohydroxylation using water as oxygen source; the two strains produced ƐC values of -3.6±0.4‰ and -2±0.1‰, accordingly. The sulfate-reducing Desulfosarcina cetonica DSM 7267 activating cresols by fumarate addition to the methyl moiety yielded ƐC values of -1.9±0.2‰ for p

  4. Correlation between microbial community and granule conductivity in anaerobic bioreactors for brewery wastewater treatment

    DEFF Research Database (Denmark)

    Shrestha, Pravin; Malvankar, Nikhil S.; Werner, Jeffrey

    2014-01-01

    granules from an aerobic bioreactor designed for phosphate removal were not. There was a moderate correlation (r = 0.67) between the abundance of Geobacter species in the UASB granules and granule conductivity, suggesting that Geobacter contributed to granule conductivity. These results, coupled...

  5. NCBI nr-aa BLAST: CBRC-DYAK-01-0032 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DYAK-01-0032 ref|ZP_01775326.1| electron transfer flavoprotein beta-subunit [G...eobacter bemidjiensis Bem] gb|EDJ79436.1| electron transfer flavoprotein beta-subunit [Geobacter bemidjiensis Bem] ZP_01775326.1 0.85 27% ...

  6. Probing Electron Transfer Mechanisms in Shewanella oneidensis MR-1 using a Nanoelectrode Platform and Single-Cell Imaging

    Science.gov (United States)

    2010-01-01

    nanowires The capability of bacteria, such as Shewanella and Geobacter ,to transfer electrons from metabolism of organic sources to electrodes without...filamentous pili growth from Shewanella and Geobacter cells report a third mechanism for extracellular electron transfer through biological nanowires (12

  7. Carboxydotrophic growth of

    NARCIS (Netherlands)

    Geelhoed, J.; Henstra, A.M.; Stams, A.J.M.

    2016-01-01

    This study shows that Geobacter sulfurreducensgrows on carbon monoxide (CO) as electron donor with fumarateas electron acceptor. Geobacter sulfurreducens wastolerant to high CO levels, with up to 150 kPa in the headspacetested. During growth, hydrogen was detected in very slightamounts (~5 Pa). In a

  8. NCBI nr-aa BLAST: CBRC-DYAK-01-0032 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DYAK-01-0032 ref|ZP_01387306.1| Electron transfer flavoprotein beta-subunit [G...eobacter sp. FRC-32] gb|EAT63524.1| Electron transfer flavoprotein beta-subunit [Geobacter sp. FRC-32] ZP_01387306.1 0.077 28% ...

  9. NCBI nr-aa BLAST: CBRC-GACU-16-0048 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GACU-16-0048 ref|YP_001231116.1| lipopolysaccharide biosynthesis protein [Geob...acter uraniumreducens Rf4] gb|ABQ26543.1| lipopolysaccharide biosynthesis protein [Geobacter uraniumreducens Rf4] YP_001231116.1 0.14 18% ...

  10. A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing.

    Science.gov (United States)

    Song, Yang; Xiao, Li; Jayamani, Indumathy; He, Zhen; Cupples, Alison M

    2015-01-01

    Stable isotope probing and high throughput sequencing were used to characterize the microbial communities involved in carbon uptake in microbial fuel cells at two levels of electricity generation. With acetate, the dominant phylotypes involved in carbon uptake included Geobacter and Rhodocyclaceae. With glucose, both Enterobacteriaceae and Geobacter were dominant.

  11. NCBI nr-aa BLAST: CBRC-TGUT-01-0002 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TGUT-01-0002 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 6e-20 36% ...

  12. NCBI nr-aa BLAST: CBRC-DRER-03-0031 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DRER-03-0031 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 2e-09 28% ...

  13. NCBI nr-aa BLAST: CBRC-HSAP-11-0358 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-11-0358 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-39 13% ...

  14. NCBI nr-aa BLAST: CBRC-LAFR-01-2641 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-2641 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 1e-17 20% ...

  15. NCBI nr-aa BLAST: CBRC-MMUS-08-0005 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-08-0005 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 8e-34 38% ...

  16. NCBI nr-aa BLAST: CBRC-MMUS-13-0130 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-13-0130 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 2e-15 33% ...

  17. NCBI nr-aa BLAST: CBRC-DNOV-01-1474 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-1474 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 1.5 31% ...

  18. NCBI nr-aa BLAST: CBRC-CJAC-01-0864 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-0864 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-21 37% ...

  19. NCBI nr-aa BLAST: CBRC-RNOR-14-0069 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RNOR-14-0069 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 2e-12 37% ...

  20. NCBI nr-aa BLAST: CBRC-DRER-16-0044 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DRER-16-0044 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-23 36% ...

  1. NCBI nr-aa BLAST: CBRC-PTRO-01-0029 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-01-0029 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 5e-17 43% ...

  2. NCBI nr-aa BLAST: CBRC-LAFR-01-0585 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-0585 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 2e-15 20% ...

  3. NCBI nr-aa BLAST: CBRC-DRER-26-0487 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DRER-26-0487 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-55 45% ...

  4. NCBI nr-aa BLAST: CBRC-CPOR-01-0327 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CPOR-01-0327 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 6e-04 34% ...

  5. NCBI nr-aa BLAST: CBRC-FCAT-01-0596 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-FCAT-01-0596 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 5e-56 53% ...

  6. NCBI nr-aa BLAST: CBRC-CJAC-01-0051 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CJAC-01-0051 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 7e-25 37% ...

  7. NCBI nr-aa BLAST: CBRC-GACU-12-0034 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GACU-12-0034 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 7e-08 28% ...

  8. NCBI nr-aa BLAST: CBRC-CFAM-09-0004 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CFAM-09-0004 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-29 43% ...

  9. NCBI nr-aa BLAST: CBRC-GGAL-35-0432 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GGAL-35-0432 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 5e-48 52% ...

  10. NCBI nr-aa BLAST: CBRC-DRER-12-0023 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DRER-12-0023 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-27 39% ...

  11. NCBI nr-aa BLAST: CBRC-DMEL-08-0093 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DMEL-08-0093 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 4e-34 34% ...

  12. NCBI nr-aa BLAST: CBRC-RMAC-07-0070 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RMAC-07-0070 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 1e-09 34% ...

  13. NCBI nr-aa BLAST: CBRC-MMUS-05-0011 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-05-0011 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 2e-34 45% ...

  14. NCBI nr-aa BLAST: CBRC-SARA-01-0796 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-SARA-01-0796 ref|ZP_01774245.1| conserved hypothetical protein [Geobacter bemi...djiensis Bem] gb|EDJ80432.1| conserved hypothetical protein [Geobacter bemidjiensis Bem] ZP_01774245.1 3e-33 39% ...

  15. NCBI nr-aa BLAST: CBRC-DNOV-01-1221 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-1221 ref|YP_001230970.1| UBA/THIF-type NAD/FAD binding protein [Geobacter uranium...reducens Rf4] gb|ABQ26397.1| UBA/THIF-type NAD/FAD binding protein [Geobacter uraniumreducens Rf4] YP_001230970.1 3.9 50% ...

  16. NCBI nr-aa BLAST: CBRC-BTAU-01-2822 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-BTAU-01-2822 ref|YP_001230511.1| lipolytic enzyme, G-D-S-L family [Geobacter uranium...reducens Rf4] gb|ABQ25938.1| lipolytic enzyme, G-D-S-L family [Geobacter uraniumreducens Rf4] YP_001230511.1 0.001 40% ...

  17. NCBI nr-aa BLAST: CBRC-LAFR-01-0322 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-LAFR-01-0322 ref|YP_001231537.1| carbon starvation protein CstA [Geobacter uranium...reducens Rf4] gb|ABQ26964.1| carbon starvation protein CstA [Geobacter uraniumreducens Rf4] YP_001231537.1 0.96 31% ...

  18. NCBI nr-aa BLAST: CBRC-DMEL-04-0042 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available ike protein [Geobacter uraniumreducens Rf4] gb|ABQ26219.1| Uncharacterized membrane-associated protein-like protein [Geobacter uraniumreducens Rf4] YP_001230792.1 4.3 28% ... ...CBRC-DMEL-04-0042 ref|YP_001230792.1| Uncharacterized membrane-associated protein-l

  19. NCBI nr-aa BLAST: CBRC-HSAP-11-0402 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-HSAP-11-0402 ref|YP_001232090.1| heavy metal efflux pump, CzcA family [Geobacter uranium...reducens Rf4] gb|ABQ27517.1| heavy metal efflux pump, CzcA family [Geobacter uraniumreducens Rf4] YP_001232090.1 1.2 30% ...

  20. NCBI nr-aa BLAST: CBRC-XTRO-01-0152 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-0152 ref|YP_001230889.1| inner-membrane translocator [Geobacter uranium...reducens Rf4] gb|ABQ26316.1| inner-membrane translocator [Geobacter uraniumreducens Rf4] YP_001230889.1 3e-34 36% ...

  1. NCBI nr-aa BLAST: CBRC-DYAK-02-0022 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DYAK-02-0022 ref|YP_001232964.1| ATP synthase F0, A subunit [Geobacter uranium...reducens Rf4] gb|ABQ28391.1| ATP synthase F0, A subunit [Geobacter uraniumreducens Rf4] YP_001232964.1 0.85 25% ...

  2. 45 CFR 5.43 - Fee schedule.

    Science.gov (United States)

    2010-10-01

    ... of a GS-15, step 7, employee. In each case, the hourly rate will be computed by taking the current... for each. (b) Computer searching and printing—the actual cost of operating the computer plus charges... machine, plus the actual cost of the materials used, plus charges for the time spent by the operator,...

  3. The Impact of Organizational Culture on the Sharing of Homeland Security Information

    Science.gov (United States)

    2008-04-04

    IMPACT OF ORGANIZATIONAL CULTURE ON THE SHARING OF HOMELAND SECURITY INFORMATION By Jeffery E. Bradey GS-15, Department of Defense...information sharing tool. 15. SUBJECT TERMS organizational culture , Homeland Security Information Network, information sharing 16. SECURITY...41 Organizational Culture .................................................................................................. 41

  4. 77 FR 16850 - Notice of Reclassification of One Investigative Field Office to Regional Office: Denver, CO

    Science.gov (United States)

    2012-03-22

    ... Colorado as well as other western US Attorneys have expressed interest in expanding work relative to HUD... limited to the pay differential between GS-14 and GS-15 pay levels. Moreover, in light of Law Enforcement... housing, schools, public services, taxes, employment, and traffic congestion will be insignificant. E...

  5. Libros colombianos raros y curiosos: agosto de 1964

    Directory of Open Access Journals (Sweden)

    Ignacio Rodríguez Guerrero

    1964-08-01

    Full Text Available El documento presenta la reseña del título: HIDALGO LARA, TOMAS (1867-- 1895. Juicio Crítico sobre la Historia General de la República del Ecuador. Imprenta del Clero. Palacio Arzobispal. Carrera Chile, No. 14. Quito, Ecuador, 1913. XIII-81 págs. 15 x 24 ctms.

  6. 5 CFR 353.303 - Restoration rights of TAPER employees.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Restoration rights of TAPER employees... Restoration rights of TAPER employees. An employee serving in the competitive service under a temporary... employee serving in a position classified above GS-15), is entitled to be restored to the position he...

  7. The electronic properties of microbial nanowires: An STM investigation

    Science.gov (United States)

    Veazey, Josh; Steidl, Becky; Reguera, Gemma; Tessmer, Stuart

    2009-03-01

    Geobacter species of bacteria present the prospect of an interesting physical system through the expression of pili that act as electrically conductive nanowires. These nanowires serve the biological role of transporting metabolically generated electrons outside the cell body to electron acceptors in the organism's native environment. We have performed scanning tunneling microscopy and spectroscopy on Geobacter sulferreducens in an effort to elucidate the mechanism of conductivity. Understanding this system may lead to the enhancement in the effectiveness of Geobacter species' roles in microbial fuel cells and the bioremediation of hazardous waste, such as uranium and petroleum.

  8. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Shrestha, Pravin M.; Liu, Fanghua

    2013-01-01

    , the most abundant bacteria in the aggregates, highly expressed genes for ethanol metabolism and for extracellular electron transfer via electrically conductive pili, suggesting that Geobacter and Methanosaeta species were exchanging electrons via direct interspecies electron transfer (DIET...

  9. Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

    Science.gov (United States)

    Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

    2016-02-01

    Studies with pure cultures of dissimilatory metal-reducing microorganisms have demonstrated that outer-surface c-type cytochromes are important electron transfer agents for the reduction of metals, but previous environmental proteomic studies have typically not recovered cytochrome sequences from subsurface environments in which metal reduction is important. Gel-separation, heme-staining and mass spectrometry of proteins in groundwater from in situ uranium bioremediation experiments identified a putative c-type cytochrome, designated Geobacter subsurface c-type cytochrome A (GscA), encoded within the genome of strain M18, a Geobacter isolate previously recovered from the site. Homologs of GscA were identified in the genomes of other Geobacter isolates in the phylogenetic cluster known as subsurface clade 1, which predominates in a diversity of Fe(III)-reducing subsurface environments. Most of the gscA sequences recovered from groundwater genomic DNA clustered in a tight phylogenetic group closely related to strain M18. GscA was most abundant in groundwater samples in which Geobacter sp. predominated. Expression of gscA in a strain of Geobacter sulfurreducens that lacked the gene for the c-type cytochrome OmcS, thought to facilitate electron transfer from conductive pili to Fe(III) oxide, restored the capacity for Fe(III) oxide reduction. Atomic force microscopy provided evidence that GscA was associated with the pili. These results demonstrate that a c-type cytochrome with an apparent function similar to that of OmcS is abundant when Geobacter sp. are abundant in the subsurface, providing insight into the mechanisms for the growth of subsurface Geobacter sp. on Fe(III) oxide and suggesting an approach for functional analysis of other Geobacter proteins found in the subsurface.

  10. A Code Of Ethics And Professional Conduct For NSA Intelligence Professionals

    Science.gov (United States)

    2015-02-17

    113. 43 Project Management Institute, “Code of Ethics and Professional Conduct,” http://www.pmi.org/~/ media /PDF/ Ethics /ap_pmicodeofethics.ashx... Ethics and Professional Conduct." PMI Project Management Institute. Accessed December 13, 2014. http://www.pmi.org/~/ media /PDF/ Ethics ...7 AIR WAR COLLEGE AIR UNIVERSITY A CODE OF ETHICS AND PROFESSIONAL CONDUCT FOR NSA INTELLIGENCE PROFESSIONALS By Katherine A. Anderson/GS15

  11. HUMAN CAPITAL: Opportunities Exist for DOD to Enhance its Approach for Determining Civilian Senior Leader Workforce Needs

    Science.gov (United States)

    2010-11-01

    Information from the defense intelligence community was included in appendix 8, titled “Intelligence.” Tab A is called “Report of 120 Day Review of DISES ...Intelligence Senior Executive Service ( DISES ) allocations. That is not accurate and contradicts the last sentence of the first paragraph on page 23...addition to validating that any additional DISES requirements involve responsibilities that exceed the GS-15 level as required by statute, we also

  12. 32 CFR 286.29 - Collection of fees and fee rates.

    Science.gov (United States)

    2010-07-01

    ...) Audiovisual documentary materials. Search costs are computed as for any other record. Duplication cost is the... Component has determined that the fee will be in excess of $250 (see § 286.28(e)). (b) Search time—(1) Manual search. Type Grade Hourly Rate Clerical E1-E9/GS1-GS8 $20.00 Professional O1-O6/GS9-GS15...

  13. A combination of parabolic and grid slope interpolation for 2D tissue displacement estimations.

    Science.gov (United States)

    Albinsson, John; Ahlgren, Åsa Rydén; Jansson, Tomas; Cinthio, Magnus

    2017-08-01

    Parabolic sub-sample interpolation for 2D block-matching motion estimation is computationally efficient. However, it is well known that the parabolic interpolation gives a biased motion estimate for displacements greater than |y.2| samples (y = 0, 1, …). Grid slope sub-sample interpolation is less biased, but it shows large variability for displacements close to y.0. We therefore propose to combine these sub-sample methods into one method (GS15PI) using a threshold to determine when to use which method. The proposed method was evaluated on simulated, phantom, and in vivo ultrasound cine loops and was compared to three sub-sample interpolation methods. On average, GS15PI reduced the absolute sub-sample estimation errors in the simulated and phantom cine loops by 14, 8, and 24% compared to sub-sample interpolation of the image, parabolic sub-sample interpolation, and grid slope sub-sample interpolation, respectively. The limited in vivo evaluation of estimations of the longitudinal movement of the common carotid artery using parabolic and grid slope sub-sample interpolation and GS15PI resulted in coefficient of variation (CV) values of 6.9, 7.5, and 6.8%, respectively. The proposed method is computationally efficient and has low bias and variance. The method is another step toward a fast and reliable method for clinical investigations of longitudinal movement of the arterial wall.

  14. Characterization and Transcription of Arsenic Respiration and Resistance Genes During In Situ Uranium Bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Giloteaux, L.; Holmes, Dawn E.; Williams, Kenneth H.; Wrighton, Kelly C.; Wilkins, Michael J.; Montgomery, Alison P.; Smith, Jessica A.; Orellana, Roberto; Thompson, Courtney A.; Roper, Thomas J.; Long, Philip E.; Lovley, Derek R.

    2013-02-04

    The possibility of arsenic release and the potential role of Geobacter in arsenic biogeochemistry during in situ uranium bioremediation was investigated because increased availability of organic matter has been associated with substantial releases of arsenic in other subsurface environments. In a field experiment conducted at the Rifle, CO study site, groundwater arsenic concentrations increased when acetate was added. The number of transcripts from arrA, which codes for the alpha subunit of dissimilatory As(V) reductase, and acr3, which codes for the arsenic pump protein Acr3, were determined with quantitative RT-PCR. Most of the arrA (> 60%) and acr3-1 (> 90%) sequences that were recovered were most similar to Geobacter species, while the majority of acr3-2 (>50%) sequences were most closely related to Rhodoferax ferrireducens. Analysis of transcript abundance demonstrated that transcription of acr3-1 by the subsurface Geobacter community was correlated with arsenic concentrations in the groundwater. In contrast, Geobacter arrA transcript numbers lagged behind the major arsenic release and remained high even after arsenic concentrations declined. This suggested that factors other than As(V) availability regulated transcription of arrA in situ even though the presence of As(V) increased transcription of arrA in cultures of G. lovleyi, which was capable of As(V) reduction. These results demonstrate that subsurface Geobacter species can tightly regulate their physiological response to changes in groundwater arsenic concentrations. The transcriptomic approach developed here should be useful for the study of a diversity of other environments in which Geobacter species are considered to have an important influence on arsenic biogeochemistry.

  15. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Mouser, P.J.; N' Guessan, A.L.; Elifantz, H.; Holmes, D.E.; Williams, K.H.; Wilkins, M.J.; Long, P.E.; Lovley, D.R.

    2009-04-01

    The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.

  16. Transcriptomic and genetic analysis of direct interspecies electron transfer

    DEFF Research Database (Denmark)

    Shrestha, Pravin Malla; Rotaru, Amelia-Elena; Summers, Zarath M

    2013-01-01

    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 elect......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....... 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....

  17. Magnetite Compensates for the Lack of a Pilin-Associated c-Type Cytochrome in Extracellular Electron Exchange

    DEFF Research Database (Denmark)

    Liu, Fanghua; Rotaru, Amelia-Elena; Shrestha, Pravin

    2015-01-01

    investigation revealed that magnetite attached to the electrically conductive pili of Geobacter species in a manner reminiscent of the association of the multi-heme c-type cytochrome OmcS with the pili of Geobacter sulfurreducens. Magnetite conferred extracellular electron capabilities on an Omc......S-deficient strain unable to participate in interspecies electron transfer or Fe(III) oxide reduction. In the presence of magnetite wild-type cells repressed expression of the OmcS gene, suggesting that cells might need to produce less OmcS when magnetite was available. The finding that magnetite can compensate...

  18. Bacterias, fuente de energía para el futuro

    Directory of Open Access Journals (Sweden)

    Alba Ayde Romero Mejía

    2012-06-01

    Full Text Available This paper presents a family of bacteria called Geobacter that have the ability to produce power as a renewable source in a microbial fuel cell. These bacteria can completely oxidize organic compounds using different elements or substances as electron acceptors. The paper addresses key features of the bacteria, the mechanisms used to harness the electricity generated and an approximation of the system required to become a competitive source of renewable energy. The results show a comparative analysis of sources of conventional and unconventional energy with respect to the Geobacter family of bacteria.

  19. Identification of several soybean cytosolic glutamine synthetase transcripts highly or specifically expressed in nodules: expression studies using one of the corresponding genes in transgenic Lotus corniculatus.

    Science.gov (United States)

    Marsolier, M C; Debrosses, G; Hirel, B

    1995-01-01

    A DNA fragment containing sequences hybridizing to the 5' region of GS15, a gene encoding soybean cytosolic glutamine synthetase, was isolated from a soybean genomic library. Mapping and partial sequence analysis of the genomic clone revealed that it encodes a cytosolic GS gene, GS21, which is different from GS15. In parallel, a number of cDNA clones encoding cytosolic GS were isolated using the coding region of pGS20 as a probe (pGS20 is a cDNA clone which corresponds to a transcript of the GS15 gene). Two new full-length cDNAs designated pGS34 and pGS38 were isolated and sequenced. In the 5' non-coding region a strong homology was found between the two clones and the GS21 gene. However, none of these sequences were identical, which suggests that there are at least three members in this group of genes. In order to determine their relative levels of transcription, specific sequences from pGS34, pGS38 and GS21 were used in an RNAse protection assay. This experiment clearly showed that GS21 and the gene encoding pGS38 are specifically expressed in young or mature nodules, whereas the gene encoding pGS34 is highly transcribed in nodules and constitutively expressed at a lower level in other soybean organs. In order to further analyse the molecular mechanisms controlling GS21 transcription, different fragments of the promoter region were fused to the Escherichia coli reporter gene encoding beta-glucuronidase (GUS) and the constructs were introduced into Lotus corniculatus via Agrobacterium rhizogenes-mediated transformation. Analysis of GUS activity showed that the GS21 promoter-GUS constructs were expressed in the vasculature of all vegetative organs. This result is discussed in relation to species-specific metabolic and developmental characteristics of soybean and Lotus.

  20. Geobacteraceae strains and methods

    Science.gov (United States)

    Lovley, Derek R.; Nevin, Kelly P.; Yi, Hana

    2015-07-07

    Embodiments of the present invention provide a method of producing genetically modified strains of electricigenic microbes that are specifically adapted for the production of electrical current in microbial fuel cells, as well as strains produced by such methods and fuel cells using such strains. In preferred embodiments, the present invention provides genetically modified strains of Geobacter sulfurreducens and methods of using such strains.

  1. Enrichment of dissimilatory Fe(III)-reducing bacteria from groundwater of the Siklós BTEX-contaminated site (Hungary).

    Science.gov (United States)

    Farkas, Milán; Szoboszlay, Sándor; Benedek, Tibor; Révész, Fruzsina; Veres, Péter Gábor; Kriszt, Balázs; Táncsics, András

    2017-01-01

    Dissimilatory iron-reducing bacteria are commonly found in microbial communities of aromatic hydrocarbon-contaminated subsurface environments where they often play key role in the degradation of the contaminants. The Siklós benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated area is one of the best characterized petroleum hydrocarbon-contaminated sites of Hungary. Continuous monitoring of the microbial community in the center of the contaminant plume indicated the presence of an emerging Geobacter population and a Rhodoferax phylotype highly associated with aromatic hydrocarbon-contaminated subsurface environments. The aim of the present study was to make an initial effort to enrich Rhodoferax-related and other dissimilatory iron-reducing bacteria from this environment. Accordingly, four slightly different freshwater media were used to enrich Fe(III) reducers, differing only in the form of nitrogen source (organic, inorganic nitrogen or gaseous headspace nitrogen). Although enrichment of the desired Rhodoferax phylotype was not succeeded, Geobacter-related bacteria were readily enriched. Moreover, the different nitrogen sources caused the enrichment of different Geobacter species. Investigation of the diversity of benzylsuccinate synthase gene both in the enrichments and in the initial groundwater sample indicated that the Geobacter population in the center of the contaminant plume may not play a significant role in the anaerobic degradation of toluene.

  2. Digestion of algal biomass for electricity generation in microbial fuel cells.

    Science.gov (United States)

    Nishio, Koichi; Hashimoto, Kazuhito; Watanabe, Kazuya

    2013-01-01

    Algal biomass serves as a fuel for electricity generation in microbial fuel cells. This study constructed a model consortium comprised of an alga-digesting Lactobacillus and an iron-reducing Geobacter for electricity generation from photo-grown Clamydomonas cells. Total power-conversion efficiency (from Light to electricity) was estimated to be 0.47%.

  3. Dicty_cDB: CHH502 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available _1( AY495652 |pid:none) Cochliobolus heterostrophus polyke... 32 8.8 CP001090_72( CP001090 |pid:none) Geobac...ter lovleyi SZ plasmid pGLO... 32 8.8 protein update 2008.10.31 PSORT psg: 0.96 gvh: 0.39 alm: 0.43 top: 0.5

  4. Influence of ammonium availability on expression of nifD and amtB genes during biostimulation of a U(VI) contaminated aquifer: implications for U(VI) removal and monitoring the metabolic state of Geobacteraceae

    Energy Technology Data Exchange (ETDEWEB)

    Mouser, Paula J.; N' Guessan, A. Lucie; Elifantz, Hila; Holmes, Dawn E.; Williams, Kenneth H; Wilkins, Michael J.; Long, Philip E.; Lovley, Derek R.

    2009-03-25

    The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by 2 orders of magnitude (<4 to 400 ?M) across the study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during uranium reduction. The abundance of amtB was inversely correlated to ammonium levels, whereas nifD transcript levels were similar across all sites examined. These results suggest that nifD and amtB expression are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB transcript expression appears to be a useful approach for monitoring the nitrogen-related physiological status of subsurface Geobacter species. This study also emphasizes the need for more detailed analysis of geochemical and physiological interactions at the field scale in order to adequately model subsurface microbial processes during bioremediation.

  5. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    Science.gov (United States)

    Sparks, N. H. C.; Mann, S.; Bazylinski, D. A.; Lovley, D. R.; Jannasch, H. W.; Frankel, R. B.

    1990-04-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo¨ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 × 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of 110 faces which are capped and truncated by 111 end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization.

  6. 新疆数字化重力观测台站的场地勘选、建设、运行及其资料评价%THE FIELD SELECTION, CONSTRUCTION, OPERATION AND OBSERVATION DATA ASSESSMENT OF DIGITAL GRAVITY STATION IN XINJIANG

    Institute of Scientific and Technical Information of China (English)

    杨又陵; 赵建政; 李晓东; 马世贵; 哈斯高娃

    2009-01-01

    简要介绍了新疆数字化重力台站的勘选和建设情况,建成后的台站完全达到了设计目标,取得了令人满意的观测结果.GS-15型重力仪的改造是成功的,但气压干扰问题有待进一步解决.PET潮汐重力仪的性能优良,潮汐分析的精度≤0.001.%The paper gives a general overview of field selection and construction of digital gravity station in Xinjiang.The finished stations realized the prospective aim and obtained satisfactory observation result. The transformation of GS-15 gravimeter is successful, but the interference of atmospheric pressure will be solved in future. The function of PET gravimeter is better and the accuracy of tide analysis is not more than 0.01.

  7. 直接微生物燃料电池的构建及初步研究%Construction and Preliminary Studies on the Direct Microbial Fuel Cell

    Institute of Scientific and Technical Information of China (English)

    连静; 冯雅丽; 李浩然; 刘志丹; 周良

    2006-01-01

    利用Geobacter metallireducens能够以Fe(OH)3固体作电子受体进行呼吸的特性,用其构建直接微生物燃料电池,初步考察了产电情况和产电原理.实验证明,Geobacter metallireducens直接微生物燃料电池的电能产出主要依赖于吸附在电极上的细菌.燃料醋酸钠可以完全氧化至CO2,反应结束后其浓度低于检测下限(<10μmol/L).电子回收率达80%,电流密度达704.4 mA/m2.

  8. Progress in Research for Non-mediator Microbial Fuel Cell%无介体微生物燃料电池研究进展

    Institute of Scientific and Technical Information of China (English)

    冯雅丽; 联静; 杜竹玮; 李浩然

    2005-01-01

    介绍微生物燃料电池特点,综述相关的研究进展.从深海沉积物中分离到微生物Rhodoferax ferrireducens、Geobacter metallireducens和Geobacter sulfereducens在分解有机底物(海底沉积物、葡萄糖、废糖蜜)进行自身代谢过程中,易在固体表面吸附成膜,无需介体可直接将电子传递到电池的阳极.能量转换为电能的效率大于70%,电流密度为30mA/m2,电池输出功率密度达到3W/m2(0.2V).

  9. Iron Cycling at Corroding Carbon Steel Surfaces

    Science.gov (United States)

    2013-01-01

    Tian J. 1998. Manganite reduction by Shewanella putrefaciens mr-4. Am Mineral. 83:1564–1572. Larsen O, Postma D. 2001. Kinetics of reductive bulk...of the genus Shewanella ). Inhibitor and competition experiments suggest that Fe3+ is an efficient electron acceptor similar to nitrate in redox abil... Shewanella sp. and Lovley et al. (1987) working with Geobacter sp. demonstrated that solid manganese and iron oxides, respectively, could serve as electron

  10. The design of long-term effective uranium bioremediation strategy using a community metabolic model.

    Science.gov (United States)

    Zhuang, K; Ma, E; Lovley, Derek R; Mahadevan, Radhakrishnan

    2012-10-01

    Acetate amendment at uranium contaminated sites in Rifle, CO. leads to an initial bloom of Geobacter accompanied by the removal of U(VI) from the groundwater, followed by an increase of sulfate-reducing bacteria (SRBs) which are poor reducers of U(VI). One of the challenges associated with bioremediation is the decay in Geobacter abundance, which has been attributed to the depletion of bio-accessible Fe(III), motivating the investigation of simultaneous amendments of acetate and Fe(III) as an alternative bioremediation strategy. In order to understand the community metabolism of Geobacter and SRBs during artificial substrate amendment, we have created a genome-scale dynamic community model of Geobacter and SRBs using the previously described Dynamic Multi-species Metabolic Modeling framework. Optimization techniques are used to determine the optimal acetate and Fe(III) addition profile. Field-scale simulation of acetate addition accurately predicted the in situ data. The simulations suggest that batch amendment of Fe(III) along with continuous acetate addition is insufficient to promote long-term bioremediation, while continuous amendment of Fe(III) along with continuous acetate addition is sufficient to promote long-term bioremediation. By computationally minimizing the acetate and Fe(III) addition rates as well as the difference between the predicted and target uranium concentration, we showed that it is possible to maintain the uranium concentration below the environmental safety standard while minimizing the cost of chemical additions. These simulations show that simultaneous addition of acetate and Fe(III) has the potential to be an effective uranium bioremediation strategy. They also show that computational modeling of microbial community is an important tool to design effective strategies for practical applications in environmental biotechnology.

  11. C-13 Stable Isotope Probing of Biostimulation Experiments to Identify Acetate Utilizers

    Science.gov (United States)

    Jaffe, P. R.; Tan, H.; Kerkhof, L.; McGuinness, L.; Peacock, A.; Long, P. E.

    2011-12-01

    In order to determine which microorganisms take up acetate during biostimulation and how the uptake of acetate by specific organisms, especially Geobacter species, changes over time, a 120-day column biostimulation experiment was performed. A total of eight columns were loaded with Rifle sediments and operated under continuous flow conditions using Rifle groundwater, amended with 3 mM C-12 acetate. At regular time intervals, C-12 acetate flow into a specific column was switched to C-13 acetate. That column was then operated under C-13 acetate amendment for 36 hours before it was sacrificed for detailed geochemical and microbiological analyses. Column operation started under iron reduction (based on the measured Fe(II) in the column effluent), while sulfate reduction (based on removal of sulfate between influent and outflow), was noted at about 25 days of operation. The microbial characterization consisted of phospholipid fatty acid analysis (PLFA) and stable isotope probing (SIP). All microbial characterization was done to differentiate between the C-12 and C-13 incorporation into the biomass. Results showed that there was a differentiation between the community that was taking up acetate actively throughout the 120 days of operation and the overall microbial community. Of interest was that the fraction of Geobacter population remained fairly constant throughout the duration of the experiment, as well as its acetate uptake. Results also showed that of the acetate incorporated into the overall biomass, about 40% was incorporated into Geobacter biomass. These results are key for the proper numerical simulations of biostimulation via acetate amendment and the biostimulation of Geobacter.

  12. 生物化学工程

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    膜材料与生物分子相互作用的分子模拟;基于蛋白质结构知识解析活性多肽的酶解制备反应行为(Ⅱ)酶解反应过程的集总动力学模型;利用微生物燃料电池研究Geobacter metallireducens异化还原铁氧化物;

  13. AcEST: DK961649 [AcEST

    Lifescience Database Archive (English)

    Full Text Available =Geobacter metallir... 29 6.4 sp|Q9HCB6|SPON1_HUMAN Spondin-1 OS=Homo sapiens GN=SPON1... 164 L GMGA L +E+ +EK+++A L+KAEG Sbjct: 702 LTGMGA-LRHIQELEDEKRQIAALMKAEG 729 >sp|Q9HCB6|SPON1..._HUMAN Spondin-1 OS=Homo sapiens GN=SPON1 PE=1 SV=2 Length = 807 Score = 29.3 bits (64), Expect

  14. Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation.

    Science.gov (United States)

    Zhao, Jiao; Scheibe, Timothy D; Mahadevan, R

    2011-07-01

    Uranium contamination is a serious concern at several sites motivating the development of novel treatment strategies such as the Geobacter-mediated reductive immobilization of uranium. However, this bioremediation strategy has not yet been optimized for the sustained uranium removal. While several reactive-transport models have been developed to represent Geobacter-mediated bioremediation of uranium, these models often lack the detailed quantitative description of the microbial process (e.g., biomass build-up in both groundwater and sediments, electron transport system, etc.) and the interaction between biogeochemical and hydrological process. In this study, a novel multi-scale model was developed by integrating our recent model on electron capacitance of Geobacter (Zhao et al., 2010) with a comprehensive simulator of coupled fluid flow, hydrologic transport, heat transfer, and biogeochemical reactions. This mechanistic reactive-transport model accurately reproduces the experimental data for the bioremediation of uranium with acetate amendment. We subsequently performed global sensitivity analysis with the reactive-transport model in order to identify the main sources of prediction uncertainty caused by synergistic effects of biological, geochemical, and hydrological processes. The proposed approach successfully captured significant contributing factors across time and space, thereby improving the structure and parameterization of the comprehensive reactive-transport model. The global sensitivity analysis also provides a potentially useful tool to evaluate uranium bioremediation strategy. The simulations suggest that under difficult environments (e.g., highly contaminated with U(VI) at a high migration rate of solutes), the efficiency of uranium removal can be improved by adding Geobacter species to the contaminated site (bioaugmentation) in conjunction with the addition of electron donor (biostimulation). The simulations also highlight the interactive effect of

  15. Live wires: direct extracellular electron exchange for bioenergy and the bioremediation of energy-related contamination

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, DR

    2011-12-01

    Microorganisms that can form direct electrical connections with insoluble minerals, electrodes, or other microorganisms can play an important role in some traditional as well as novel bioenergy strategies and can be helpful in the remediation of environmental contamination resulting from the use of more traditional energy sources. The surprising discovery that microorganisms in the genus Geobacter are capable of forming highly conductive networks of filaments that transfer electrons along their length with organic metallic-like conductivity, rather than traditional molecule to molecule electron exchange, provides an explanation for the ability of Geobacter species to grow in subsurface environments with insoluble Fe(III) oxides as the electron acceptor, and effectively remediate groundwater contaminated with hydrocarbon fuels or uranium and similar contaminants associated with the mining and processing of nuclear fuel. A similar organic metallic-like conductivity may be an important mechanism for microorganisms to exchange electrons in syntrophic associations, such as those responsible for the conversion of organic wastes to methane in anaerobic digesters, a proven bioenergy technology. Biofilms with conductivities rivaling those of synthetic polymers help Geobacter species generate the high current densities in microbial fuel cells producing electric current from organic compounds. Electron transfer in the reverse direction, i.e. from electrodes to microbes, is the basis for microbial electrosynthesis, in which microorganisms reduce carbon dioxide to fuels and other useful organic compounds with solar energy in a form of artificial photosynthesis that is more efficient and avoids many of the environmental sustainability concerns associated with biomass-based bioenergy strategies. The ability of Geobacter species to produce highly conductive electronic networks that function in water opens new possibilities in the emerging field of bioelectronics.

  16. Multi-heme cytochromes--new structures, new chemistry.

    Science.gov (United States)

    Mowat, Christopher G; Chapman, Stephen K

    2005-11-07

    Heme is one of the most pervasive cofactors in nature and the c-type cytochromes represent one of the largest families of heme-containing proteins. Recent progress in bacterial genomic analysis has revealed a vast range of genes encoding novel c-type cytochromes that contain multiple numbers of heme cofactors. The genome sequence of Geobacter sulfurreducens, for example, includes some one hundred genes encoding c-type cytochromes, with around seventy of these containing two, or more, heme groups and with one protein containing an astonishing twenty seven heme groups. This wealth of cytochromes is of great significance in the respiratory flexibility shown by bacteria such as Geobacter. In addition, we are now discovering that many of these multi-heme cytochromes have associated enzymatic activities and in some cases this is revealing new chemistries. The purpose of this perspective is to describe recent progress in the structural and functional analyses of these new multi-heme cytochromes. To illustrate this we have chosen to focus on three of these cytochromes which exhibit catalytic activities; nitrite reductase, hydroxylamine oxidoreductase and tetrathionate reductase. In addition we consider the multi-heme cytochromes from Geobacter and Desulfovibrio species. Finally, we consider and contrast the repeating structural modules found in these multi-heme cytochromes.

  17. Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours.

    Directory of Open Access Journals (Sweden)

    Cesar E Guzman

    Full Text Available The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0-20 mins after birth, day 1 (24 ± 1 h after birth, day 2 (48 ± 1 h after birth, and day 3 (72 ± 1 h after birth. Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose.

  18. Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.

    Directory of Open Access Journals (Sweden)

    Michael J Wilkins

    Full Text Available While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.

  19. Diversity and Characterization of Potential H2-Dependent Fe(Ⅲ)-Reducing Bacteria in Paddy Soils

    Institute of Scientific and Technical Information of China (English)

    LI Hui-Juan; PENG Jing-Jing; LI Hong-Bo

    2012-01-01

    Microbial ferric iron reduction,with organic carbon or hydrogen as the electron donor,is one of the most important biogeochemical processes in anoxic paddy soils; however,the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown.Potential H2-dependent Fe(Ⅲ)-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor.Terminal restriction fragment length polymorphism (T-RFLP) analysis and cloning/sequencing were conducted to reveal bacterial comnunity structure.Results showed that Geobacter and Clostridium were the dominant bacteria in the enrichment cultures.Fe(Ⅲ) oxide mineral phases showed a strong effect on the community structure; Geobacter and Clostridium were dominant in the ferrihydrite treatment,while Clostridium spp were dominant in the goethite treatment.These suggested that H2-dependent Fe(Ⅲ)-reducing bacteria might be widely distributed in paddy soils and that besides Geobacter,Clostridium spp.might also be an important group of H2-dependent Fe(Ⅲ)-reducing microorganisms.

  20. Electromicrobiology: Electron Transfer via Biowires in Nature and Practical Applications

    Directory of Open Access Journals (Sweden)

    Lovley Derek

    2016-01-01

    Full Text Available One of the most exciting developments in the field of electromicrobiology has been the discovery of electrically conductive pili (e-pili in Geobacter species that transport electrons with a metallic-like mechanism. The e-pili are essential for extracellular electron transport to Fe(III oxides and longrange electron transport through the conductive biofilms that form on the anodes of microbial fuel cells. The e-pili also facilitate direct interspecies electron transfer between Geobacter and Methanosaeta or Methanosarcina species. Metatranscriptomic studies have demonstrated that Geobacter/Methanosaeta DIET is an important process in anaerobic digesters converting brewery wastes to methane. Increasing e-pili expression through genetic modification of regulatory systems or adaptive evolution yields strains with enhanced rates of extracellular electron transfer. Measurement of the conductivity of individual e-pili has demonstrated that they have conductivities higher than those of a number of synthetic conducting organic polymers. Multiple lines of evidence have demonstrated that aromatic amino acids play an important role in the electron transport along e-pili, suggesting opportunities to tune e-pili conductivity via genetic manipulation of the amino acid composition of e-pili. It is expected that e-pili will be harnessed to improve microbe-electrode processes such as microbial electrosynthesis and for the development of novel biosensors. Also, e-pili show promise as a sustainable ‘green’ replacement for electronic materials that contain toxic components and/or are produced with harsh chemicals.

  1. Analog Design for Digital Deployment of a Serious Leadership Game

    Science.gov (United States)

    Maxwell, Nicholas; Lang, Tristan; Herman, Jeffrey L.; Phares, Richard

    2012-01-01

    This paper presents the design, development, and user testing of a leadership development simulation. The authors share lessons learned from using a design process for a board game to allow for quick and inexpensive revision cycles during the development of a serious leadership development game. The goal of this leadership simulation is to accelerate the development of leadership capacity in high-potential mid-level managers (GS-15 level) in a federal government agency. Simulation design included a mixed-method needs analysis, using both quantitative and qualitative approaches to determine organizational leadership needs. Eight design iterations were conducted, including three user testing phases. Three re-design iterations followed initial development, enabling game testing as part of comprehensive instructional events. Subsequent design, development and testing processes targeted digital application to a computer- and tablet-based environment. Recommendations include pros and cons of development and learner testing of an initial analog simulation prior to full digital simulation development.

  2. Molecular analysis of phosphate limitation in Geobacteraceae during the bioremediation of a uranium-contaminated aquifer

    Energy Technology Data Exchange (ETDEWEB)

    N' Guessan, L.A.; Elifantz, H.; Nevin, K.P.; Mouser, P.J.; Methe, B.; Woodard, T. L.; Manley, K.; Williams, K. H.; Wilkins, M. J.; Larsen, J.T.; Long, P. E.; Lovley, D. R.

    2009-09-01

    Nutrient limitation is an environmental stress that may reduce the effectiveness of bioremediation strategies, especially when the contaminants are organic compounds or when organic compounds are added to promote microbial activities such as metal reduction. Genes indicative of phosphate-limitation were identified via microarray analysis of chemostat cultures of Geobacter sulfureducens. This analysis revealed that genes in the pst-pho operon, which is associated with a high affinity phosphate uptake system in other microorganisms, had significantly higher transcript abundance under phosphate-limiting conditions, with the genes pstB and phoU the most up-regulated. Quantitative PCR analysis of pstB and phoU transcript levels in G. sulfurreducens grown in chemostats demonstrated that the expression of these genes increased when phosphate was removed from the culture medium. Transcripts of pstB and phoU within the subsurface Geobacter species predominating during an in situ uranium bioremediation field experiment were more abundant than in chemostat cultures of G. sulfurreducens that were not limited for phosphate. Addition of phosphate to incubations of subsurface sediments did not stimulate dissimilatory metal reduction. The added phosphate was rapidly adsorbed onto the sediments. The results demonstrate that Geobacter species can effectively reduce U(VI) even when experiencing suboptimal phosphate concentrations and that increasing phosphate availability with phosphate additions is difficult to achieve due to the high reactivity of this compound. This transcript-based approach developed for diagnosing phosphate limitation should be applicable to assessing the potential need for additional phosphate in other bioremediation processes.

  3. Thermodynamic analysis of regulation in metabolic networks using constraint-based modeling

    Directory of Open Access Journals (Sweden)

    Mahadevan Radhakrishnan

    2010-05-01

    Full Text Available Abstract Background Geobacter sulfurreducens is a member of the Geobacter species, which are capable of oxidation of organic waste coupled to the reduction of heavy metals and electrode with applications in bioremediation and bioenergy generation. While the metabolism of this organism has been studied through the development of a stoichiometry based genome-scale metabolic model, the associated regulatory network has not yet been well studied. In this manuscript, we report on the implementation of a thermodynamics based metabolic flux model for Geobacter sulfurreducens. We use this updated model to identify reactions that are subject to regulatory control in the metabolic network of G. sulfurreducens using thermodynamic variability analysis. Findings As a first step, we have validated the regulatory sites and bottleneck reactions predicted by the thermodynamic flux analysis in E. coli by evaluating the expression ranges of the corresponding genes. We then identified ten reactions in the metabolic network of G. sulfurreducens that are predicted to be candidates for regulation. We then compared the free energy ranges for these reactions with the corresponding gene expression fold changes under conditions of different environmental and genetic perturbations and show that the model predictions of regulation are consistent with data. In addition, we also identify reactions that operate close to equilibrium and show that the experimentally determined exchange coefficient (a measure of reversibility is significant for these reactions. Conclusions Application of the thermodynamic constraints resulted in identification of potential bottleneck reactions not only from the central metabolism but also from the nucleotide and amino acid subsystems, thereby showing the highly coupled nature of the thermodynamic constraints. In addition, thermodynamic variability analysis serves as a valuable tool in estimating the ranges of ΔrG' of every reaction in the model

  4. Evidence of a dynamic microbial community structure and predation through combined microbiological and stable isotope characterization

    Science.gov (United States)

    Druhan, J. L.; Bill, M.; Lim, H. C.; Wu, C.; Conrad, M. E.; Williams, K. H.; DePaolo, D. J.; Brodie, E.

    2014-12-01

    The speciation, reactivity and mobility of carbon in the near surface environment is intimately linked to the prevalence, diversity and dynamics of native microbial populations. We utilize this relationship by introducing 13C-labeled acetate to sediments recovered from a shallow aquifer system to track both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Results demonstrate a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples analyzed weekly for microbial composition by pyrosequencing of ribosomal RNA genes showed a transient microbial community structure, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identifiable in the partitioning of carbon isotopes. The impact of predator-prey relationships on subsurface microbial community dynamics and therefore the flux of carbon through a system via the microbial biomass

  5. Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Holmes, Dawn; Giloteaux, L.; Williams, Kenneth H.; Wrighton, Kelly C.; Wilkins, Michael J.; Thompson, Courtney A.; Roper, Thomas J.; Long, Philip E.; Lovley, Derek

    2013-07-28

    The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well-recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, acetate amendments initially promoted the growth of metal-reducing Geobacter species followed by the growth of sulfate-reducers, as previously observed. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater prior to the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the amoeboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity, and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

  6. Convergent development of anodic bacterial communities in microbial fuel cells.

    KAUST Repository

    Yates, Matthew D

    2012-05-10

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m(-2)). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

  7. The presence of hydrogenotrophic methanogens in the inoculum improves methane gas production in microbial electrolysis cells

    Directory of Open Access Journals (Sweden)

    Michael eSiegert

    2015-01-01

    Full Text Available High current densities in microbial electrolysis cells (MECs result from the predominance of various Geobacter species on the anode. MECs inoculated from different sources often converge in terms of current production and predominance of Geobacter species despite variability in the inoculum community. Relatively less is known about the effects of inoculum source on methane gas production in MECs, and specifically whether archaeal communities similarly converge to one specific genus. MECs were examined here on the basis of maximum methane production and current density relative to the inoculum community structure. We used anaerobic digester (AD sludge dominated by acetoclastic Methanosaeta species, and an anaerobic bog sediment where hydrogenotrophic methanogens were detected. Inoculation using solids to medium ratio of 25% w/v resulted in the highest methane production rates (0.27 mL mL–1 cm–2, gas volume normalized by liquid volume and cathode projected area and highest peak current densities (0.5 mA cm–2 for the bog sample. Methane production was independent of solid to medium ratio when AD sludge was used as the inoculum. 16S rRNA gene community analysis using pyrosequencing and qPCR confirmed the convergence of Archaea to Methanobacterium and Methanobrevibacter, and of Bacteria to Geobacter, despite their absence in AD sludge. Combined with other studies, these findings suggest that Archaea of the hydrogenotrophic genera Methanobacterium and Methanobrevibacter are the most important microorganisms for methane production in MECs and that their presence in the inoculum improves the performance.

  8. Gene expression correlates with process rates quantified for sulfate- and Fe(III-reducing bacteria in U(VI-contaminated sediments

    Directory of Open Access Journals (Sweden)

    Denise M Akob

    2012-08-01

    Full Text Available Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III and sulfate reduction pathways in order to monitor these processes during in situ U(VI remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA and the dissimilatory (bisulfite reductase gene (dsrA, were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC site at Oak Ridge, Tennessee. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically-active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.

  9. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

    Science.gov (United States)

    Ding, Long-Jun; Su, Jian-Qiang; Xu, Hui-Juan; Jia, Zhong-Jun; Zhu, Yong-Guan

    2015-03-01

    Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.

  10. Dicty_cDB: Contig-U08982-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Name: Full=E3 ubiquitin-protein ligase highwire; ... 56 1e-06 CP000698_1764( CP000698 |pid:none) Geobacter u...-06 AF262977_1( AF262977 |pid:none) Drosophila melanogaster highwire (... 56 1e-06 CP001159_266( CP001159 |p...-06 ( P25183 ) RecName: Full=Regulator of chromosome condensation; &D... 53 7e-06 AY325887_1( AY325887 |pid:...none) Mus musculus highwire (Phr1) mRNA,... 53 9e-06 AB046783_1( AB046783 |pid:no

  11. Acetate availability and its influence on sustainable bioremediation of Uranium-contaminated groundwater

    Science.gov (United States)

    Williams, K.H.; Long, P.E.; Davis, J.A.; Wilkins, M.J.; N'Guessan, A. L.; Steefel, Carl; Yang, L.; Newcomer, D.; Spane, F.A.; Kerkhof, L.J.; Mcguinness, L.; Dayvault, R.; Lovley, D.R.

    2011-01-01

    Field biostimulation experiments at the U.S. Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, Colorado, have demonstrated that uranium concentrations in groundwater can be decreased to levels below the U.S. Environmental Protection Agency's (EPA) drinking water standard (0.126??M).During successive summer experiments - referred to as "Winchester" (2007) and "Big Rusty" (2008) - acetate was added to the aquifer to stimulate the activity of indigenous dissimilatory metal reducing bacteria capable of reductively immobilizing uranium. The two experiments differed in the length of injection (31 vs. 110 days), the maximum concentration of acetate (5 vs. 30 mM),and the extent to which iron reduction ("Winchester") or sulfate reduction("Big Rusty") was the predominant metabolic process. In both cases, rapid removal of U(VI) from groundwater occurred at calcium concentrations (6 mM) and carbonate alkalinities (8 meq/L) where Ca-UO2-CO3 ternary complexes constitute >90% of uranyl species in groundwater. Complete consumption of acetate and increased alkalinity (>30 meq/L) accompanying the onset of sulfate reduction corresponded to temporary increases in U(VI);however, by increasing acetate concentrations in excess of available sulfate (10 mM), low U(VI) concentrations (0.1-0.05 ??M) were achieved for extended periods of time (>140 days). Uniform delivery of acetate during "Big Rusty" was impeded due to decreases in injection well permeability, likely resulting from biomass accumulation and carbonate and sulfide mineral precipitation. Such decreases were not observed during the short-duration "Winchester" experiment. Terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes demonstrated that Geobacter sp. and Geobacter-like strains dominated the groundwater community profile during iron reduction, with 13C stable isotope probing (SIP) results confirming these strains were actively utilizing acetate to replicate their

  12. Dicty_cDB: Contig-U10742-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 76_1( BC071576 |pid:none) Homo sapiens amyotrophic lateral s... 52 7e-05 AB046783.... 50 3e-04 BC046828_1( BC046828 |pid:none) Mus musculus amyotrophic lateral s... 50 3e-04 CP000474_3011( CP0...114261_1( AC114261 |pid:none) Dictyostelium discoideum chromosom... 57 4e-06 BC123947_1( BC123947 |pid:none) Xenopus tropicalis amyot...rophic lat... 57 4e-06 AE017180_2260( AE017180 |pid:none) Geobacter sulfurreducens

  13. 材料科学基础学科

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Geobacter metallireducens异化还原铁氧化物三种方式,功能材料二氧化钛光催化降解酸性黑染料,Al2O3/WC-10Co/ZrO2金属陶瓷的制备与性能,闪光法测量半透明材料热扩散率的理论研究,汽车用TWIP钢的力学性能与微观组织……

  14. Long range electronic transport in microbial nanowires bridging an electrode and scanned probe

    Science.gov (United States)

    Veazey, Joshua; Lampa-Pastirk, Sanela; Walsh, Kathy; Sun, Jiebing; Zhang, Pengpeng; Reguera, Gemma; Tessmer, Stuart

    2011-03-01

    The filament-like appendages known as pili, expressed by the bacterium Geobacter sulfurreducens, are believed to act as electrically conductive nanowires. Previously, we used scanning tunneling microscopy to study the local density of states at different positions along the wire. However, the long range electron transfer believed to occur in this protein has not been directly observed. Here we discuss a system for verifying long range transport using a scanning probe technique. Transport at distances of more than a few nanometers would require a novel biological electron transfer process. The authors gratefully acknowledge support from the National Science Foundation (MCB-1021948) and the Michigan State University Foundation (Strategic Partnership Grant).

  15. Low-temperature STM studies of electronic properties of microbial nanowires

    Science.gov (United States)

    Walsh, Kathy; Lampa-Pastirk, Sanela; Veazey, Joshua; Reguera, Gemma; Tessmer, Stuart

    2013-03-01

    Geobacter sulfurreducens expresses pili that act as electrically conductive nanowires. These microbial nanowires transport metabolically generated electrons outside the cell body to electron acceptors in the organism's environment. We have performed scanning tunneling microscopy and spectroscopy on these pili in an endeavor to elucidate the mechanism of conductivity. In particular, we will discuss spectroscopy curves acquired at a temperature of 77 K. This work supported by the NSF-MCB Grant No. 1021948 and a Strategic Partnership Grant from the Michigan State University Foundation. K.W. acknowledges support from a U.S. Department of Education GAANN fellowship.

  16. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D

    2011-06-01

    Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

  17. Nuclear technology in research and everyday life; Kerntechnik in Forschung und Alltag

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2015-12-15

    The paper.. discusses the impact of nuclear technology in research and everyday life covering the following issues: miniaturization of memory devices, neutron radiography in material science, nuclear reactions in the universe, sterilization of food, medical applies, cosmetics and packaging materials using beta and gamma radiation, neutron imaging for radioactive waste analysis, microbial transformation of uranium (geobacter uraniireducens), nuclear technology knowledge preservation, spacecrafts voyager 1 and 2, future fusion power plants, prompt gamma activation analysis in archeology, radiation protection and radioecology and nuclear medicine (radiotherapy).

  18. Thermally activated charge transport in microbial protein nanowires.

    Science.gov (United States)

    Lampa-Pastirk, Sanela; Veazey, Joshua P; Walsh, Kathleen A; Feliciano, Gustavo T; Steidl, Rebecca J; Tessmer, Stuart H; Reguera, Gemma

    2016-03-24

    The bacterium Geobacter sulfurreducens requires the expression of conductive protein filaments or pili to respire extracellular electron acceptors such as iron oxides and uranium and to wire electroactive biofilms, but the contribution of the protein fiber to charge transport has remained elusive. Here we demonstrate efficient long-range charge transport along individual pili purified free of metal and redox organic cofactors at rates high enough to satisfy the respiratory rates of the cell. Carrier characteristics were within the orders reported for organic semiconductors (mobility) and inorganic nanowires (concentration), and resistivity was within the lower ranges reported for moderately doped silicon nanowires. However, the pilus conductance and the carrier mobility decreased when one of the tyrosines of the predicted axial multistep hopping path was replaced with an alanine. Furthermore, low temperature scanning tunneling microscopy demonstrated the thermal dependence of the differential conductance at the low voltages that operate in biological systems. The results thus provide evidence for thermally activated multistep hopping as the mechanism that allows Geobacter pili to function as protein nanowires between the cell and extracellular electron acceptors.

  19. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Directory of Open Access Journals (Sweden)

    Ayaka Yamamuro

    Full Text Available Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2 (based on the projected area of the anode. In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  20. The presence of hydrogenotrophic methanogens in the inoculum improves methane gas production in microbial electrolysis cells.

    KAUST Repository

    Siegert, Michael

    2014-01-01

    High current densities in microbial electrolysis cells (MECs) result from the predominance of various Geobacter species on the anode, but it is not known if archaeal communities similarly converge to one specific genus. MECs were examined here on the basis of maximum methane production and current density relative to the inoculum community structure. We used anaerobic digester (AD) sludge dominated by acetoclastic Methanosaeta, and an anaerobic bog sediment where hydrogenotrophic methanogens were detected. Inoculation using solids to medium ratio of 25% (w/v) resulted in the highest methane production rates (0.27 mL mL(-1) cm(-2), gas volume normalized by liquid volume and cathode projected area) and highest peak current densities (0.5 mA cm(-2)) for the bog sample. Methane production was independent of solid to medium ratio when AD sludge was used as the inoculum. 16S rRNA gene community analysis using pyrosequencing and quantitative PCR confirmed the convergence of Archaea to Methanobacterium and Methanobrevibacter, and of Bacteria to Geobacter, despite their absence in AD sludge. Combined with other studies, these findings suggest that Archaea of the hydrogenotrophic genera Methanobacterium and Methanobrevibacter are the most important microorganisms for methane production in MECs and that their presence in the inoculum improves the performance.

  1. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Science.gov (United States)

    Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2014-01-01

    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  2. Set anode potentials affect the electron fluxes and microbial community structure in propionate-fed microbial electrolysis cells

    KAUST Repository

    Rao, Hari Ananda

    2016-12-09

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; −0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49–71%) and CH4 (22.9–41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of −0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, but their relative abundance varied among the tested SAPs. Microbial community analysis implies that complete degradation of propionate in all the tested SAPs was facilitated by syntrophic interactions between fermenters and Geobacter at the anode and ferementers and hydrogenotrophic methanogens in suspension.

  3. Microbial fuel cell coupled to biohydrogen reactor: a feasible technology to increase energy yield from cheese whey.

    Science.gov (United States)

    Wenzel, J; Fuentes, L; Cabezas, A; Etchebehere, C

    2017-02-20

    An important pollutant produced during the cheese making process is cheese whey which is a liquid by-product with high content of organic matter, composed mainly by lactose and proteins. Hydrogen can be produced from cheese whey by dark fermentation but, organic matter is not completely removed producing an effluent rich in volatile fatty acids. Here we demonstrate that this effluent can be further used to produce energy in microbial fuel cells. Moreover, current production was not feasible when using raw cheese whey directly to feed the microbial fuel cell. A maximal power density of 439 mW/m(2) was obtained from the reactor effluent which was 1000 times more than when using raw cheese whey as substrate. 16S rRNA gene amplicon sequencing showed that potential electroactive populations (Geobacter, Pseudomonas and Thauera) were enriched on anodes of MFCs fed with reactor effluent while fermentative populations (Clostridium and Lactobacillus) were predominant on the MFC anode fed directly with raw cheese whey. This result was further demonstrated using culture techniques. A total of 45 strains were isolated belonging to 10 different genera including known electrogenic populations like Geobacter (in MFC with reactor effluent) and known fermentative populations like Lactobacillus (in MFC with cheese whey). Our results show that microbial fuel cells are an attractive technology to gain extra energy from cheese whey as a second stage process during raw cheese whey treatment by dark fermentation process.

  4. Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

    Science.gov (United States)

    Hu, Haiyan; Lin, Hui; Zheng, Wang; Tomanicek, Stephen J.; Johs, Alexander; Feng, Xinbin; Elias, Dwayne A.; Liang, Liyuan; Gu, Baohua

    2013-09-01

    Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury. One strain of sulphate-reducing bacteria (Desulfovibrio desulphuricans ND132) can also methylate elemental mercury. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidize and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally relevant concentrations of elemental mercury. We report differences in the ability of these organisms to oxidize and methylate elemental mercury. In line with recent findings, we show that D.desulphuricans ND132 can both oxidize and methylate elemental mercury. We find that the rate of methylation of elemental mercury is about one-third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidize, but not methylate, elemental mercury. Geobacter sulphurreducens PCA is able to oxidize and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.

  5. Anoxic iron cycling bacteria from an iron sulfide- and nitrate-rich freshwater environment

    Directory of Open Access Journals (Sweden)

    Suzanne Caroline Marianne Haaijer

    2012-02-01

    Full Text Available In this study, both culture-dependent and culture-independent methods were used to determine whether the iron sulfide mineral- and nitrate-rich freshwater nature reserve Het Zwart Water accommodates anoxic microbial iron cycling. Molecular analyses (16S rRNA gene clone library and FISH showed that sulfur-oxidizing denitrifiers dominated the microbial population. In addition, bacteria resembling the iron-oxidizing, nitrate-reducing Acidovorax strain BrG1 accounted for a major part of the microbial community in the groundwater of this ecosystem. Despite the apparent abundance of strain BrG1-like bacteria, iron-oxidizing nitrate reducers could not be isolated, likely due to the strictly autotrophic cultivation conditions adopted in our study. In contrast an iron-reducing Geobacter sp. was isolated from this environment while FISH and 16S rRNA gene clone library analyses did not reveal any Geobacter sp.-related sequences in the groundwater. Our findings indicate that iron-oxidizing nitrate reducers may be of importance to the redox cycling of iron in the groundwater of our study site and illustrate the necessity of employing both culture-dependent and independent methods in studies on microbial processes.

  6. Structural basis underlying the metallic-like conductivity of microbial nanowires

    Science.gov (United States)

    Malvankar, Nikhil; Vargas, Madeline; Tuominen, Mark; Lovley, Derek

    2014-03-01

    Microbial nanowires are electrically conductive proteinaceous pili nanofilaments secreted by Geobacter sulfurreducens. In contrast to current biochemical understanding that proteins are insulators, G. sulfurreducens pili show organic metallic-like conductivity. Pili also enable direct exchange of electrons among Geobacter co-cultures. Site-directed mutagenesis studies revealed that aromatic amino acids confer conductivity to pili. In order to develop a structural understanding of the pili to probe the conduction mechanism at a molecular level, we employed three complementary structural methods - X-ray microdiffraction using synchrotron radiation, rocking curve X-ray diffraction, and electron diffraction. Studies performed with all these three methods revealed a 3.2 Å periodic spacing in wild-type G. sulfurreducens pili, expected for metal-like conductivity and a lack of such spacing in genetically modified non-conductive pili. Notably, both the peak intensity and the conductivity increased 100-fold with lowering the pH from pH 10.5 to pH 2, demonstrating a structure-function correlation in pili. We also reconstructed the three dimensional tertiary structure of pili with homology modeling, which further suggested the 3.2 Å spacing among aromatics associated with metal-like conductivity. Funded by Office of Naval Research, DOE Genomic Sciences and NSF-NSEC Center for Hierarchical Manufacturing grant no. CMMI-1025020.

  7. Effect of ferrihydrite biomineralization on methanogenesis in an anaerobic incubation from paddy soil

    Science.gov (United States)

    Zhuang, Li; Xu, Jielong; Tang, Jia; Zhou, Shungui

    2015-05-01

    Microbial reduction of Fe(III) can be one of the major factors controlling methane production from anaerobic sedimentary environments, such as paddy soils and wetlands. Although secondary iron mineralization following Fe(III) reduction is a process that occurs naturally over time, it has not yet been considered in methanogenic systems. This study performed a long-term anaerobic incubation of a paddy soil and ferrihydrite-supplemented soil cultures to investigate methanogenesis during ferrihydrite biomineralization. The results revealed that the long-term effect of ferrihydrite on methanogenesis may be enhancement rather than suppression documented in previous studies. During initial microbial ferrihydrite reduction, methanogenesis was suppressed; however, the secondary minerals of magnetite formation was simultaneous with facilitated methanogenesis in terms of average methane production rate and acetate utilization rate. In the phase of magnetite formation, microbial community analysis revealed a strong stimulation of the bacterial Geobacter, Bacillus, and Sedimentibacter and the archaeal Methanosarcina in the ferrihydrite-supplemented cultures. Direct electric syntrophy between Geobacter and Methanosarcina via conductive magnetite is the plausible mechanism for methanogenesis acceleration along with magnetite formation. Our data suggested that a change in iron mineralogy might affect the conversion of anaerobic organic matter to methane and might provide a fresh perspective on the mitigation of methane emissions from paddy soils by ferric iron fertilization.

  8. Screen-Printed Electrodes: New Tools for Developing Microbial Electrochemistry at Microscale Level

    Directory of Open Access Journals (Sweden)

    Marta Estevez-Canales

    2015-11-01

    Full Text Available Microbial electrochemical technologies (METs have a number of potential technological applications. In this work, we report the use of screen-printed electrodes (SPEs as a tool to analyze the microbial electroactivity by using Geobacter sulfurreducens as a model microorganism. We took advantage of the small volume required for the assays (75 μL and the disposable nature of the manufactured strips to explore short-term responses of microbial extracellular electron transfer to conductive materials under different scenarios. The system proved to be robust for identifying the bioelectrochemical response, while avoiding complex electrochemical setups, not available in standard biotechnology laboratories. We successfully validated the system for characterizing the response of Geobacter sulfurreducens in different physiological states (exponential phase, stationary phase, and steady state under continuous culture conditions revealing different electron transfer responses. Moreover, a combination of SPE and G. sulfurreducens resulted to be a promising biosensor for quantifying the levels of acetate, as well as for performing studies in real wastewater. In addition, the potential of the technology for identifying electroactive consortia was tested, as an example, with a mixed population with nitrate-reducing capacity. We therefore present SPEs as a novel low-cost platform for assessing microbial electrochemical activity at the microscale level.

  9. Set anode potentials affect the electron fluxes and microbial community structure in propionate-fed microbial electrolysis cells

    Science.gov (United States)

    Hari, Ananda Rao; Katuri, Krishna P.; Logan, Bruce E.; Saikaly, Pascal E.

    2016-01-01

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; −0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49–71%) and CH4 (22.9–41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of −0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, but their relative abundance varied among the tested SAPs. Microbial community analysis implies that complete degradation of propionate in all the tested SAPs was facilitated by syntrophic interactions between fermenters and Geobacter at the anode and ferementers and hydrogenotrophic methanogens in suspension. PMID:27934925

  10. Molecular Basis for Electron Flow Within Metal-and Electrode-Reducing Biofilms

    Energy Technology Data Exchange (ETDEWEB)

    Bond, Daniel R. [Univ. of Minnesota, Minneapolis, MN (United States)

    2016-11-01

    Electrochemical, spectral, genetic, and biochemical techniques were developed to reveal that a diverse suite of redox proteins and structural macromolecules outside the cell work together to move electrons long distances between Geobacter cells to metals and electrodes. In this project, we greatly expanded the known participants in the electron transfer pathway of Geobacter. For example, in addition to well-studied pili, polysaccharides contribute to anchoring, different cytochromes are required under different conditions, strategies change with redox potential, and the localization of these components can change depending on where cells are located in a biofilm. By inventing new electrodes compatible with real-time spectral measurements, we were able to visualize the redox status of biofilms in action, leading to a hypothesis that long-distance electron transfer is ultimately limiting in these systems and redox potentials change within biofilms. The goals of this project were met, as we were able to 1) identify new elements crucial to the expression, assembly and function of the extracellular electron transfer phenotype 2) expand spectral and electrochemical techniques to define the mechanism and route of electron transfer through the matrix, and 3) combine this knowledge to build the next generation of genetic tools for study of this complex process.

  11. Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell.

    Science.gov (United States)

    Ding, Jing; Lu, Yong-Ze; Fu, Liang; Ding, Zhao-Wei; Mu, Yang; Cheng, Shuk H; Zeng, Raymond J

    2017-03-01

    Anaerobic oxidation of methane (AOM) contributes significantly to the global methane sink. Previously, studies of anaerobic methanotrophic (ANME) archaea have been limited as they have not been separable from their bacterial partners during the AOM process because of their dependence on the bacteria. A microbial fuel cell (MFC) is a device capable of directly transforming chemical energy to electrical energy via electrochemical reactions involving biochemical pathways. In this study, decoupling of denitrifying anaerobic methane oxidation (DAMO) archaea and DAMO bacteria was investigated in an microbial fuel cell (MFC) using methane as the fuel. The DAMO fuel cell worked successfully but demonstrated weak electrogenic capability with around 25 mV production. After 45 days' enrichment, the sequencing and fluorescence in situ hybridization results showed the DAMO archaea percentage had increased from 26.96% (inoculum) to 65.77% (electrode biofilm), while the DAMO bacteria percentage decreased from 24.39% to 2.07%. Moreover, the amount of ANME-2d had doubled in the electrode biofilm compared with the inoculum. The sequencing results also showed substantial enrichment of the Ignavibacterium and Geobacter genera. The roles of Ignavibacterium and Geobacter in the MFC system need to be further investigated. Nevertheless, these results illustrate that an MFC device may provide a possible approach to separate DAMO archaea from DAMO bacteria.

  12. Strategies for Reducing the Start-up Operation of Microbial Electrochemical Treatments of Urban Wastewater

    Directory of Open Access Journals (Sweden)

    Zulema Borjas

    2015-12-01

    Full Text Available Microbial electrochemical technologies (METs constitute the core of a number of emerging technologies with a high potential for treating urban wastewater due to a fascinating reaction mechanism—the electron transfer between bacteria and electrodes to transform metabolism into electrical current. In the current work, we focus on the model electroactive microorganism Geobacter sulfurreducens to explore both the design of new start-up procedures and electrochemical operations. Our chemostat-grown plug and play cells, were able to reduce the start-up period by 20-fold while enhancing chemical oxygen demand (COD removal by more than 6-fold during this period. Moreover, a filter-press based bioreactor was successfully tested for both acetate-supplemented synthetic wastewater and real urban wastewater. This proof-of-concept pre-pilot treatment included a microbial electrolysis cell (MEC followed in time by a microbial fuel cell (MFC to finally generate electrical current of ca. 20 A·m−2 with a power of 10 W·m−2 while removing 42 g COD day−1·m−2. The effective removal of acetate suggests a potential use of this modular technology for treating acetogenic wastewater where Geobacter sulfurreducens outcompetes other organisms.

  13. Spatial distribution of bacterial communities on volumetric and planar anodes in single-chamber air-cathode microbial fuel cells

    KAUST Repository

    Vargas, Ignacio T.

    2013-05-29

    Pyrosequencing was used to characterize bacterial communities in air-cathode microbial fuel cells across a volumetric (graphite fiber brush) and a planar (carbon cloth) anode, where different physical and chemical gradients would be expected associated with the distance between anode location and the air cathode. As expected, the stable operational voltage and the coulombic efficiency (CE) were higher for the volumetric anode than the planar anode (0.57V and CE=22% vs. 0.51V and CE=12%). The genus Geobacter was the only known exoelectrogen among the observed dominant groups, comprising 57±4% of recovered sequences for the brush and 27±5% for the carbon-cloth anode. While the bacterial communities differed between the two anode materials, results showed that Geobacter spp. and other dominant bacterial groups were homogenously distributed across both planar and volumetric anodes. This lends support to previous community analysis interpretations based on a single biofilm sampling location in these systems. © 2013 Wiley Periodicals, Inc.

  14. Effects of proton exchange membrane on the performance and microbial community composition of air-cathode microbial fuel cells.

    Science.gov (United States)

    Lee, Yun-Yeong; Kim, Tae Gwan; Cho, Kyung-Suk

    2015-10-10

    This study investigated the effects of proton exchange membranes (PEMs) on performance and microbial community of air-cathode microbial fuel cells (MFCs). Air-cathode MFCs with reactor volume of 1L were constructed in duplicate with or without PEM (designated as ACM-MFC and AC-MFC, respectively) and fed with a mixture of glucose and acetate (1:1, w:w). The maximum power density and coulombic efficiency did not differ between MFCs in the absence or presence of a PEM. However, PEM use adversely affected maximum voltage production and the rate of organic compound removal (p0.9 and p<0.05). Geobacter, which is known as an exoelectrogen, was positively associated with maximum power density and negatively associated with PEM. Thus, these results suggest that the absence of PEM favored the growth of Geobacter, a key player for electricity generation in MFC systems. Taken together, these findings demonstrate that MFC systems without PEM are more efficient with respect to power production and COD removal as well as exoelectrogen growth.

  15. An Electrode-based approach for monitoring in situ microbial activity during subsurface bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Williams, K.H.; Nevin, K.P.; Franks, A.; Englert, A.; Long, P.E.; Lovley, D.R.

    2009-11-15

    Current production by microorganisms colonizing subsurface electrodes and its relationship to substrate availability and microbial activity was evaluated in an aquifer undergoing bioremediation. Borehole graphite anodes were installed downgradient from a region of acetate injection designed to stimulate bioreduction of U(VI); cathodes consisted of graphite electrodes embedded at the ground surface. Significant increases in current density ({<=}50 mA/m{sup 2}) tracked delivery of acetate to the electrodes, dropping rapidly when acetate inputs were discontinued. An upgradient control electrode not exposed to acetate produced low, steady currents ({<=}0.2 mA/m{sup 2}). Elevated current was strongly correlated with uranium removal but minimal correlation existed with elevated Fe(II). Confocal laser scanning microscopy of electrodes revealed firmly attached biofilms, and analysis of 16S rRNA gene sequences indicated the electrode surfaces were dominated (67-80%) by Geobacter species. This is the first demonstration that electrodes can produce readily detectable currents despite long-range (6 m) separation of anode and cathode, and these results suggest that oxidation of acetate coupled to electron transfer to electrodes by Geobacter species was the primary source of current. Thus it is expected that current production may serve as an effective proxy for monitoring in situ microbial activity in a variety of subsurface anoxic environments.

  16. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    Science.gov (United States)

    Dhar, Bipro Ranjan; Ryu, Hodon; Santo Domingo, Jorge W.; Lee, Hyung-Sool

    2016-11-01

    Multi-anode microbial electrochemical cells (MxCs) are considered as one of the most promising configurations for scale-up of MxCs, but understanding of anode kinetics in multiple anodes is limited in the MxCs. In this study we assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MxC to better comprehend anode fundamentals. Microbial community analysis targeting 16S rRNA Illumina sequencing showed that Geobacter genus was abundant (87%) only on the biofilm anode closest to a reference electrode (low ohmic energy loss) in which current density was the highest among three anodes. In comparison, Geobacter populations were less than 1% for biofilms on other two anodes distant from the reference electrode (high ohmic energy loss), generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest biofilm anode to the reference electrode, while EKA was as high as -0.134 V for the farthest anode. Our study proves that electric potential of individual anodes changed by ohmic energy loss shifts biofilm communities on individual anodes and consequently influences electron transfer kinetics on each anode in the multi-anode MxC.

  17. Phase Preference by Active, Acetate-Utilizing Bacteria at the Rifle, CO Integrated Field Research Challenge Site

    Energy Technology Data Exchange (ETDEWEB)

    Kerkhof, L.; Williams, K.H.; Long, P.E.; McGuinness, L.

    2011-02-21

    Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC) site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via {sup 13}C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 {micro}m), groundwater (0.2-8 {micro}m)] over a 24-day time frame. TRFLP results generally indicated a stronger signal in {sup 13}C-DNA in the 'fines' fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized {sup 13}C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the {sup 13}C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater, while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.

  18. Electrochemical evaluation of Ti/TiO{sub 2}-polyaniline anodes for microbial fuel cells using hypersaline microbial consortia for synthetic-wastewater treatment

    Energy Technology Data Exchange (ETDEWEB)

    Benetton, X.D.; Navarro-Avila, S.G. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Biotecnologia y Bioingenieria; Carrera-Figueiras, C. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Quimica Fundamental y Aplicada

    2010-07-01

    This paper described the development of a titanium (Ti/TiO{sub 2}) polyaniline composite electrode. The electrode was designed for use with a microbial fuel cell (MFC) that generated electricity through the microbial biodegradation of organic compounds. A modified NBAF medium was used with a 20 mM acetate as an electron donor and 53 mM fumarate as an electron acceptor for a period of 96 hours at 37 degrees C. Strains were cultured under strict anaerobic conditions. Two microbial cultures were used: (1) pure cultures of Geobacter sulfur-reducens; and (2) an uncharacterized stable microbial consortia isolated from hypersaline swamp sediments. The anodes were made with an emeraldine form of PANI deposited over Ti/TiO{sub 2} electrodes. Electrochemical impedance spectroscopy (EIS) monitoring was used to determine the open circuit potential of the MFC. Negative real impedances were obtained and reproduced in all systems studied with the Ti/TiO{sub 2}-PANI anodes. The highest power density was obtained using the Geobacter sulfur-reducens culture. Further research is needed to study the mechanisms that contribute to the occurrence of negative real impedances. 23 refs., 1 tab., 5 figs.

  19. Impact of acclimation methods on microbial communities and performance of anaerobic fluidized bed membrane bioreactors

    KAUST Repository

    Labarge, Nicole

    2016-10-17

    An anaerobic fluidized bed membrane bioreactor (AFMBR) is a new and effective method for energy-efficient treatment of low strength wastewater, but the factors that affect performance are not well known. Different inocula and acclimation methods of the granular activated carbon (GAC) used in the reactor were examined here to determine their impact on chemical oxygen demand (COD) removal and microbial community composition of domestic wastewater-fed AFMBRs. AFMBRs inoculated with anaerobic digester sludge (D) or domestic wastewater (W) and fed domestic wastewater, or inoculated with a microbiologically diverse anaerobic bog sediment and acclimated using methanol (M), all produced the same COD removal of 63 ± 12% using a diluted wastewater feed (100 ± 21 mg L−1 COD). However, an AFMBR with GAC inoculated with anaerobic digester sludge and acclimated using acetate (A) showed significantly increased wastewater COD removal to 84 ± 6%. In addition, feeding the AFMBR with the M-acclimated GAC with an acetate medium for one week subsequently increased COD removal to 70 ± 6%. Microbial communities enriched on the GAC included Geobacter, sulfur-reducing bacteria, Syntrophaceae, and Chlorobiaceae, with reactor A having the highest relative abundance of Geobacter. These results showed that acetate was the most useful substrate for acclimation of GAC communities, and GAC harbors unique communities relative to those in the AFMBR influent and recirculated solution.

  20. Dissimilatory Fe(III) and Mn(IV) reduction.

    Science.gov (United States)

    Lovley, Derek R; Holmes, Dawn E; Nevin, Kelly P

    2004-01-01

    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

  1. Isolation and Characterization of Microbes Mediating Thermodynamically Favorable Coupling of Anaerobic Oxidation of Methane and Metal Reduction

    Science.gov (United States)

    Glass, J. B.; Reed, B. C.; Sarode, N. D.; Kretz, C. B.; Bray, M. S.; DiChristina, T. J.; Stewart, F. J.; Fowle, D. A.; Crowe, S.

    2014-12-01

    Methane is the third most reduced environmentally relevant electron donor for microbial metabolisms after organic carbon and hydrogen. In anoxic ecosystems, the major sink for methane is anaerobic oxidation of methane (AOM) mediated by syntrophic microbial consortia that couple AOM to reduction of an oxidized electron acceptor to yield free energy. In marine sediments, AOM is generally coupled to reduction of sulfate despite an extremely small amount of free energy yield because sulfate is the most abundant electron acceptor in seawater. While AOM coupled to Fe(III) and Mn(IV) reduction (Fe- and Mn-AOM) is 10-30x more thermodynamically favorable than sulfate-AOM, and geochemical data suggests that it occurs in diverse environments, the microorganisms mediating Fe- and Mn-AOM remain unknown. Lake Matano, Indonesia is an ideal ecosystem to enrich for Fe- and Mn-AOM microbes because its anoxic ferruginous deep waters and sediments contain abundant Fe(III), Mn(IV) and methane, and extremely low sulfate and nitrate. Our research aims to isolate and characterize the microbes mediating Fe- and Mn-AOM from three layers of Lake Matano sediments through serial enrichment cultures in minimal media lacking nitrate and sulfate. 16S rRNA amplicon sequencing of sediment inoculum revealed the presence of the Fe(III)-reducing bacterium Geobacter (5-10% total microbial community in shallow sediment and 35-60% in deeper sediment) as well as 1-2% Euryarchaeota implicated in methane cycling, including ANME-1 and 2d and Methanosarcinales. After 90 days of primary enrichment, all three sediment layers showed high levels of Fe(III) reduction (60-90 μM Fe(II) d-1) in the presence of methane compared to no methane and heat-killed controls. Treatments with added Fe(III) as goethite contained higher abundances of Geobacter than the inoculum (60-80% in all layers), suggesting that Geobacter may be mediating Fe(III) reduction in these enrichments. Quantification of AOM rates is underway, and

  2. Phvlogenetic diversity of dissimilatory Fe (Ⅲ) -reducing bacteria in paddy soil%水稻土中铁还原菌多样性

    Institute of Scientific and Technical Information of China (English)

    黎慧娟; 彭静静

    2011-01-01

    Microorganism-mediated dissimilatory Fe (III) reduction is recognized as the dominant mechanism for Fe(III) reduction to Fe(II) in non-sulfidogenic anaerobic environments, but the microorganisms involved, especially in paddy soil, are still poorly understood. In this paper, an enrichment culture was conducted to study the phylogenetic diversity of Fe (III) -reducing bacteria in paddy soil, with acetate or hydrogen as the electron donor and with ferrihydrite or goethite as the electron acceptor, and by the methods of terminal-restriction fragment length polymorphism ( T-RFLP) technology and 16S rRNA genes cloning and sequencing. No matter what the electron donor and electron acceptor were supplemented, the most abundant microorganisms were Geobacter and Clostridiales, and Rhodocyclaceae were also abundant, when acetate was supplemented as electron donor, which suggested that besides Geobacter, Clostridiales and Rhodocyclaceae could be also the important Fe (III)-reducing bacteria in paddy soil.%微生物介导的异化Fe(Ⅲ)还原是非硫厌氧环境中Fe (Ⅲ)还原生成Fe(Ⅱ)的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性(T-RFLP)技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明:无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌(Geobacter)和梭茵(Clostridiales)是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌(Rhodocyclaceae);因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.

  3. Removal of Ni (Ⅱ) and microbial dynamics in single-chamber microbial electrolysis cell%单室微生物电解池除镍途径分析及微生物群落动态特征

    Institute of Scientific and Technical Information of China (English)

    赵欣; 吴忆宁; 王岭; 李伟明; 靳敏; 李帅

    2016-01-01

    [目的]为探究UASB颗粒污泥启动的单室微生物电解池(Single-chamber microbial electrolysis cell,SMEC)对Ni(Ⅱ)的去除途径和SMEC中微生物群落的动态特征.[方法]以乙酸钠为底物,采用单因子控制方法分析SMEC对Ni(Ⅱ)的去除途径和应用Illumina高通量测序技术解析SMEC启动过程中微生物群落的组成和结构动态学特征.[结果]结果表明,SMEC对重金属的去除主要通过吸附和微生物作用.经培养驯化功能菌群发生变化.成熟单室微生物燃料电池(Single-chamber microbial fuel cell,SMFC)阳极生物膜菌群主要是Proteobacteria(变形菌门,91.42%)中的Geobacter sp.(地杆菌属,76.25%);阴极生物膜菌群主要是Bacteroidetes(拟杆菌门,47.99%)中的Niabella sp.(布鲁氏菌属,33.01%)和Proteobacteria(45.74%)中的Ochrobactrum sp.(苍白杆菌属,10.80%).成熟SMFC改装成的SMEC在12.5 mg-Ni(Ⅱ)/L下,阳极生物膜菌群由单一优势菌Geobacter sp.转变为Geobacter sp.(41.56%)和Proteobacteria中的Azospirillum sp.(固氮螺菌属,5.97%);阴极生物膜菌群由Niabella sp.和Ochrobactrum sp.转变为Firmicutes(厚壁菌门,25.21%)中的Acetoanaerobium sp.(19.28%)、Proteobacteria (51.42%)中的Dokdonella sp.(16.48%)和Azospirillum sp.(9.49%).[结论]本研究表明,污泥微生物经SMFC和SMEC驯化过程及Ni(Ⅱ)的淘汰和选择,在电极上形成了稳定、高效产电与除镍菌群,优势菌群为Proteobacteria.

  4. Using proteomic data to assess a genome-scale "in silico" model of metal reducing bacteria in the simulation of field-scale uranium bioremediation

    Science.gov (United States)

    Yabusaki, S.; Fang, Y.; Wilkins, M. J.; Long, P.; Rifle IFRC Science Team

    2011-12-01

    A series of field experiments in a shallow alluvial aquifer at a former uranium mill tailings site have demonstrated that indigenous bacteria can be stimulated with acetate to catalyze the conversion of hexavalent uranium in a groundwater plume to immobile solid-associated uranium in the +4 oxidation state. While this bioreduction of uranium has been shown to lower groundwater concentrations below actionable standards, a viable remediation methodology will need a mechanistic, predictive and quantitative understanding of the microbially-mediated reactions that catalyze the reduction of uranium in the context of site-specific processes, properties, and conditions. At the Rifle IFRC site, we are investigating the impacts on uranium behavior of pulsed acetate amendment, acetate-oxidizing iron and sulfate reducing bacteria, seasonal water table variation, spatially-variable physical (hydraulic conductivity, porosity) and geochemical (reactive surface area) material properties. The simulation of three-dimensional, variably saturated flow and biogeochemical reactive transport during a uranium bioremediation field experiment includes a genome-scale in silico model of Geobacter sp. to represent the Fe(III) terminal electron accepting process (TEAP). The Geobacter in silico model of cell-scale physiological metabolic pathways is comprised of hundreds of intra-cellular and environmental exchange reactions. One advantage of this approach is that the TEAP reaction stoichiometry and rate are now functions of the metabolic status of the microorganism. The linkage of in silico model reactions to specific Geobacter proteins has enabled the use of groundwater proteomic analyses to assess the accuracy of the model under evolving hydrologic and biogeochemical conditions. In this case, the largest predicted fluxes through in silico model reactions generally correspond to high abundances of proteins linked to those reactions (e.g. the condensation reaction catalyzed by the protein

  5. Long-term effects of the transient COD concentration on the performance of microbial fuel cells.

    Science.gov (United States)

    Mateo, S; Gonzalez Del Campo, A; Lobato, J; Rodrigo, M; Cañizares, P; Fernandez-Morales, F J

    2016-07-08

    In this work, the long-term effects of transient chemical oxygen demands (COD) concentrations over the performance of a microbial fuel cell were studied. From the obtained results, it was observed that the repetitive change in the COD loading rate during 12 h conditioned the behavior of the system during periods of up to 7 days. The main modifications were the enhancement of the COD consumption rate and the exerted current. These enhancements yielded increasing Coulombic efficiencies (CEs) when working with COD concentrations of 300 mg/L, but constant CEs when working with COD concentrations from 900 to 1800 mg/L. This effect could be explained by the higher affinity for the substrate of Geobacter than that of the nonelectrogenic organisms such as Clostridia. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:883-890, 2016.

  6. Microbial characterization and degradation of linear alkylbenzene sulfonate in an anaerobic reactor treating wastewater containing soap powder.

    Science.gov (United States)

    Carosia, Mariana Fronja; Okada, Dagoberto Yukio; Sakamoto, Isabel Kimiko; Silva, Edson Luiz; Varesche, Maria Bernadete Amâncio

    2014-09-01

    The aim of this study was to evaluate the removal of linear alkylbenzene sulfonate (LAS) in an anaerobic fluidized bed reactor (AFBR) treating wastewater containing soap powder as LAS source. At Stage I, the AFBR was fed with a synthetic substrate containing yeast extract and ethanol as carbon sources, and without LAS; at Stage II, soap powder was added to this synthetic substrate obtaining an LAS concentration of 14 ± 3 mg L(-1). The compounds of soap powder probably inhibited some groups of microorganisms, increasing the concentration of volatile fatty acids (VFA) from 91 to 143 mg HAc L(-1). Consequently, the LAS removal rate was 48 ± 10% after the 156 days of operation. By sequencing, 16S rRNA clones belonging to the phyla Proteobacteria and Synergistetes were identified in the samples taken at the end of the experiment, with a remarkable presence of Dechloromonas sp. and Geobacter sp.

  7. Microbial engineering of nano-heterostructures; biological synthesis of a magnetically-recoverable palladium nanocatalyst

    Energy Technology Data Exchange (ETDEWEB)

    Coker, V. S.; Bennett, J. A.; Telling, N.; Charnock, J. M.; van der Laan, G.; Pattrick, R. A. D.; Pearce, C. I; Cutting, R. S.; Shannon, I. J.; Wood, J.; Arenholz, E.; Vaughan, D. J.; Lloyd, J. R.

    2009-12-01

    Precious metals supported on ferrimagnetic particles form a diverse range of catalysts. Here we show a novel biotechnological route for the synthesis of a heterogeneous catalyst consisting of reactive palladium nanoparticles arrayed on a biomagnetite support. The magnetic support was synthesized at ambient temperature by the Fe(III)-reducing bacterium, Geobacter sulfurreducens, and facilitated ease of recovery of the catalyst with superior performance due to reduced agglomeration. Arrays of palladium nanoparticles were deposited on the nanomagnetite using a simple one-step method without the need to modify the biomineral surface most likely due to an organic coating priming the surface for Pd adsorption. A combination of EXAFS and XPS showed the particles to be predominantly metallic in nature. The Pd{sup 0}-biomagnetite was tested for catalytic activity in the Heck Reaction coupling iodobenzene to ethyl acrylate or styrene and near complete conversion to ethyl cinnamate or stilbene was achieved within 90 and 180 min, respectively.

  8. Control of bacterial exoelectrogenesis by c-AMP-GMP.

    Science.gov (United States)

    Nelson, James W; Sudarsan, Narasimhan; Phillips, Grace E; Stav, Shira; Lünse, Christina E; McCown, Phillip J; Breaker, Ronald R

    2015-04-28

    Major changes in bacterial physiology including biofilm and spore formation involve signaling by the cyclic dinucleotides c-di-GMP and c-di-AMP. Recently, another second messenger dinucleotide, c-AMP-GMP, was found to control chemotaxis and colonization by Vibrio cholerae. We have identified a superregulon of genes controlled by c-AMP-GMP in numerous Deltaproteobacteria, including Geobacter species that use extracellular insoluble metal oxides as terminal electron acceptors. This exoelectrogenic process has been studied for its possible utility in energy production and bioremediation. Many genes involved in adhesion, pilin formation, and others that are important for exoelectrogenesis are controlled by members of a variant riboswitch class that selectively bind c-AMP-GMP. These RNAs constitute, to our knowledge, the first known specific receptors for c-AMP-GMP and reveal that this molecule is used by many bacteria to control specialized physiological processes.

  9. Removal Kinetics of Organic Matter and Nitrogen Using Microbial Electrochemical Based - Constructed Wetlands (iMETland)

    DEFF Research Database (Denmark)

    Ramírez Vargas, Carlos Andrés; Arias, Carlos Alberto; Carvalho, Pedro

    In recent years the combination of Constructed Wetlands and Microbial Fuel Cell (MFC), has led to an innovative set- up for wastewater treatment and energy harvesting, relaying on electrodes and external circuits (CW – MFC). Based on this approach, a new concept is being developed to create...... the Microbial Electrochemical-based Constructed Wetland (iMETland). In this system electro- active bacteria – EAB (e.g. Geobacter sp., Shewanella spp) are stimulated to release and transfer electrons to an electro-conductive material that act as unlimited electron acceptor, maximizing the substrate consumption....... The iMETland technology is still in development and therefore uncertainties still exist regarding the dynamics in the removal of pollutants, as well as in its performance along time. To elucidate these uncertainties, a benchmark study is being conducted to characterize the processes and interactions n...

  10. The genetic basis for bacterial mercury methylation.

    Science.gov (United States)

    Parks, Jerry M; Johs, Alexander; Podar, Mircea; Bridou, Romain; Hurt, Richard A; Smith, Steven D; Tomanicek, Stephen J; Qian, Yun; Brown, Steven D; Brandt, Craig C; Palumbo, Anthony V; Smith, Jeremy C; Wall, Judy D; Elias, Dwayne A; Liang, Liyuan

    2013-03-15

    Methylmercury is a potent neurotoxin produced in natural environments from inorganic mercury by anaerobic bacteria. However, until now the genes and proteins involved have remained unidentified. Here, we report a two-gene cluster, hgcA and hgcB, required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In either bacterium, deletion of hgcA, hgcB, or both genes abolishes mercury methylation. The genes encode a putative corrinoid protein, HgcA, and a 2[4Fe-4S] ferredoxin, HgcB, consistent with roles as a methyl carrier and an electron donor required for corrinoid cofactor reduction, respectively. Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in nonmethylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.

  11. Controlled cobalt doping in biogenic magnetite nanoparticles

    Science.gov (United States)

    Byrne, J. M.; Coker, V. S.; Moise, S.; Wincott, P. L.; Vaughan, D. J.; Tuna, F.; Arenholz, E.; van der Laan, G.; Pattrick, R. A. D.; Lloyd, J. R.; Telling, N. D.

    2013-01-01

    Cobalt-doped magnetite (CoxFe3 −xO4) nanoparticles have been produced through the microbial reduction of cobalt–iron oxyhydroxide by the bacterium Geobacter sulfurreducens. The materials produced, as measured by superconducting quantum interference device magnetometry, X-ray magnetic circular dichroism, Mössbauer spectroscopy, etc., show dramatic increases in coercivity with increasing cobalt content without a major decrease in overall saturation magnetization. Structural and magnetization analyses reveal a reduction in particle size to less than 4 nm at the highest Co content, combined with an increase in the effective anisotropy of the magnetic nanoparticles. The potential use of these biogenic nanoparticles in aqueous suspensions for magnetic hyperthermia applications is demonstrated. Further analysis of the distribution of cations within the ferrite spinel indicates that the cobalt is predominantly incorporated in octahedral coordination, achieved by the substitution of Fe2+ site with Co2+, with up to 17 per cent Co substituted into tetrahedral sites. PMID:23594814

  12. Tunable metallic-like conductivity in microbial nanowire networks

    Science.gov (United States)

    Malvankar, Nikhil S.; Vargas, Madeline; Nevin, Kelly P.; Franks, Ashley E.; Leang, Ching; Kim, Byoung-Chan; Inoue, Kengo; Mester, Tünde; Covalla, Sean F.; Johnson, Jessica P.; Rotello, Vincent M.; Tuominen, Mark T.; Lovley, Derek R.

    2011-09-01

    Electronic nanostructures made from natural amino acids are attractive because of their relatively low cost, facile processing and absence of toxicity. However, most materials derived from natural amino acids are electronically insulating. Here, we report metallic-like conductivity in films of the bacterium Geobacter sulfurreducens and also in pilin nanofilaments (known as microbial nanowires) extracted from these bacteria. These materials have electronic conductivities of ~5 mS cm-1, which are comparable to those of synthetic metallic nanostructures. They can also conduct over distances on the centimetre scale, which is thousands of times the size of a bacterium. Moreover, the conductivity of the biofilm can be tuned by regulating gene expression, and also by varying the gate voltage in a transistor configuration. The conductivity of the nanofilaments has a temperature dependence similar to that of a disordered metal, and the conductivity could be increased by processing.

  13. Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria

    Science.gov (United States)

    Byrne, James M.; Klueglein, Nicole; Pearce, Carolyn; Rosso, Kevin M.; Appel, Erwin; Kappler, Andreas

    2015-03-01

    Microorganisms are a primary control on the redox-induced cycling of iron in the environment. Despite the ability of bacteria to grow using both Fe(II) and Fe(III) bound in solid-phase iron minerals, it is currently unknown whether changing environmental conditions enable the sharing of electrons in mixed-valent iron oxides between bacteria with different metabolisms. We show through magnetic and spectroscopic measurements that the phototrophic Fe(II)-oxidizing bacterium Rhodopseudomonas palustris TIE-1 oxidizes magnetite (Fe3O4) nanoparticles using light energy. This process is reversible in co-cultures by the anaerobic Fe(III)-reducing bacterium Geobacter sulfurreducens. These results demonstrate that Fe ions bound in the highly crystalline mineral magnetite are bioavailable as electron sinks and electron sources under varying environmental conditions, effectively rendering magnetite a naturally occurring battery.

  14. Potentially direct interspecies electron transfer of methanogenesis for syntrophic metabolism under sulfate reducing conditions with stainless steel.

    Science.gov (United States)

    Li, Yue; Zhang, Yaobin; Yang, Yafei; Quan, Xie; Zhao, Zhiqiang

    2017-06-01

    Direct interspecies electron transfer (DIET) is an alternative to syntrophic metabolism in natural carbon cycle as well as in anaerobic digesters, but its function in anaerobic treatment of sulfate-containing wastewater have not yet to be described. Here, conductive stainless steel was added into anaerobic digesters for treating sulfate-containing wastewater to investigate the potential role of DIET in the response to the sulfate impact. Results showed that adding the conductive stainless steel made the anaerobic digestion less affected by the sulfate reduction than adding insulative plastic material. With adding stainless steel, methane production of the digesters increased by 7.5%-24.6%. Microbial analysis showed that the dissimilatory Fe (III) reducers like Geobacter species were enriched on the surface of the stainless steel. These results implied that the potential DIET of methanogenesis was established associating with stainless steel to outcompete the sulfate reduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane

    DEFF Research Database (Denmark)

    Rotaru, Amelia-Elena; Shrestha, Pravin M.; Liu, Fanghua

    2013-01-01

    Anaerobic conversion of organic wastes and biomass to methane is an important bioenergy strategy, which depends on poorly understood mechanisms of interspecies electron transfer to methanogenic microorganisms. Metatranscriptomic analysis of methanogenic aggregates from a brewery wastewater digester......, coupled with fluorescence in situ hybridization with specific 16S rRNA probes, revealed that Methanosaeta species were the most abundant and metabolically active methanogens. Methanogens known to reduce carbon dioxide with H2 or formate as the electron donor were rare. Although Methanosaeta have......, the most abundant bacteria in the aggregates, highly expressed genes for ethanol metabolism and for extracellular electron transfer via electrically conductive pili, suggesting that Geobacter and Methanosaeta species were exchanging electrons via direct interspecies electron transfer (DIET...

  16. A comparative evaluation of different types of microbial electrolysis desalination cells for malic acid production.

    Science.gov (United States)

    Liu, Guangli; Zhou, Ying; Luo, Haiping; Cheng, Xing; Zhang, Renduo; Teng, Wenkai

    2015-12-01

    The aim of this study was to investigate different microbial electrolysis desalination cells for malic acid production. The systems included microbial electrolysis desalination and chemical-production cell (MEDCC), microbial electrolysis desalination cell (MEDC) with bipolar membrane and anion exchange membrane (BP-A MEDC), MEDC with bipolar membrane and cation exchange membrane (BP-C MEDC), and modified microbial desalination cell (M-MDC). The microbial electrolysis desalination cells performed differently in terms of malic acid production and energy consumption. The MEDCC performed best with the highest malic acid production rate (18.4 ± 0.6 mmol/Lh) and the lowest energy consumption (0.35 ± 0.14 kWh/kg). The best performance of MEDCC was attributable to the neutral pH condition in the anode chamber, the lowest internal resistance, and the highest Geobacter percentage of the anode biofilm population among all the reactors.

  17. Phenol-degrading anode biofilm with high coulombic efficiency in graphite electrodes microbial fuel cell.

    Science.gov (United States)

    Zhang, Dongdong; Li, Zhiling; Zhang, Chunfang; Zhou, Xue; Xiao, Zhixing; Awata, Takanori; Katayama, Arata

    2017-03-01

    A microbial fuel cell (MFC), with graphite electrodes as both the anode and cathode, was operated with a soil-free anaerobic consortium for phenol degradation. This phenol-degrading MFC showed high efficiency with a current density of 120 mA/m(2) and a coulombic efficiency of 22.7%, despite the lack of a platinum catalyst cathode and inoculation of sediment/soil. Removal of planktonic bacteria by renewing the anaerobic medium did not decrease the performance, suggesting that the phenol-degrading MFC was not maintained by the planktonic bacteria but by the microorganisms in the anode biofilm. Cyclic voltammetry analysis of the anode biofilm showed distinct oxidation and reduction peaks. Analysis of the microbial community structure of the anode biofilm and the planktonic bacteria based on 16S rRNA gene sequences suggested that Geobacter sp. was the phenol degrader in the anode biofilm and was responsible for current generation.

  18. Increased performance of hydrogen production in microbial electrolysis cells under alkaline conditions.

    Science.gov (United States)

    Rago, Laura; Baeza, Juan A; Guisasola, Albert

    2016-06-01

    This work reports the first successful enrichment and operation of alkaline bioelectrochemical systems (microbial fuel cells, MFC, and microbial electrolysis cells, MEC). Alkaline (pH=9.3) bioelectrochemical hydrogen production presented better performance (+117%) compared to conventional neutral conditions (2.6 vs 1.2 litres of hydrogen gas per litre of reactor per day, LH2·L(-1)REACTOR·d(-1)). Pyrosequencing results of the anodic biofilm showed that while Geobacter was mainly detected under conventional neutral conditions, Geoalkalibacter sp. was highly detected in the alkaline MFC (21%) and MEC (48%). This is the first report of a high enrichment of Geoalkalibacter from an anaerobic mixed culture using alkaline conditions in an MEC. Moreover, Alkalibacter sp. was highly present in the anodic biofilm of the alkaline MFC (37%), which would indicate its potentiality as a new exoelectrogen.

  19. Microbial community analysis in a long-term membrane-less microbial electrolysis cell with hydrogen and methane production.

    Science.gov (United States)

    Rago, Laura; Ruiz, Yolanda; Baeza, Juan A; Guisasola, Albert; Cortés, Pilar

    2015-12-01

    A single-chamber microbial electrolysis cell (MEC) aiming at hydrogen production with acetate as sole carbon source failed due to methanogenesis build-up despite the significant amount of 2-bromoethanesulfonate (BES) dosage, 50 mM. Specific batch experiments and a thorough microbial community analysis, pyrosequencing and qPCR, of cathode, anode and medium were performed to understand these observations. The experimental data rebuts different hypothesis and shows that methanogenesis at high BES concentration was likely due to the capacity of some Archaea (hydrogen-oxidizing genus Methanobrevibacter) to resist high BES concentration up to 200 mM. Methanobrevibacter, of the Methanobacteriales order, represented almost the 98% of the total Archaea in the cathode whereas Geobacter was highly abundant in the anode (72% of bacteria). Moreover, at higher BES concentration (up to 200 mM), methanogenesis activity decreased resulting in an increase of homoacetogenic activity, which challenged the performance of the MEC for H2 production.

  20. Electricity generation from food wastes and microbial community structure in microbial fuel cells.

    Science.gov (United States)

    Jia, Jianna; Tang, Yu; Liu, Bingfeng; Wu, Di; Ren, Nanqi; Xing, Defeng

    2013-09-01

    Microbial fuel cell (MFC) was studied as an alternate and a novel way to dispose food wastes (FWs) in a waste-to-energy form. Different organic loading rate obviously affected the performance of MFCs fed with FWs. The maximum power density of ~18 W/m(3) (~556 mW/m(2)) was obtained at COD of 3200±400 mg/L and the maximum coulombic efficiency (CE) was ~27.0% at COD of 4900±350 mg/L. The maximum removals of COD, total carbohydrate (TC) and total nitrogen (TN) were ~86.4%, ~95.9% and ~16.1%, respectively. Microbial community analysis using 454 pyrosequencing of 16S rRNA gene demonstrated the combination of the dominant genera of the exoelectrogenic Geobacter and fermentative Bacteroides effectively drove highly efficient and reliable MFC systems with functions of organic matters degradation and electricity generation.

  1. Strategies for merging microbial fuel cell technologies in water desalination processes: Start-up protocol and desalination efficiency assessment

    Science.gov (United States)

    Borjas, Zulema; Esteve-Núñez, Abraham; Ortiz, Juan Manuel

    2017-07-01

    Microbial Desalination Cells constitute an innovative technology where microbial fuel cell and electrodialysis merge in the same device for obtaining fresh water from saline water with no energy-associated cost for the user. In this work, an anodic biofilm of the electroactive bacteria Geobacter sulfurreducens was able to efficiently convert the acetate present in synthetic waste water into electric current (j = 0.32 mA cm-2) able to desalinate water. .Moreover, we implemented an efficient start-up protocol where desalination up to 90% occurred in a desalination cycle (water production:0.308 L m-2 h-1, initial salinity: 9 mS cm-1, final salinity: treatment method combined with other well established desalination technologies such as reverse osmosis (RO) or reverse electrodialysis.

  2. Protozoan grazing reduces the current output of microbial fuel cells.

    Science.gov (United States)

    Holmes, Dawn E; Nevin, Kelly P; Snoeyenbos-West, Oona L; Woodard, Trevor L; Strickland, Justin N; Lovley, Derek R

    2015-10-01

    Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells.

  3. Characterization of microbial current production as a function of microbe-electrode-interaction.

    Science.gov (United States)

    Dolch, Kerstin; Danzer, Joana; Kabbeck, Tobias; Bierer, Benedikt; Erben, Johannes; Förster, Andreas H; Maisch, Jan; Nick, Peter; Kerzenmacher, Sven; Gescher, Johannes

    2014-04-01

    Microbe-electrode-interactions are keys for microbial fuel cell technology. Nevertheless, standard measurement routines to analyze the interplay of microbial physiology and material characteristics have not been introduced yet. In this study, graphite anodes with varying surface properties were evaluated using pure cultures of Shewanella oneidensis and Geobacter sulfurreducens, as well as defined and undefined mixed cultures. The evaluation routine consisted of a galvanostatic period, a current sweep and an evaluation of population density. The results show that surface area correlates only to a certain extent with population density and anode performance. Furthermore, the study highlights a strain-specific microbe-electrode-interaction, which is affected by the introduction of another microorganism. Moreover, evidence is provided for the possibility of translating results from pure culture to undefined mixed species experiments. This is the first study on microbe-electrode-interaction that systematically integrates and compares electrochemical and biological data.

  4. Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.

    Science.gov (United States)

    Qiu, Yu; Nagarajan, Harish; Embree, Mallory; Shieu, Wendy; Abate, Elisa; Juárez, Katy; Cho, Byung-Kwan; Elkins, James G; Nevin, Kelly P; Barrett, Christian L; Lovley, Derek R; Palsson, Bernhard O; Zengler, Karsten

    2013-01-01

    Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.

  5. Characterizing the interplay betwen mulitple levels of organization within bacterial sigma factor regulatory networks

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Qiu [University of California, San Diego; Nagarajan, Harish [University of California, San Diego; Embree, Mallory [University of California, San Diego; Shieu, Wendy [University of California, San Diego; Abate, Elisa [University of California, San Diego; Juarez, Katy [Universidad Nacional Autonoma de Mexico (UNAM); Cho, Byung-Kwan [University of California, San Diego; Elkins, James G [ORNL; Nevin, Kelly P. [University of Massachusetts, Amherst; Barrett, Christian [University of California, San Diego; Lovley, Derek [University of Massachusetts, Amherst; Palsson, Bernhard O. [University of California, San Diego; Zengler, Karsten [University of California, San Diego

    2013-01-01

    Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with sN being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.

  6. Multiple redox states of multiheme cytochromes may enable bacterial response to changing redox environments

    Science.gov (United States)

    Arbour, T.; Wrighton, K. C.; Mullin, S. W.; Castelle, C.; Luef, B.; Gilbert, B.; Banfield, J. F.

    2013-12-01

    Multiheme c-type cytochromes (MHCs) are key components in electron-transport pathways that enable some microorganisms to transfer electron byproducts of metabolism to a variety of minerals. As a response to changes in mineral redox potential, microbial communities may shift their membership, or individual organisms may adjust protein expression. Alternatively, the ability to respond may be conferred by the innate characteristics of certain electron-transport-chain components. Here, we used potentiostat-controlled microbial fuel cells (MFCs) to measure the timescale of response to imposed changes in redox conditions, thus placing constraints on the importance of these different mechanisms. In the experiments, a solid electrode acts as an electron-accepting mineral whose redox potential can be precisely controlled. We inoculated duplicate MFCs with a sediment/groundwater mixture from an aquifer at Rifle, Colorado, supplied acetate as an electron donor, and obtained stable, mixed-species biofilms dominated by Geobacter and a novel Geobacter-related family. We poised the anode at potentials spanning the range of natural Fe(III)-reduction, then performed cyclic voltammetry (CV) to characterize the overall biofilm redox signature. The apparent biofilm midpoint potential shifted directly with anode set potential when the latter was changed within the range from about -250 to -50 mV vs. SHE. Following a jump in set potential by 200 mV, the CV-midpoint shift by ~100 mV over a timescale of ~30 minutes to a few hours, depending on the direction of the potential change. The extracellular electron transfer molecules, whose overall CV signature is very similar to those of purified MHCs, appear to span a broad redox range (~200 mV), supporting the hypothesis that MHCs confer substantial redox flexibility. This flexibility may be a principle reason for the abundance of MHCs expressed by microorganisms capable of extracellular electron transfer to minerals.

  7. Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes

    Science.gov (United States)

    Holmes, Dawn E.; Nevin, Kelly P.; O'Neil, Regina A.; Ward, Joy E.; Adams, Lorrie A.; Woodard, Trevor L.; Vrionis, Helen A.; Lovely, Derek R.

    2005-01-01

    The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.

  8. Reactor performance in terms of COD and nitrogen removal and bacterial community structure of a three-stage rotating bioelectrochemical contactor

    KAUST Repository

    Sayess, Rassil R.

    2013-02-01

    Integrating microbial fuel cell (MFC) into rotating biological contactor (RBC) creates an opportunity for enhanced removal of COD and nitrogen coupled with energy generation from wastewater. In this study, a three-stage rotating bioelectrochemical contactor (referred to as RBC-MFC unit) integrating MFC with RBC technology was constructed for simultaneous removal of carbonaceous and nitrogenous compounds and electricity generation from a synthetic medium containing acetate and ammonium. The performance of the RBC-MFC unit was compared to a control reactor (referred to as RBC unit) that was operated under the same conditions but without current generation (i.e. open-circuit mode). The effect of hydraulic loading rate (HLR) and COD/N ratio on the performance of the two units was investigated. At low (3.05 gCOD g-1N) and high COD/N ratio (6.64 gCOD g-1N), both units achieved almost similar COD and ammonia-nitrogen removal. However, the RBC-MFC unit achieved significantly higher denitrification and nitrogen removal compared to the RBC unit indicating improved denitrification at the cathode due to current flow. The average voltage under 1000 Ω external resistance ranged between 0.03 and 0.30 V and between 0.02 and 0.21 V for stages 1 and 2 of the RBC-MFC unit. Pyrosequencing analysis of bacterial 16S rRNA gene revealed high bacterial diversity at the anode and cathode of both units. Genera that play a role in nitrification (Nitrospira; Nitrosomonas), denitrification (Comamonas; Thauera) and electricity generation (Geobacter) were identified at the electrodes. Geobacter was only detected on the anode of the RBC-MFC unit. Nitrifiers and denitrifiers were more abundant in the RBC-MFC unit compared to the RBC unit and were largely present on the cathode of both units suggesting that most of the nitrogen removal occurred at the cathode. © 2012 Elsevier Ltd.

  9. Ecophysiology of Fe-cycling bacteria in acidic sediments.

    Science.gov (United States)

    Lu, Shipeng; Gischkat, Stefan; Reiche, Marco; Akob, Denise M; Hallberg, Kevin B; Küsel, Kirsten

    2010-12-01

    Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 10(5) gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.

  10. Cd Mobility in Anoxic Fe-Mineral-Rich Environments - Potential Use of Fe(III)-Reducing Bacteria in Soil Remediation

    Science.gov (United States)

    Muehe, E. M.; Adaktylou, I. J.; Obst, M.; Schröder, C.; Behrens, S.; Hitchcock, A. P.; Tylsizczak, T.; Michel, F. M.; Krämer, U.; Kappler, A.

    2014-12-01

    Agricultural soils are increasingly burdened with heavy metals such as Cd from industrial sources and impure fertilizers. Metal contaminants enter the food chain via plant uptake from soil and negatively affect human and environmental health. New remediation approaches are needed to lower soil metal contents. To apply these remediation techniques successfully, it is necessary to understand how soil microbes and minerals interact with toxic metals. Here we show that microbial Fe(III) reduction initially mobilizes Cd before its immobilization under anoxic conditions. To study how microbial Fe(III) reduction influences Cd mobility, we isolated a new Cd-tolerant, Fe(III)-reducing Geobacter sp. from a heavily Cd-contaminated soil. In lab experiments, this Geobacter strain first mobilized Cd from Cd-loaded Fe(III) hydroxides followed by precipitation of Cd-bearing mineral phases. Using Mössbauer spectroscopy and scanning electron microscopy, the original and newly formed Cd-containing Fe(II) and Fe(III) mineral phases, including Cd-Fe-carbonates, Fe-phosphates and Fe-(oxyhydr)oxides, were identified and characterized. Using energy-dispersive X-ray spectroscopy and synchrotron-based scanning transmission X-ray microscopy, Cd was mapped in the Fe(II) mineral aggregates formed during microbial Fe(III) reduction. Microbial Fe(III) reduction mobilizes Cd prior to its precipitation in Cd-bearing mineral phases. The mobilized Cd could be taken up by phytoremediating plants, resulting in a net removal of Cd from contaminated sites. Alternatively, Cd precipitation could reduce Cd bioavailability in the environment, causing less toxic effects to crops and soil microbiota. However, the stability and thus bioavailability of these newly formed Fe-Cd mineral phases needs to be assessed thoroughly. Whether phytoremediation or immobilization of Cd in a mineral with reduced Cd bioavailability are feasible mechanisms to reduce toxic effects of Cd in the environment remains to be

  11. Phylogenetic diversity of dissimilatory ferric iron reducers in paddy soil of Hunan, South China

    Energy Technology Data Exchange (ETDEWEB)

    Wang Xin-Jun [State Key Lab. of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, BJ (China); Graduate Univ., Chinese Academy of Sciences, BJ (China); Yang Jing; Chen Xue-Ping; Sun Guo-Xin [State Key Lab. of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, BJ (China); Zhu Yong-Guan [State Key Lab. of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, BJ (China); Key Lab. of Urban Environment and Health, Inst. of Urban Environment, Chinese Academy of Sciences, Xiamen (China)

    2009-12-15

    Purpose: Dissimilatory iron-reducing bacteria have been described by both culture-dependent and -independent methods in various environments, including freshwater, marine sediments, natural wetlands, and contaminated aquifers. However, little is known about iron-reducing microbial communities in paddy soils. The goal of this study was to characterize iron-reducing microbial communities in paddy soil. Moreover, the effect of dissolved and solid-phase iron (III) species on the iron-reducing microbial communities was also investigated by enrichment cultures. Methods: Ferric citrate and ferrihydrite were used respectively to set up enrichment cultures of dissimilatory ironreducing microorganisms using 1% inoculum of soil samples, and the iron reduction was measured. Moreover, bacterial DNA was extracted and 16S rRNA genes were PCR-amplified, and subsequently analyzed by the clone library and terminal restriction fragment length polymorphism (T-RFLP). Results: Phylogenetic analysis of 16S rRNA gene sequences extracted from the enrichment cultures revealed that Bradyrhizobium, Bacteroides, Clostridium and Ralstonia species were the dominant bacteria in the ferric citrate enrichment. However, members of the genera Clostridium, Bacteroides, and Geobacter were the dominant micro-organisms in the ferrihydrite enrichment. Analysis of enrichment cultures by T-RFLP strongly supported the cloning and sequencing results. Conclusions: The present study demonstrated that dissimilatory iron-reducing consortia in As-contaminated paddy soil are phylogenetically diverse. Moreover, iron (III) sources as a key factor have a strong effect on the iron (III)-reducing microbial community structure and relative abundance in the enrichments. In addition, Geobacter species are selectively enriched by ferrihydrite enrichment cultures. (orig.)

  12. Comparative Analysis of Type IV Pilin in Desulfuromonadales

    Science.gov (United States)

    Shu, Chuanjun; Xiao, Ke; Yan, Qin; Sun, Xiao

    2016-01-01

    During anaerobic respiration, the bacteria Geobacter sulfurreducens can transfer electrons to extracellular electron accepters through its pilus. G. sulfurreducens pili have been reported to have metallic-like conductivity that is similar to doped organic semiconductors. To study the characteristics and origin of conductive pilin proteins found in the pilus structure, their genetic, structural, and phylogenetic properties were analyzed. The genetic relationships, and conserved structures and sequences that were obtained were used to predict the evolution of the pilins. Homologous genes that encode conductive pilin were found using PilFind and Cluster. Sequence characteristics and protein tertiary structures were analyzed with MAFFT and QUARK, respectively. The origin of conductive pilins was explored by building a phylogenetic tree. Truncation is a characteristic of conductive pilin. The structures of truncated pilins and their accompanying proteins were found to be similar to the N-terminal and C-terminal ends of full-length pilins respectively. The emergence of the truncated pilins can probably be ascribed to the evolutionary pressure of their extracellular electron transporting function. Genes encoding truncated pilins and proteins similar to the C-terminal of full-length pilins, which contain a group of consecutive anti-parallel beta-sheets, are adjacent in bacterial genomes. According to the genetic, structure, and phylogenetic analyses performed in this study, we inferred that the truncated pilins and their accompanying proteins probably evolved from full-length pilins by gene fission through duplication, degeneration, and separation. These findings provide new insights about the molecular mechanisms involved in long-range electron transport along the conductive pili of Geobacter species. PMID:28066394

  13. Stability of Ferrihydrite and Organic Matter in Ferrihydrite-Organic Matter Associations

    Science.gov (United States)

    Eusterhues, K.; Totsche, K. U.

    2015-12-01

    Iron oxides can bind particularly large amounts of organic matter (OM) and seem to be an important control on OM storage in many soils. To better understand the interactions between Fe oxides and OM, we produced ferrihydrite-OM associations by adsorption and coprecipitation in laboratory experiments. Because ferrihydrites are often formed in OM-rich solutions, we assume that coprecipitation is a common process in nature. In contrast to adsorption on pre-existing ferrihydrite surfaces, coprecipitation involves adsorption, occlusion (physical entrapment of OM), formation of Fe-OM complexes, and poisoning of ferrihydrite growth. The reactivity of coprecipitates may therefore differ from ferriydrites with adsorbed OM. Incubation experiments with an inoculum extracted from a Podzol forest-floor were carried out to quantify the mineralization of the adsorbed and coprecipitated organic matter. These experiments showed that the association with ferrihydrite stabilized the associated organic matter, but that differences in the degradability of adsorbed and coprecipitated organic matter were small. We therefore conclude that coprecipitation does not lead to a significant formation of microbial inaccessible organic matter domains. Microbial reduction experiments were performed using Geobacter bremensis. We observed that increasing amounts of associated OM led to decreasing initial reaction rates and a decreasing degree of dissolution. Reduction of coprecipitated ferrihydrites was faster than reduction of ferrihydrites with adsorbed OM. Our data demonstrate that the association with ferrihydrite can effectively stabilize labile polysaccharides. Vice versa, these polysaccharides may protect ferrihydrite from reduction by Geobacter-like bacteria. However, a challenge for future studies will be to link formation and degradation of mineral-organic associations to natural porous systems, that is, to the complex interplay of mass transport and microbial distribution in the

  14. Reactor performance in terms of COD and nitrogen removal and bacterial community structure of a three-stage rotating bioelectrochemical contactor.

    Science.gov (United States)

    Sayess, Rassil R; Saikaly, Pascal E; El-Fadel, Mutasem; Li, Dong; Semerjian, Lucy

    2013-02-01

    Integrating microbial fuel cell (MFC) into rotating biological contactor (RBC) creates an opportunity for enhanced removal of COD and nitrogen coupled with energy generation from wastewater. In this study, a three-stage rotating bioelectrochemical contactor (referred to as RBC-MFC unit) integrating MFC with RBC technology was constructed for simultaneous removal of carbonaceous and nitrogenous compounds and electricity generation from a synthetic medium containing acetate and ammonium. The performance of the RBC-MFC unit was compared to a control reactor (referred to as RBC unit) that was operated under the same conditions but without current generation (i.e. open-circuit mode). The effect of hydraulic loading rate (HLR) and COD/N ratio on the performance of the two units was investigated. At low (3.05 gCOD g⁻¹N) and high COD/N ratio (6.64 gCOD g⁻¹N), both units achieved almost similar COD and ammonia-nitrogen removal. However, the RBC-MFC unit achieved significantly higher denitrification and nitrogen removal compared to the RBC unit indicating improved denitrification at the cathode due to current flow. The average voltage under 1000 Ω external resistance ranged between 0.03 and 0.30 V and between 0.02 and 0.21 V for stages 1 and 2 of the RBC-MFC unit. Pyrosequencing analysis of bacterial 16S rRNA gene revealed high bacterial diversity at the anode and cathode of both units. Genera that play a role in nitrification (Nitrospira; Nitrosomonas), denitrification (Comamonas; Thauera) and electricity generation (Geobacter) were identified at the electrodes. Geobacter was only detected on the anode of the RBC-MFC unit. Nitrifiers and denitrifiers were more abundant in the RBC-MFC unit compared to the RBC unit and were largely present on the cathode of both units suggesting that most of the nitrogen removal occurred at the cathode.

  15. Influence of Oxygen and Nitrate on Fe (Hydr)oxide Mineral Transformation and Soil Microbial Communities during Redox Cycling.

    Science.gov (United States)

    Mejia, Jacqueline; Roden, Eric E; Ginder-Vogel, Matthew

    2016-04-05

    Oscillations between reducing and oxidizing conditions are observed at the interface of anaerobic/oxic and anaerobic/anoxic environments, and are often stimulated by an alternating flux of electron donors (e.g., organic carbon) and electron acceptors (e.g., O2 and NO3(-)). In iron (Fe) rich soils and sediments, these oscillations may stimulate the growth of both Fe-reducing bacteria (FeRB) and Fe-oxidizing bacteria (FeOB), and their metabolism may induce cycling between Fe(II) and Fe(III), promoting the transformation of Fe (hydr)oxide minerals. Here, we examine the mineralogical evolution of lepidocrocite and ferrihydrite, and the adaptation of a natural microbial community to alternating Fe-reducing (anaerobic with addition of glucose) and Fe-oxidizing (with addition of nitrate or air) conditions. The growth of FeRB (e.g., Geobacter) is stimulated under anaerobic conditions in the presence of glucose. However, the abundance of these organisms depends on the availability of Fe(III) (hydr)oxides. Redox cycling with nitrate results in decreased Fe(II) oxidation thereby decreasing the availability of Fe(III) for FeRB. Additionally, magnetite is detected as the main product of both lepidocrocite and ferrihydrite reduction. In contrast, introduction of air results in increased Fe(II) oxidation, increasing the availability of Fe(III) and the abundance of Geobacter. In the lepidocrocite reactors, Fe(II) oxidation by dissolved O2 promotes the formation of ferrihydrite and lepidocrocite, whereas in the ferrihydrite reactors we observe a decrease in magnetite stoichiometry (e.g., oxidation). Understanding Fe (hydr)oxide transformation under environmentally relevant redox cycling conditions provides insight into nutrient availability and transport, contaminant mobility, and microbial metabolism in soils and sediments.

  16. Exoelectrogenic biofilm as a template for sustainable formation of a catalytic mesoporous structure

    KAUST Repository

    Yates, Matthew D.

    2014-06-04

    © 2014 Wiley Periodicals, Inc. Actively respiring biofilms of Geobacter sulfurreducens were used as a biotemplate to form a palladium mesoporous layer directly on an electrode surface. Cells and proteins within the biofilm acted as the reductant and stabilizer to facilitate the reduction, dispersion, and attachment of palladium nanoparticles to the electrode surface without using synthetic chemicals. © 2014 Wiley Periodicals, Inc. Mesoporous structures can increase catalytic activity by maximizing the ratio of surface area to volume, but current synthesis techniques utilize expensive polymers and toxic chemicals. A Geobacter sulfurreducens biofilm was used as a sustainable template to form mesoporous Pd structures while eliminating the need for synthetic chemicals. The bulk of the biofilm material was removed by thermal treatments after nanoparticle formation, producing a catalytic Pd mesoporous (pore size 9.7±0.1nm) structure attached to the graphite electrode with a 1.5-2μm thick backbone composed of nanoparticles (~200nm). A control electrode electrochemically plated with Pd in the absence of a biofilm exhibited a variable planar Pd base (~0.5-3μm thick) with sporadic Pd extrusions (~2μm across, 1-5μm tall) from the surface. The biotemplated mesoporous structure produced 15-20% higher stable current densities during H2 oxidation tests than the electrochemically plated control electrode, even though 30% less Pd was present in the biotemplated catalyst. These results indicate that electroactive biofilms can be used as a sustainable base material to produce nanoporous structures without the need for synthetic polymers. Biotechnol. Bioeng. 2014;111: 2349-2354.

  17. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth.

    Science.gov (United States)

    Luef, Birgit; Fakra, Sirine C; Csencsits, Roseann; Wrighton, Kelly C; Williams, Kenneth H; Wilkins, Michael J; Downing, Kenneth H; Long, Philip E; Comolli, Luis R; Banfield, Jillian F

    2013-02-01

    Iron-reducing bacteria (FeRB) play key roles in anaerobic metal and carbon cycling and carry out biogeochemical transformations that can be harnessed for environmental bioremediation. A subset of FeRB require direct contact with Fe(III)-bearing minerals for dissimilatory growth, yet these bacteria must move between mineral particles. Furthermore, they proliferate in planktonic consortia during biostimulation experiments. Thus, a key question is how such organisms can sustain growth under these conditions. Here we characterized planktonic microbial communities sampled from an aquifer in Rifle, Colorado, USA, close to the peak of iron reduction following in situ acetate amendment. Samples were cryo-plunged on site and subsequently examined using correlated two- and three-dimensional cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission X-ray microscopy (STXM). The outer membranes of most cells were decorated with aggregates up to 150 nm in diameter composed of ∼3 nm wide amorphous, Fe-rich nanoparticles. Fluorescent in situ hybridization of lineage-specific probes applied to rRNA of cells subsequently imaged via cryo-TEM identified Geobacter spp., a well-studied group of FeRB. STXM results at the Fe L(2,3) absorption edges indicate that nanoparticle aggregates contain a variable mixture of Fe(II)-Fe(III), and are generally enriched in Fe(III). Geobacter bemidjiensis cultivated anaerobically in the laboratory on acetate and hydrous ferric oxyhydroxides also accumulated mixed-valence nanoparticle aggregates. In field-collected samples, FeRB with a wide variety of morphologies were associated with nano-aggregates, indicating that cell surface Fe(III) accumulation may be a general mechanism by which FeRB can grow while in planktonic suspension.

  18. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth

    Energy Technology Data Exchange (ETDEWEB)

    Luef, Birgit; Fakra, Sirine C.; Csencsits, Roseann; Wrighton, Kelly C.; Williams, Kenneth H.; Wilkins, Michael J.; Downing, Kenneth H.; Long, Philip E.; Comolli, Luis R.; Banfield, Jillian F.

    2013-02-04

    Iron-reducing bacteria (FeRB) play key roles in anaerobic metal and carbon cycling and carry out biogeochemical transformations that can be harnessed for environmental bioremediation. A subset of FeRB require direct contact with Fe(III) bearing minerals for dissimilatory growth, yet these bacteria must move between mineral particles. Further, they proliferate in planktonic consortia during biostimulation experiments. Thus, a key question is how such organisms can sustain growth under these conditions. Here we characterized planktonic microbial communities sampled from an aquifer in Rifle, Colorado, USA close to the peak of iron reduction following in situ acetate amendment. Samples were cryo-plunged on site and subsequently examined using correlated 2- and 3- dimensional cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission X-ray microscopy (STXM). Most cells had their outer membranes decorated with up to 150 nm diameter aggregates composed of a few nm wide amorphous, Fe-rich nanoparticles. Fluorescent in situ hybridization of lineage-specific probes applied to rRNA of cells subsequently imaged via cryo-TEM identified Geobacter spp., a well studied group of FeRB. STXM results at the Fe L2,3 absorption edges indicate that nanoparticle aggregates contain a variable mixture of Fe(II)-Fe(III), and are generally enriched in Fe(III). Geobacter bemidjiensis cultivated anaerobically in the laboratory on acetate and hydrous ferric oxyhydroxides also accumulated mixed valence nanoparticle aggregates. In field-collected samples, FeRB with a wide variety of morphologies were associated with nano-aggregates, indicating that cell-surface Fe(III) accumulation may be a general mechanism by which FeRB can grow while in planktonic suspension.

  19. Genomic Analyses of Bacterial Porin-Cytochrome Gene Clusters

    Directory of Open Access Journals (Sweden)

    Liang eShi

    2014-11-01

    Full Text Available The porin-cytochrome (Pcc protein complex is responsible for trans-outer membrane electron transfer during extracellular reduction of Fe(III by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens PCA. The identified and characterized Pcc complex of G. sulfurreducens PCA consists of a porin-like outer-membrane protein, a periplasmic 8-heme c-type cytochrome (c-Cyt and an outer-membrane 12-heme c-Cyt, and the genes encoding the Pcc proteins are clustered in the same regions of genome (i.e., the pcc gene clusters of G. sulfurreducens PCA. A survey of additionally microbial genomes has identified the pcc gene clusters in all sequenced Geobacter spp. and other bacteria from six different phyla, including Anaeromyxobacter dehalogenans 2CP-1, A. dehalogenans 2CP-C, Anaeromyxobacter sp. K, Candidatus Kuenenia stuttgartiensis, Denitrovibrio acetiphilus DSM 12809, Desulfurispirillum indicum S5, Desulfurivibrio alkaliphilus AHT2, Desulfurobacterium thermolithotrophum DSM 11699, Desulfuromonas acetoxidans DSM 684, Ignavibacterium album JCM 16511, and Thermovibrio ammonificans HB-1. The numbers of genes in the pcc gene clusters vary, ranging from two to nine. Similar to the metal-reducing (Mtr gene clusters of other Fe(III-reducing bacteria, such as Shewanella spp., additional genes that encode putative c-Cyts with predicted cellular localizations at the cytoplasmic membrane, periplasm and outer membrane often associate with the pcc gene clusters. This suggests that the Pcc-associated c-Cyts may be part of the pathways for extracellular electron transfer reactions. The presence of pcc gene clusters in the microorganisms that do not reduce solid-phase Fe(III and Mn(IV oxides, such as D. alkaliphilus AHT2 and I. album JCM 16511, also suggests that some of the pcc gene clusters may be involved in extracellular electron transfer reactions with the substrates other than Fe(III and Mn(IV oxides.

  20. Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface

    Science.gov (United States)

    Lovley, Derek R.; Anderson, Robert T.

    Dissimilatory Fe(III)-reducing microorganisms have the ability to destroy organic contaminants under anaerobic conditions by oxidizing them to carbon dioxide. Some Fe(III)-reducing microorganisms can also reductively dechlorinate chlorinated contaminants. Fe(III)-reducing microorganisms can reduce a variety of contaminant metals and convert them from soluble forms to forms that are likely to be immobilized in the subsurface. Studies in petroleum-contaminated aquifers have demonstrated that Fe(III)-reducing microorganisms can be effective agents in removing aromatic hydrocarbons from groundwater under anaerobic conditions. Laboratory studies have demonstrated the potential for Fe(III)-reducing microorganisms to remove uranium from contaminated groundwaters. The activity of Fe(III)-reducing microorganisms can be stimulated in several ways to enhance organic contaminant oxidation and metal reduction. Molecular analyses in both field and laboratory studies have demonstrated that microorganisms of the genus Geobacter become dominant members of the microbial community when Fe(III)-reducing conditions develop as the result of organic contamination, or when Fe(III) reduction is artificially stimulated. These results suggest that further understanding of the ecophysiology of Geobacter species would aid in better prediction of the natural attenuation of organic contaminants under anaerobic conditions and in the design of strategies for the bioremediation of subsurface metal contamination. Des micro-organismes simulant la réduction du fer ont la capacité de détruire des polluants organiques dans des conditions anérobies en les oxydant en dioxyde de carbone. Certains micro-organismes réducteurs de fer peuvent aussi dé-chlorer par réduction des polluants chlorés. Des micro-organismes réducteurs de fer peuvent réduire tout un ensemble de métaux polluants et les faire passer de formes solubles à des formes qui sont susceptibles d'être immobilisées dans le milieu

  1. A 200 years record of multidecadal oceanographic changes from offshore North Iceland

    Science.gov (United States)

    Perner, Kerstin; Moros, Matthias; Jansen, Eystein

    2016-04-01

    A 200 years record of multidecadal oceanographic changes from offshore North Iceland During the cruise GS15-198 of the RV G.O. Sars in summer 2015, new sediments cores have been collected from the North Iceland shelf at 66°N, an area known for its high sedimentation rates. Here, offshore North Iceland an offshoot of the East Greenland Current, the surface flowing East Icelandic Current (EIC) transports a mixture of cooled Atlantic Water and cold/fresh Polar Water eastwards and at intermediate depths (100-350 m water depth), flows the relatively warm (4-7°C) North Irminger Icelandic Current (NIIC). Beneath this Atlantic Water layer, less saline and cooled (area offshore North Iceland is suitably located to investigate multidecadal changes in the southward fluxes of freshwater from the EGC, via the EIC and in the relative contribution/water mass characteristics (i.e. temperature and salinity) of the NIIC and shifts in the location of the Polar Front. Oceanographic variability recorded offshore North Iceland is closely linked to broader scale climatic and oceanographic shifts/variations in the North Atlantic region. Samples for foraminiferal analyses were wet sieved at 63 μm and counted at 1-2 cm intervals, which equals a resolution of ~ 2 years. The foraminiferal assemblage is characterized by a divers fauna and a total of 76 foraminiferal species were identified, 6 planktic, 19 agglutinated and 51 calcareous species. The absolute abundance of foraminifera averages 400 specimens per 1g of wet sediment. Our high-resolution palaeoceanographic reconstructions reveal distinct multidecadal oceanographic variability that relate to climatic changes during the last 200 years, i.e. transition from the Little Ice Age into the modern warm phase.

  2. Shipborne LiDAR system for coastal change monitoring

    Science.gov (United States)

    Kim, chang hwan; Park, chang hong; Kim, hyun wook; hyuck Kim, won; Lee, myoung hoon; Park, hyeon yeong

    2016-04-01

    Coastal areas, used as human utilization areas like leisure space, medical care, ports and power plants, etc., are regions that are continuously changing and interconnected with oceans and land and the sea level has risen by about 8cm (1.9mm / yr) due to global warming from 1964 year to 2006 year in Korea. Coastal erosion due to sea-level rise has caused the problem of marine ecosystems and loss of tourism resources, etc. Regular monitoring of coastal erosion is essential at key locations with such volatility. But the survey method of land mobile LiDAR (light detection and ranging) system has much time consuming and many restrictions. For effective monitoring beach erosion, KIOST (Korea Institute of Ocean Science & Technology) has constructed a shipborne mobile LiDAR system. The shipborne mobile LiDAR system comprised a land mobile LiDAR (RIEGL LMS-420i), an INS (inertial navigation system, MAGUS Inertial+), a RTKGPS (LEICA GS15 GS25), and a fixed platform. The shipborne mobile LiDAR system is much more effective than a land mobile LiDAR system in the measuring of fore shore areas without shadow zone. Because the vessel with the shipborne mobile LiDAR system is continuously moved along the shoreline, it is possible to efficiently survey a large area in a relatively short time. Effective monitoring of the changes using the constructed shipborne mobile LiDAR system for seriously eroded coastal areas will be able to contribute to coastal erosion management and response.

  3. Ammonia-regulated expression of a soybean gene encoding cytosolic glutamine synthetase in transgenic Lotus corniculatus.

    Science.gov (United States)

    Miao, G H; Hirel, B; Marsolier, M C; Ridge, R W; Verma, D P

    1991-01-01

    A full-length cDNA clone encoding cytosolic glutamine synthetase (GS), expressed in roots and root nodules of soybean, was isolated by direct complementation of an Escherichia coli gln A- mutant. This sequence is induced in roots by the availability of ammonia. A 3.5-kilobase promoter fragment of a genomic clone (lambda GS15) corresponding to this cDNA was isolated and fused with a reporter [beta-glucuronidase (GUS)] gene. The GS-GUS fusion was introduced into a legume (Lotus corniculatus) and a nonlegume (tobacco) plant by way of Agrobacterium-mediated transformations. This chimeric gene was found to be expressed in a root-specific manner in both tobacco and L. corniculatus, the expression being restricted to the growing root apices and the vascular bundles of the mature root. Treatment with ammonia increased the expression of this chimeric gene in the legume background (i.e., L. corniculatus); however, no induction was observed in tobacco roots. Histochemical localization of GUS activity in ammonia-treated transgenic L. corniculatus roots showed a uniform distribution across all cell types. These data suggest that the tissue specificity of the soybean cytosolic GS gene is conserved in both tobacco and L. corniculatus; however, in the latter case, this gene is ammonia inducible. Furthermore, the ammonia-enhanced GS gene expression in L. corniculatus is due to an increase in transcription. That this gene is directly regulated by externally supplied or symbiotically fixed nitrogen is also evident from the expression of GS-GUS in the infection zone, including the uninfected cells, and the inner cortex of transgenic L. corniculatus nodules, where a flux of ammonia is encountered by this tissue. The lack of expression of GS-GUS in the outer cortex of the nodules suggests that ammonia may not be able to diffuse outside the endodermis.

  4. Overexpression of a soybean gene encoding cytosolic glutamine synthetase in shoots of transgenic Lotus corniculatus L. plants triggers changes in ammonium assimilation and plant development.

    Science.gov (United States)

    Vincent, R; Fraisier, V; Chaillou, S; Limami, M A; Deleens, E; Phillipson, B; Douat, C; Boutin, J P; Hirel, B

    1997-01-01

    A soybean cytosolic glutamine synthetase gene (GS15) was fused with the constitutive 35S cauliflower mosaic virus (CaMV) promoter in order to direct overexpression in Lotus corniculatus L. plants. Following transformation with Agrobacterium rhizogenes, eight independent Lotus transformants were obtained which synthesized additional cytosolic glutamine synthetase (GS) in the shoots. To eliminate any interference caused by the T-DNA from the Ri plasmid, three primary transformants were crossed with untransformed plants and progeny devoid of TL- and TR-DNA sequences were chosen for further analyses. These plants had a 50-80% increase in total leaf GS activity. Plants were grown under different nitrogen regimes (4 or 12 mM NH4+) and aspects of carbon and nitrogen metabolism were examined. In roots, an increase in free amino acids and ammonium was accompanied by a decrease in soluble carbohydrates in the transgenic plants cultivated with 12 mM NH4+ in comparison to the wild type grown under the same conditions. Labelling experiments using 15NH4+ were carried out in order to monitor the influx of ammonium and its subsequent incorporation into amino acids. This experiment showed that both ammonium uptake in the roots and the subsequent translocation of amino acids to the shoots was lower in plants overexpressing GS. It was concluded that the build up of ammonium and the increase in amino acid concentration in the roots was the result of shoot protein degradation. Moreover, following three weeks of hydroponic culture early floral development was observed in the transformed plants. As all these properties are characteristic of senescent plants, these findings suggest that expression of cytosolic GS in the shoots may accelerate plant development, leading to early senescence and premature flowering when plants are grown on an ammonium-rich medium.

  5. Single fiber analyses of glycogen-related proteins reveal their differential association with glycogen in rat skeletal muscle.

    Science.gov (United States)

    Murphy, Robyn M; Xu, Hongyang; Latchman, Heidy; Larkins, Noni T; Gooley, Paul R; Stapleton, David I

    2012-12-01

    To understand how glycogen affects skeletal muscle physiology, we examined enzymes essential for muscle glycogen synthesis and degradation using single fibers from quiescent and stimulated rat skeletal muscle. Presenting a shift in paradigm, we show these proteins are differentially associated with glycogen granules. Protein diffusibility and/or abundance of glycogenin, glycogen branching enzyme (GBE), debranching enzyme (GDE), phosphorylase (GP), and synthase (GS) were examined in fibers isolated from rat fast-twitch extensor digitorum longus (EDL) and slow-twitch soleus (SOL) muscle. GDE and GP proteins were more abundant (~10- to 100-fold) in fibers from EDL compared with SOL muscle. GS and glycogenin proteins were similar between muscles while GBE had an approximately fourfold greater abundance in SOL muscle. Mechanically skinned fibers exposed to physiological buffer for 10 min showed ~70% total pools of GBE and GP were diffusible (nonbound), whereas GDE and GS were considerably less diffusible. Intense in vitro stimulation, sufficient to elicit a ~50% decrease in intracellular glycogen, increased diffusibility of GDE, GP, and GS (~15-60%) and decreased GBE diffusibility (~20%). Amylase treatment, which breaks α-1,4 linkages of glycogen, indicated differential diffusibilities and hence glycogen associations of GDE and GS. Membrane solubilization (1% Triton-X-100) allowed a small additional amount of GDE and GS to diffuse from fibers, suggesting the majority of nonglycogen-associated GDE/GS is associated with myofibrillar/contractile network of muscle rather than membranes. Given differences in enzymes required for glycogen metabolism, the current findings suggest glycogen particles have fiber-type-dependent structures. The greater catabolic potential of glycogen breakdown in fast-twitch fibers may account for different contraction induced rates of glycogen utilization.

  6. A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation

    Science.gov (United States)

    Druhan, Jennifer L.; Bill, Markus; Lim, HsiaoChien; Wu, Cindy; Conrad, Mark E.; Williams, Kenneth H.; DePaolo, Donald J.; Brodie, Eoin L.

    2014-01-01

    Here we report a combined analysis of carbon mass balance based on isotopic labeling and microbiological characterization during organic carbon stimulated bioreduction of a subsurface sediment in a large laboratory column experimental system. This combination of approaches allows quantification of both the cycling of carbon through multiple redox pathways and the associated spatial and temporal evolution of bacterial communities in response to this nutrient source. Carbon isotope mass balance facilitated by the use of 13C-labeled acetate as the electron donor showed evidence for a net loss of sediment organic carbon over the course of the amendment experiment. Furthermore, these data clearly demonstrated a source of isotopically labeled inorganic carbon that was not attributable to primary metabolism by acetate-oxidizing microorganisms. Fluid samples collected weekly over the duration of the 43-day amendment at composition by pyrosequencing of ribosomal RNA genes. The microbial community composition was transient, with distinct occurrences of Azoarcus, Geobacter and multiple sulfate reducing species over the course of the experiment. In combination with DNA sequencing data, the anomalous carbon cycling process is shown to occur exclusively during the period of predominant Geobacter species growth. Pyrosequencing indicated, and targeted cloning and sequencing confirmed the presence of several bacteriovorous protozoa, including species of the Breviata, Planococcus and Euplotes genera. Cloning and qPCR analysis demonstrated that Euplotes species were most abundant and displayed a growth trajectory that closely followed that of the Geobacter population. These results suggest a previously undocumented secondary turnover of biomass carbon related to protozoan grazing that was not sufficiently prevalent to be observed in bulk concentrations of carbon species in the system, but was clearly identified in the partitioning of carbon isotopes. This study demonstrates evidence

  7. Microbial Community Structure and Function at an Aquifer Contaminated with Landfill Leachate (Norman,OK)

    Science.gov (United States)

    Weiss, J. V.; Voytek, M. A.; Lowit, M. B.; Cozzarelli, I. M.; Kirshtein, J. D.

    2006-05-01

    Geochemical research at an aquifer contaminated with landfill leachate (Norman, OK) has shown that contaminated areas have significant increases in the concentration of dissolved organic carbon (DOC) and persistent anaerobic conditions as compared to uncontaminated areas. As a result, sulfate is depleted in the center of the contaminant plume with concomitant increases in Fe(II) and methane. These observations have been used to infer the dominant biogeochemical processes in this ecosystem which include Fe reduction, sulfate reduction, and methanogenesis. Because each of these processes is microbially-mediated, the goal of this study was to use a combination of culture-based and molecular methods to determine the composition and diversity of the microbial community in the contaminant plume. Groundwater and sediment samples were collected along the flow path of contamination in June 2005. We used most probable number (MPN) analyses to determine the abundances of key functional groups of bacteria including methanogens, sulfate-reducers (SRB), and iron-reducers (FeRB). Quantitative PCR (qPCR) was performed to determine abundances of functional genes of the dissimilatory sulfite reductase (dsr) and methyl coenzyme M-reductase (mcr) genes and the 16 rRNA genes targeting Geobacter spp. Results from the MPN analyses confirmed the presence of a relatively abundant and diverse anaerobic community in the groundwater at the landfill (e.g. 102 SRB, FeRB ml-1. In general, with increasing distance from the source of contamination, abundances of FeRB, SRB, and methanogens decreased to < 101 cells ml-1 groundwater and < 102 cells g soil. In fact, most of these groups were undetectable throughout much of the sampling transect, particularly in the groundwater. For example, methanogens were largely absent despite the presence of high concentrations of methane. In contrast to these estimates obtained with MPN analyses, the results of qPCR indicated that there were measurable, and many

  8. Improved Understanding of Microbial Iron and Sulfate Reduction Through a Combination of Bottom-up and Top-down Functional Proteomics Assays

    Energy Technology Data Exchange (ETDEWEB)

    Richardson, Ruth [Cornell Univ., Ithaca, NY (United States)

    2016-02-28

    Our overall goal was to improve the understanding of microbial iron and sulfate reduction by evaluating a diverse iron and sulfate reducing organisms utilizing a multi-omics approach combining “top-down” and “bottom-up” omics methodologies. We initiated one of the first combined comparative genomics, shotgun proteomics, RTqPCR, and heterologous expression studies in pursuit of our project objectives. Within the first year of this project, we created a new bioinformatics tool for ortholog identification (“SPOCS”). SPOCS is described in our publication, Curtis et al., 2013. Using this tool we were able to identify conserved orthologous groups across diverse iron and sulfate reducing microorganisms from Firmicutes, gamma-proteobacteria and delta-proteobacteria. For six iron and sulfate reducers we also performed shotgun proteomics (“bottom-up” proteomics including accurate mass and time (AMT) tag and iTRAQ approaches). Cultures include Gram (-) and Gram (+) microbes. Gram (-) were: Geobacter sulfureducens (grown on iron citrate and fumarate), Geobacter bemidjiensis (grown on iron citrate and fumarate), Shewanella oneidiensis (grown on iron citrate and fumarate) and Anaeromyxobacter dehalogenans (grown on iron citrate and fumarate). Although all cultures grew on insoluble iron, the iron precipitates interfered with protein extraction and analysis; which remains a major challenge for researchers in disparate study systems. Among the Gram (-) organisms studied, Anaeromyxobacter dehalogenans remains the most poorly characterized. Yet, it is arguably the most versatile organisms we studied. In this work we have used comparative proteomics to hypothesize which two of the dozens of predicted c-type cytochromes within Anaeromyxobacter dehalogenans may be directly involved in soluble iron reduction. Unfortunately, heterologous expression of these Anaeromyxobacter dehalogenans ctype cytochromes led to poor protein production and/or formation of inclusion bodies

  9. 用于产电纯菌研究的MFC反应器的开发%Development of Microbial Fuel Cell Reactor for Pure Electricigen Research

    Institute of Scientific and Technical Information of China (English)

    曹效鑫; 梁鹏; 范明志; 黄霞

    2012-01-01

    Further improvement of the microbial fuel cell (MFC) power output urges to better understand the interaction mechanism between the electricigen and the electrode. In order to accomplish this goal, pure culture study is a better approach. However, strict sterile and anaerobic requirements make such experiments difficult to carry out. Therefore, a sterile two bottle MFC was developed. The modules were compared, and the electricity generation performance of MFC inoculated with Geobacter sul-furreducens was investigated. It was shown that sterilized condition could be achieved in the two bottle MFC during operation. Using potassium ferricyanide could effectively reduce cathode polarization and maintain anaerobic condition in the anode chamber. Further applications of this MFC system should provide a fundament for pure electricigen research.%以纯菌为对象进行产电机理研究是微生物燃料电池( MFC)技术进一步提高输出功率、走向实用的重要基础之一,然而由于产电纯菌研究要求的无菌性、厌氧性较为苛刻,给此类反应器的搭建、运行造成诸多困难.基于此,设计搭建了一种可灭菌的组件式两瓶型MFC,对其各组件进行了比较研究,并考察了接种Geobacter sulfurreducens后MFC的运行情况.研究结果表明,该反应器在运行周期内可保持良好的灭菌状态;使用铁氰化钾可有效地降低阴极极化,并保持阳极室的厌氧状态;该反应器可以较好地满足MFC对纯菌研究的要求.

  10. Monitoring Subsurface Microbial Biomass, Community Composition and Physiological Status during Biological Uranium Reduction with Acetate Addition using Lipid Analysis, DNA Arrays and q-PCR

    Science.gov (United States)

    Peacock, A. D.; Long, P. E.; N'Guessan, L.; Williams, K. H.; Chandler, D.

    2011-12-01

    Our objectives for this effort were to investigate microbial community dynamics during each of the distinct terminal electron acc