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

USGS Publications Warehouse

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aklujkar, Muktak; Young, Nelson D; Holmes, Dawn

2010-01-01

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-subsurfacemore » 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 Geobacteraceae in

Mineralogical and morphological constraints on the reduction of Fe(III) minerals by Geobacter sulfurreducens

NASA Astrophysics Data System (ADS)

Cutting, R. S.; Coker, V. S.; Fellowes, J. W.; Lloyd, J. R.; Vaughan, D. J.

2009-07-01

The biologically-mediated reduction of synthetic samples of the Fe(III)-bearing minerals hematite, goethite, lepidocrocite, feroxhyte, ford ferrihydrite, akaganeite and schwertmannite by Geobacter sulfurreducens has been investigated using microbiological techniques in conjunction with X-ray Diffraction (XRD), Transmission Electron Microscopy (TEM) and X-ray Photoelectron Spectroscopy (XPS). This combination of approaches offers unique insights into the influence of subtle variations in the crystallinity of a given mineral on biogeochemical processes, and has highlighted the importance of (oxyhydr)oxide crystallite morphology in determining the changes occurring in a given mineral phase. Problems arising from normalising the biological Fe(III) reduction rates relative to the specific surface areas of the starting materials are also highlighted. These problems are caused primarily by particle aggregation, and compounded when using spectrophotometric assays to monitor reduction. For example, the initial rates of Fe(III) reduction observed for two synthetic feroxyhytes with different crystallinities (as shown by XRD and TEM studies) but almost identical surface areas, differ substantially. Both microbiological and high-resolution TEM studies show that hematite and goethite are susceptible to limited amounts of Fe(III) reduction, as evidenced by the accumulation of Fe(II) during incubation with G. sulfurreducens and the growth of nodular structures on crystalline goethite laths during incubation. Lepidocrocite and akaganeite readily transform into mixtures of magnetite and goethite, and XRD data indicate that the proportion of magnetite increases within the transformation products as the crystallinity of the starting material decreases. The presence of anthraquinone-2,6-disulfonate (AQDS) as an electron shuttle increases both the initial rate and longer term extent of biological Fe(III) reduction for all of the synthetic minerals examined. High-resolution XPS indicates

Mechanisms for Fe(III) oxide reduction in sedimentary environments

USGS Publications Warehouse

Nevin, Kelly P.; Lovely, Derek R.

2002-01-01

Although it was previously considered that Fe(III)-reducing microorganisms must come into direct contact with Fe(III) oxides in order to reduce them, recent studies have suggested that electron-shuttling compounds and/or Fe(III) chelators, either naturally present or produced by the Fe(III)-reducing microorganisms themselves, may alleviate the need for the Fe(III) reducers to establish direct contact with Fe(III) oxides. Studies with Shewanella alga strain BrY and Fe(III) oxides sequestered within microporous beads demonstrated for the first time that this organism releases a compound(s) that permits electron transfer to Fe(III) oxides which the organism cannot directly contact. Furthermore, as much as 450 w M dissolved Fe(III) was detected in cultures of S. alga growing in Fe(III) oxide medium, suggesting that this organism releases compounds that can solublize Fe(III) from Fe(III) oxide. These results contrast with previous studies, which demonstrated that Geobacter metallireducens does not produce electron-shuttles or Fe(III) chelators. Some freshwater aquatic sediments and groundwaters contained compounds, which could act as electron shuttles by accepting electrons from G. metallireducens and then transferring the electrons to Fe(III). However, other samples lacked significant electron-shuttling capacity. Spectroscopic studies indicated that the electron-shuttling capacity of the waters was not only associated with the presence of humic substances, but water extracts of walnut, oak, and maple leaves contained electron-shuttling compounds did not appear to be humic substances. Porewater from a freshwater aquatic sediment and groundwater from a petroleum-contaminated aquifer contained dissolved Fe(III) (4-16 w M), suggesting that soluble Fe(III) may be available as an electron acceptor in some sedimentary environments. These results demonstrate that in order to accurately model the mechanisms for Fe(III) reduction in sedimentary environments it will be necessary

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

USGS Publications Warehouse

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.

Paenibacillus guangzhouensis sp. nov., an Fe(III)- and humus-reducing bacterium from a forest soil.

PubMed

Li, Jibing; Lu, Qin; Liu, Ting; Zhou, Shungui; Yang, Guiqin; Zhao, Yong

2014-11-01

A Gram-reaction-variable, rod-shaped, motile, facultatively aerobic and endospore-forming bacterium, designated strain GSS02(T), was isolated from a forest soil. Strain GSS02(T) was capable of reducing humic substances and Fe(III) oxides. Strain GSS02(T) grew optimally at 35 °C, at pH 78 and in the presence of 1% NaCl. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C(15:0) and iso-C(16:0) and the polar lipid profile contained mainly phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol, with moderate amounts of two unknown aminophospholipids and a minor amount of one unknown lipid. The DNA G+C content was 53.4 mol%. Comparative 16S rRNA gene sequence analysis showed that strain GSS02(T) was related most closely to Paenibacillus terrigena JCM 21741(T) (98.1% similarity). Mean DNA-DNA relatedness between strain GSS02(T) and P. terrigena JCM 21741(T) was 58.8 ± 0.5%. The phylogenetic, chemotaxonomic and phenotypic results clearly demonstrated that strain GSS02(T) belongs to the genus Paenibacillus and represents a novel species, for which the name Paenibacillus guangzhouensis sp. nov. is proposed. The type strain is GSS02(T) ( =KCTC 33171(T) =CCTCC AB 2013236(T)). © 2014 IUMS.

Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

USGS Publications Warehouse

Caccavo, F.; Coates, J.D.; Rossello-Mora, R. A.; Ludwig, W.; Schleifer, K.H.; Lovley, D.R.; McInerney, M.J.

1996-01-01

A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAI-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAI-1 differs from all other described bacteria, and represents the type strain of a new genus and species. Geovibrio ferrireducens.

Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA.

PubMed

Otwell, Anne E; Callister, Stephen J; Sherwood, Robert W; Zhang, Sheng; Goldman, Abby R; Smith, Richard D; Richardson, Ruth E

2018-06-15

We established Fe(III)-reducing co-cultures of two species of metal-reducing bacteria, the Gram-positive Desulfotomaculum reducens MI-1 and the Gram-negative Geobacter sulfurreducens PCA. Co-cultures were given pyruvate, a substrate that D. reducens can ferment and use as electron donor for Fe(III) reduction. G. sulfurreducens relied upon products of pyruvate oxidation by D. reducens (acetate, hydrogen) for use as electron donor in the co-culture. Co-cultures reduced Fe(III) to Fe(II) robustly, and Fe(II) was consistently detected earlier in co-cultures than pure cultures. Notably, faster cell growth, and correspondingly faster pyruvate oxidation, was observed by D. reducens in co-cultures. Global comparative proteomic analysis was performed to observe differential protein abundance during co-culture vs. pure culture growth. Proteins previously associated with Fe(III) reduction in G. sulfurreducens, namely c-type cytochromes and type IV pili proteins, were significantly increased in abundance in co-cultures relative to pure cultures. D. reducens ribosomal proteins were significantly increased in co-cultures, likely a reflection of faster growth rates observed for D. reducens cells while in co-culture. Furthermore, we developed multiple reaction monitoring (MRM) assays to quantitate specific biomarker peptides. The assays were validated in pure and co-cultures, and protein abundance ratios from targeted MRM and global proteomic analysis correlate significantly. © 2018 John Wiley & Sons Ltd.

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

PubMed

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.

Identification of Genes Involved in Biofilm Formation and Respiration via Mini-Himar Transposon Mutagenesis of Geobacter sulfurreducens▿ †

PubMed Central

Rollefson, Janet B.; Levar, Caleb E.; Bond, Daniel R.

2009-01-01

Electron transfer from cells to metals and electrodes by the Fe(III)-reducing anaerobe Geobacter sulfurreducens requires proper expression of redox proteins and attachment mechanisms to interface bacteria with surfaces and neighboring cells. We hypothesized that transposon mutagenesis would complement targeted knockout studies in Geobacter spp. and identify novel genes involved in this process. Escherichia coli mating strains and plasmids were used to develop a conjugation protocol and deliver mini-Himar transposons, creating a library of over 8,000 mutants that was anaerobically arrayed and screened for a range of phenotypes, including auxotrophy for amino acids, inability to reduce Fe(III) citrate, and attachment to surfaces. Following protocol validation, mutants with strong phenotypes were further characterized in a three-electrode system to simultaneously quantify attachment, biofilm development, and respiratory parameters, revealing mutants defective in Fe(III) reduction but unaffected in electron transfer to electrodes (such as an insertion in GSU1330, a putative metal export protein) or defective in electrode reduction but demonstrating wild-type biofilm formation (due to an insertion upstream of the NHL domain protein GSU2505). An insertion in a putative ATP-dependent transporter (GSU1501) eliminated electrode colonization but not Fe(III) citrate reduction. A more complex phenotype was demonstrated by a mutant containing an insertion in a transglutaminase domain protein (GSU3361), which suddenly ceased to respire when biofilms reached approximately 50% of the wild-type levels. As most insertions were not in cytochromes but rather in transporters, two-component signaling proteins, and proteins of unknown function, this collection illustrates how biofilm formation and electron transfer are separate but complementary phenotypes, controlled by multiple loci not commonly studied in Geobacter spp. PMID:19395486

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

USGS Publications Warehouse

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%, P<0.05 in all cases). The percentage of poorly crystalline Fe(III) was significantly correlated with the percentage of FeRB (r=0.76), reflecting the fact that poorly crystalline Fe(III) minerals are labile with respect to microbial reduction. Abiotic reductive dissolution consumed about 75% of the rhizosphere Fe(III)-oxide pool in 4 h compared to 23% of the soil 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.

Electron Donors Supporting Growth and Electroactivity of Geobacter sulfurreducens Anode Biofilms

PubMed Central

Speers, Allison M.

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. PMID:22101036

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

PubMed

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.

Anaerobic Benzene Oxidation via Phenol in Geobacter metallireducens

PubMed Central

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

2013-01-01

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 (<0.5 μM) of phenol accumulated in cultures of 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 18O during growth in H218O, 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. PMID:24096430

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

PubMed

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pokkuluri, P. R.; Londer, Y. Y.; Yang, X.

2010-02-01

Periplasmic cytochromes c{sub 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{sub 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, inmore » 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{sub 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{sub 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{sub 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.« less

Enhanced Uranium Immobilization and Reduction by Geobacter sulfurreducens Biofilms

PubMed Central

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

2014-01-01

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. PMID:25128347

Enhanced uranium immobilization and reduction by Geobacter sulfurreducens biofilms.

PubMed

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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feist, AM; Nagarajan, H; Rotaru, AE

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 withmore » 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

Release of 226Ra from uranium mill tailings by microbial Fe(III) reduction

USGS Publications Warehouse

Landa, E.R.; Phillips, E.J.P.; Lovley, D.R.

1991-01-01

Uranium mill tailings were anaerobically incubated in the presence of H2 with Alteromonas putrefaciens, a bacterium known to couple the oxidation of H2 and organic compounds to the reduction of Fe(III) oxides. There was a direct correlation between the extent of Fe(III) reduction and the accumulation of dissolved 226Ra. In sterile tailings in which Fe(III) was not reduced, there was negligible leaching of 226Ra. The behavior of Ba was similar to that of Ra in inoculated and sterile systems. These results demonstrate that under anaerobic conditions, microbial reduction of Fe(III) may result in the release of dissolved 226Ra from uranium mill tailings. ?? 1991.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, M.J.; Callister, S.J.; Miletto, M.

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 situmore » 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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Callister, Stephen J.; Miletto, Marzia

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 situmore » 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.« less

Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slobodkin, A.; Wiegel, J.; Reysenbach, A.L.

1997-04-01

A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2.more » The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.« less

Significance of a Posttranslational Modification of the PilA Protein of Geobacter sulfurreducens for Surface Attachment, Biofilm Formation, and Growth on Insoluble Extracellular Electron Acceptors.

PubMed

Richter, Lubna V; Franks, Ashley E; Weis, Robert M; Sandler, Steven J

2017-04-15

Geobacter sulfurreducens , an anaerobic metal-reducing bacterium, possesses type IV pili. These pili are intrinsic structural elements in biofilm formation and, together with a number of c -type cytochromes, are thought to serve as conductive nanowires enabling long-range electron transfer (ET) to metal oxides and graphite anodes. Here, we report that a posttranslational modification of a nonconserved amino acid residue within the PilA protein, the structural subunit of the type IV pili, is crucial for growth on insoluble extracellular electron acceptors. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the secreted PilA protein revealed a posttranslational modification of tyrosine-32 with a moiety of a mass consistent with a glycerophosphate group. Mutating this tyrosine into a phenylalanine inhibited cell growth with Fe(III) oxides as the sole electron acceptor. In addition, this amino acid substitution severely diminished biofilm formation on graphite surfaces and impaired current output in microbial fuel cells. These results demonstrate that the capability to attach to insoluble electron acceptors plays a crucial role for the cells' ability to utilize them. The work suggests that glycerophosphate modification of Y32 is a key factor contributing to the surface charge of type IV pili, influencing the adhesion of Geobacter to specific surfaces. IMPORTANCE Type IV pili are bacterial appendages that function in cell adhesion, virulence, twitching motility, and long-range electron transfer (ET) from bacterial cells to insoluble extracellular electron acceptors. The mechanism and role of type IV pili for ET in Geobacter sulfurreducens is still a subject of research. In this study, we identified a posttranslational modification of the major G. sulfurreducens type IV pilin, suggested to be a glycerophosphate moiety. We show that a mutant in which the glycerophosphate-modified tyrosine-32 is replaced with a phenylalanine has reduced abilities for

Significance of a Posttranslational Modification of the PilA Protein of Geobacter sulfurreducens for Surface Attachment, Biofilm Formation, and Growth on Insoluble Extracellular Electron Acceptors

PubMed Central

Franks, Ashley E.; Weis, Robert M.; Sandler, Steven J.

2017-01-01

ABSTRACT Geobacter sulfurreducens, an anaerobic metal-reducing bacterium, possesses type IV pili. These pili are intrinsic structural elements in biofilm formation and, together with a number of c-type cytochromes, are thought to serve as conductive nanowires enabling long-range electron transfer (ET) to metal oxides and graphite anodes. Here, we report that a posttranslational modification of a nonconserved amino acid residue within the PilA protein, the structural subunit of the type IV pili, is crucial for growth on insoluble extracellular electron acceptors. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the secreted PilA protein revealed a posttranslational modification of tyrosine-32 with a moiety of a mass consistent with a glycerophosphate group. Mutating this tyrosine into a phenylalanine inhibited cell growth with Fe(III) oxides as the sole electron acceptor. In addition, this amino acid substitution severely diminished biofilm formation on graphite surfaces and impaired current output in microbial fuel cells. These results demonstrate that the capability to attach to insoluble electron acceptors plays a crucial role for the cells' ability to utilize them. The work suggests that glycerophosphate modification of Y32 is a key factor contributing to the surface charge of type IV pili, influencing the adhesion of Geobacter to specific surfaces. IMPORTANCE Type IV pili are bacterial appendages that function in cell adhesion, virulence, twitching motility, and long-range electron transfer (ET) from bacterial cells to insoluble extracellular electron acceptors. The mechanism and role of type IV pili for ET in Geobacter sulfurreducens is still a subject of research. In this study, we identified a posttranslational modification of the major G. sulfurreducens type IV pilin, suggested to be a glycerophosphate moiety. We show that a mutant in which the glycerophosphate-modified tyrosine-32 is replaced with a phenylalanine has reduced

Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring.

PubMed

Slepova, Tatiana V; Sokolova, Tatyana G; Kolganova, Tatyana V; Tourova, Tatyana P; Bonch-Osmolovskaya, Elizaveta A

2009-02-01

A novel anaerobic, thermophilic, Fe(III)-reducing, CO-utilizing bacterium, strain 1315(T), was isolated from a hot spring of Geyser Valley on the Kamchatka Peninsula. Cells of the new isolate were Gram-positive, short rods. Growth was observed at 52-70 degrees C, with an optimum at 65 degrees C, and at pH 5.5-8.5, with an optimum at pH 6.5-7.2. In the presence of Fe(III) or 9,10-anthraquinone 2,6-disulfonate (AQDS), the bacterium was capable of growth with CO and yeast extract (0.2 g l(-1)); during growth under these conditions, strain 1315(T) produced H(2) and CO(2) and Fe(II) or AQDSH(2), respectively. Strain 1315(T) also grew by oxidation of yeast extract, glucose, xylose or lactate under a N(2) atmosphere, reducing Fe(III) or AQDS. Yeast extract (0.2 g l(-1)) was required for growth. Isolate 1315(T) grew exclusively with Fe(III) or AQDS as an electron acceptor. The generation time under optimal conditions with CO as growth substrate was 9.3 h. The G+C content of the DNA was 41.5+/-0.5 mol%. 16S rRNA gene sequence analysis placed the organism in the genus Carboxydothermus (97.8 % similarity with the closest relative). On the basis of physiological features and phylogenetic analysis, it is proposed that strain 1315(T) should be assigned to a novel species, Carboxydothermus siderophilus sp. nov., with the type strain 1315(T) (=VKPM 9905B(T) =VKM B-2474(T) =DSM 21278(T)).

Arsenic Detoxification by Geobacter Species.

PubMed

Dang, Yan; Walker, David J F; Vautour, Kaitlin E; Dixon, Steven; Holmes, Dawn E

2017-02-15

Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found

Arsenic Detoxification by Geobacter Species

PubMed Central

Walker, David J. F.; Vautour, Kaitlin E.; Dixon, Steven

2016-01-01

ABSTRACT Insight into the mechanisms for arsenic detoxification by Geobacter species is expected to improve the understanding of global cycling of arsenic in iron-rich subsurface sedimentary environments. Analysis of 14 different Geobacter genomes showed that all of these species have genes coding for an arsenic detoxification system (ars operon), and several have genes required for arsenic respiration (arr operon) and methylation (arsM). Genes encoding four arsenic repressor-like proteins were detected in the genome of G. sulfurreducens; however, only one (ArsR1) regulated transcription of the ars operon. Elimination of arsR1 from the G. sulfurreducens chromosome resulted in enhanced transcription of genes coding for the arsenic efflux pump (Acr3) and arsenate reductase (ArsC). When the gene coding for Acr3 was deleted, cells were not able to grow in the presence of either the oxidized or reduced form of arsenic, while arsC deletion mutants could grow in the presence of arsenite but not arsenate. These studies shed light on how Geobacter influences arsenic mobility in anoxic sediments and may help us develop methods to remediate arsenic contamination in the subsurface. IMPORTANCE This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different

Thermodynamic Versus Surface Area Control of Microbial Fe(III) Oxide Reduction Kinetics

NASA Astrophysics Data System (ADS)

Roden, E. E.

2003-12-01

Recent experimental studies of synthetic and natural Fe(III) oxide reduction permit development of conceptual and quantitative models of enzymatic Fe(III) oxide reduction at circumneutral pH that can be compared to and contrasted with established models of abiotic mineral dissolution. The findings collectively support a model for controls on enzymatic reduction that differs fundamentally from those applied to abiotic reductive dissolution as a result of two basic phenomena: (1) the relatively minor influence of oxide mineralogical and thermodynamic properties on surface area-normalized rates of enzymatic reduction compared to abiotic reductive dissolution; and (2) the major limitation which sorption and/or surface precipitation of biogenic Fe(II) on residual oxide and Fe(III)-reducing bacterial cell surfaces poses to enzymatic electron transfer in the presence of excess electron donor. Parallel studies with two major Fe(III)-reducing bacteria genera (Shewanella and Geobacter) lead to common conclusions regarding the importance of these phenomena in regulating the rate and long-term extent of Fe(III) oxide reduction. Although the extent to which these phenomena can be traced to underlying kinetic vs. thermodynamic effects cannot be resolved with current information, models in which rates of enzymatic reduction are limited kinetically by the abundance of "available" oxide surface sites (as controlled by oxide surface area and the abundance of surface-bound Fe(II)) provide an adequate macroscopic description of controls on the initial rate and long-term extent of oxide reduction. In some instances, thermodynamic limitation posed by the accumulation of aqueous reaction end-products (i.e. Fe(II) and alkalinity) must also be invoked to explain observed long-term patterns of reduction. In addition, the abundance of Fe(III)-reducing microorganisms plays an important role in governing rates of reduction and needs to be considered in models of Fe(III) reduction in nonsteady

Cd Mobility in Anoxic Fe-Mineral-Rich Environments - Potential Use of Fe(III)-Reducing Bacteria in Soil Remediation

NASA Astrophysics Data System (ADS)

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

Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances.

PubMed

Dantas, Joana M; Ferreira, Marisa R; Catarino, Teresa; Kokhan, Oleksandr; Raj Pokkuluri, P; Salgueiro, Carlos A

2018-05-16

The bacterium Geobacter sulfurreducens can transfer electrons to the quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH 2 QDS) can also be used as energy source G. sulfurreducens. Such bi-directional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bi-functional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH 2 QDS. Using stopped-flow measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same bi-functional behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13 C, 15 N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1 H heme methyl group signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex with AQDS through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens. Copyright © 2018. Published by Elsevier B.V.

Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

NASA Astrophysics Data System (ADS)

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joyner, Dominique; Fortney, Julian; Chakraborty, Romy

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 reducingmore » 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

Identification of an Extracellular Polysaccharide Network Essential for Cytochrome Anchoring and Biofilm Formation in Geobacter sulfurreducens▿ †

PubMed Central

Rollefson, Janet B.; Stephen, Camille S.; Tien, Ming; Bond, Daniel R.

2011-01-01

Transposon insertions in Geobacter sulfurreducens GSU1501, part of an ATP-dependent exporter within an operon of polysaccharide biosynthesis genes, were previously shown to eliminate insoluble Fe(III) reduction and use of an electrode as an electron acceptor. Replacement of GSU1501 with a kanamycin resistance cassette produced a similarly defective mutant, which could be partially complemented by expression of GSU1500 to GSU1505 in trans. The Δ1501 mutant demonstrated limited cell-cell agglutination, enhanced attachment to negatively charged surfaces, and poor attachment to positively charged poly-d-lysine- or Fe(III)-coated surfaces. Wild-type and mutant cells attached to graphite electrodes, but when electrodes were poised at an oxidizing potential inducing a positive surface charge (+0.24 V versus the standard hydrogen electrode [SHE]), Δ1501 mutant cells detached. Scanning electron microscopy revealed fibrils surrounding wild-type G. sulfurreducens which were absent from the Δ1501 mutant. Similar amounts of type IV pili and pilus-associated cytochromes were detected on both cell types, but shearing released a stable matrix of c-type cytochromes and other proteins bound to polysaccharides. The matrix from the mutant contained 60% less sugar and was nearly devoid of c-type cytochromes such as OmcZ. The addition of wild-type extracellular matrix to Δ1501 cultures restored agglutination and Fe(III) reduction. The polysaccharide binding dye Congo red preferentially bound wild-type cells and extracellular matrix material over mutant cells, and Congo red inhibited agglutination and Fe(III) reduction by wild-type cells. These results demonstrate a crucial role for the xap (extracellular anchoring polysaccharide) locus in metal oxide attachment, cell-cell agglutination, and localization of essential cytochromes beyond the Geobacter outer membrane. PMID:21169487

Biological reduction of uranium coupled with oxidation of ammonium by Acidimicrobiaceae bacterium A6 under iron reducing conditions.

PubMed

Gilson, Emily R; Huang, Shan; Jaffé, Peter R

2015-11-01

This study investigated the possibility of links between the biological immobilization of uranium (U) and ammonium oxidation under iron (Fe) reducing conditions. The recently-identified Acidimicrobiaceae bacterium A6 (ATCC, PTA-122488) derives energy from ammonium oxidation coupled with Fe reduction. This bacterium has been found in various soil and wetland environments, including U-contaminated wetland sediments. Incubations of Acidimicrobiaceae bacteria A6 with nontronite, an Fe(III)-rich clay, and approximately 10 µM U indicate that these bacteria can use U(VI) in addition to Fe(III) as an electron acceptor in the presence of ammonium. Measurements of Fe(II) production and ammonium oxidation support this interpretation. Concentrations of approximately 100 µM U were found to entirely inhibit Acidimicrobiaceae bacteria A6 activity. These results suggest that natural sites of active ammonium oxidation under Fe reducing conditions by Acidimicrobiaceae bacteria A6 could be hotspots of U immobilization by bioreduction. This is the first report of biological U reduction that is not coupled to carbon oxidation.

Effect of the oxidation rate and Fe(II) state on microbial nitrate-dependent Fe(III) mineral formation

USGS Publications Warehouse

Senko, John M.; Dewers , Thomas A.; Krumholz, Lee R.

2005-01-01

A nitrate-dependent Fe(II)-oxidizing bacterium was isolated and used to evaluate whether Fe(II) chemical form or oxidation rate had an effect on the mineralogy of biogenic Fe(III) (hydr)oxides resulting from nitrate-dependent Fe(II) oxidation. The isolate (designated FW33AN) had 99% 16S rRNA sequence similarity to Klebsiella oxytoca. FW33AN produced Fe(III) (hydr)oxides by oxidation of soluble Fe(II) [Fe(II)sol] or FeS under nitrate-reducing conditions. Based on X-ray diffraction (XRD) analysis, Fe(III) (hydr)oxide produced by oxidation of FeS was shown to be amorphous, while oxidation of Fe(II)sol yielded goethite. The rate of Fe(II) oxidation was then manipulated by incubating various cell concentrations of FW33AN with Fe(II)sol and nitrate. Characterization of products revealed that as Fe(II) oxidation rates slowed, a stronger goethite signal was observed by XRD and a larger proportion of Fe(III) was in the crystalline fraction. Since the mineralogy of Fe(III) (hydr)oxides may control the extent of subsequent Fe(III) reduction, the variables we identify here may have an effect on the biogeochemical cycling of Fe in anoxic ecosystems.

Biodegradation of organic matter and anodic microbial communities analysis in sediment microbial fuel cells with/without Fe(III) oxide addition.

PubMed

Xu, Xun; Zhao, Qingliang; Wu, Mingsong; Ding, Jing; Zhang, Weixian

2017-02-01

To enhance the biodegradation of organic matter in sediment microbial fuel cell (SMFC), Fe(III) oxide, as an alternative electron acceptor, was added into the sediment. Results showed that the SMFC with Fe(III) oxide addition obtained higher removal efficiencies for organics than the SMFC without Fe(III) oxide addition and open circuit bioreactor, and produced a maximum power density (P max ) of 87.85mW/m 2 with a corresponding maximum voltage (V max ) of 0.664V. The alteration of UV-254 and specific ultraviolet absorbance (SUVA) also demonstrated the organic matter in sediments can be effectively removed. High-throughput sequencing of anodic microbial communities indicated that bacteria from the genus Geobacter were predominantly detected (21.23%) in the biofilm formed on the anode of SMFCs, while Pseudomonas was the most predominant genus (18.12%) in the presence of Fe(III) oxide. Additionally, compared with the open circuit bioreactor, more electrogenic bacteria attached to the biofilm of anode in SMFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chan, Chi Ho; Levar, Caleb E.; Zacharoff, Lori

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 flagellarmore » 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 Δ imcH 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. Lastly, these tools will enable more sophisticated genetic studies in G. sulfurreducens without polar insertion effects or need for multiple antibiotics.« less

Isolation and Characterization of Microbes Mediating Thermodynamically Favorable Coupling of Anaerobic Oxidation of Methane and Metal Reduction

NASA Astrophysics Data System (ADS)

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

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

PubMed Central

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

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

PubMed Central

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

The life cycle of iron Fe(III) oxide: impact of fungi and bacteria

NASA Astrophysics Data System (ADS)

Bonneville, Steeve

2014-05-01

properties, in particular the influence of solubility, in the kinetics of microbial iron reduction. We used the facultative anaerobic gram-positive bacterium Shewanella putrefaciens as model iron reducing bacterium, with several ferrihydrite, hematite, goethite or lepidocrocite as electron acceptor, and lactate as electron donor. Maximum microbial Fe(III) reduction rates and solubility of Fe(III) phases were found to positively correlated in a Linear Free Energy Relationship suggesting a rate limitation by the electron transfer between iron reductases and a Fe(III) center, or by the subsequent desorption of Fe2+ from the iron oxide mineral surface.

Fe(III) oxides accelerate microbial nitrate reduction and electricity generation by Klebsiella pneumoniae L17.

PubMed

Liu, Tongxu; Li, Xiaomin; Zhang, Wei; Hu, Min; Li, Fangbai

2014-06-01

Klebsiella pneumoniae L17 is a fermentative bacterium that can reduce iron oxide and generate electricity under anoxic conditions, as previously reported. This study reveals that K. pneumoniae L17 is also capable of dissimilatory nitrate reduction, producing NO2(-), NH4(+), NO and N2O under anoxic conditions. The presence of Fe(III) oxides (i.e., α-FeOOH, γ-FeOOH, α-Fe2O3 and γ-Fe2O3) significantly accelerates the reduction of nitrate and generation of electricity by K. pneumoniae L17, which is similar to a previous report regarding another fermentative bacterium, Bacillus. No significant nitrate reduction was observed upon treatment with Fe(2+) or α-FeOOH+Fe(2+), but a slight facilitation of nitrate reduction and electricity generation was observed upon treatment with L17+Fe(2+). This result suggests that aqueous Fe(II) or mineral-adsorbed Fe(II) cannot reduce nitrate abiotically but that L17 can catalyze the reduction of nitrate and generation of electricity in the presence of Fe(II) (which might exist as cell surface-bound Fe(II)). To rule out the potential effect of Fe(II) produced by L17 during microbial iron reduction, treatments with the addition of TiO2 or Al2O3 instead of Fe(III) oxides also exhibited accelerated microbial nitrate reduction and electricity generation, indicating that cell-mineral sorption did account for the acceleration effect. However, the acceleration caused by Fe(III) oxides is only partially attributed to the cell surface-bound Fe(II) and cell-mineral sorption but may be driven by the iron oxide conduction band-mediated electron transfer from L17 to nitrate or an electrode, as proposed previously. The current study extends the diversity of bacteria of which nitrate reduction and electricity generation can be facilitated by the presence of iron oxides and confirms the positive role of Fe(III) oxides on microbial nitrate reduction and electricity generation by particular fermentative bacteria in anoxic environments. Copyright �

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation

PubMed Central

Yun, Jiae; Malvankar, Nikhil S; Ueki, Toshiyuki; Lovley, Derek R

2016-01-01

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. PMID:26140532

Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

PubMed

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.

Orenia metallireducens sp. nov. strain Z6, a Novel Metal-reducing [member of the Phylum] Firmicute from the Deep Subsurface

DOE PAGES

Dong, Yiran; Sanford, Robert A.; Boyanov, Maxim I.; ...

2016-08-26

A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain 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 with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H 2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 60°C).more » At pH 6.5, strain Z6 also reduced more crystalline iron oxides, such as lepidocrocite (γ-FeOOH), goethite (α-FeOOH), and hematite (α-Fe 2O 3). 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 [Fe 3(PO 4) 2] and siderite (FeCO 3). 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-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. In conclusion, these distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov.« less

Orenia metallireducens sp. nov. Strain Z6, a Novel Metal-Reducing Member of the Phylum Firmicutes from the Deep Subsurface

PubMed Central

Sanford, Robert A.; Boyanov, Maxim I.; Kemner, Kenneth 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.

2016-01-01

ABSTRACT A novel halophilic and metal-reducing bacterium, Orenia metallireducens strain 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 with Orenia marismortui but demonstrated physiological properties previously unknown for this genus. In addition to exhibiting a fermentative metabolism typical of the genus Orenia, strain Z6 reduces various metal oxides [Fe(III), Mn(IV), Co(III), and Cr(VI)], using H2 as the electron donor. Strain Z6 actively reduced ferrihydrite over broad ranges of pH (6 to 9.6), salinity (0.4 to 3.5 M NaCl), and temperature (20 to 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-reducing Shewanella and Geobacter species, this organism lacks the c-type cytochromes for typical Fe(III) reduction. Strain Z6 represents the first bacterial species in the genus Orenia (order Halanaerobiales) reported to reduce ferric iron minerals and other metal oxides. This microbe expands both the phylogenetic and physiological scopes of iron-reducing microorganisms known to inhabit the deep subsurface and suggests new mechanisms for microbial iron reduction. These distinctions from other Orenia spp. support the designation of strain Z6 as a new species, Orenia metallireducens sp. nov. IMPORTANCE A novel iron-reducing species, Orenia metallireducens sp. nov., strain Z6, was isolated from groundwater collected from a geological formation located 2.02 km below land surface in the Illinois Basin, USA

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

REGUERA, GEMMA

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 biofilmsmore » 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.« less

Enzymatic versus nonenzymatic mechanisms for Fe(III) reduction in aquatic sediments

USGS Publications Warehouse

Lovley, D.R.; Phillips, E.J.P.; Lonergan, D.J.

1991-01-01

The potential for nonenzymatic reduction of Fe(III) either by organic compounds or by the development of a low redox potential during microbial metabolism was compared with direct, enzymatic Fe(III) reduction by Fe(III)-reducing microorganisms. At circumneutral pH, very few organic compounds nonenzymatically reduced Fe(III). In contrast, in the presence of the appropriate Fe(IH)-reducing microorganisms, most of the organic compounds examined could be completely oxidized to carbon dioxide with the reduction of Fe(III). Even for those organic compounds that could nonenzymatically reduce Fe(III), microbial Fe(III) reduction was much more extensive. The development of a low redox potential during microbial fermentation did not result in nonenzymatic Fe(III) reduction. Model organic compounds were readily oxidized in Fe(III)-reducing aquifer sediments, but not in sterilized sediments. These results suggest that microorganisms enzymatically catalyze most of the Fe(III) reduction in the Fe(III) reduction zone of aquatic sediments and aquifers.

Microbiological and Geochemical Evidence of Fe(III) Reduction in the Rhizosphere (Root-Zone) of Wetland Plants

NASA Astrophysics Data System (ADS)

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

2002-05-01

We have found that the Fe-oxide deposits (Fe-plaque) on wetland plant roots contain abundant microbes including Fe(II)-oxidizing bacteria (FeOB) (Appl. Environ. Microbiol. 1999, 65:2758-2761). In the current study, we investigated the potential for root Fe-plaque to serve as a substrate for Fe(III)-reducing bacteria (FeRB) and compared rates of Fe reduction between plaque and bulk soil. In a study at six wetland habitats located in the Mid-Atlantic region, abundances of FeRB in the rhizosphere of Typha spp. and the bulk soil were enumerated using the most probable number technique. In the rhizosphere, FeRB accounted for an average of 12% of the total cell number while in the soil they accounted for <1% of the total bacteria. We subsequently performed a sequential chemical extraction on both roots and soil to determine if FeRB abundances were driven by differences in the reducibility of Fe(III) in each environment. The roots contained a significantly higher percentage of amorphous Fe (77.4%; p<0.05 n=5 wetlands) than the bulk soil (33.8%); conversely, the soil also had significantly higher amounts of crystalline Fe (41.1%, p<0.05, n=5 wetlands) than the roots (8.1%). A significant correlation was observed between the percentage of amorphous Fe and the percentage of FeRB (r2=0.583; p<0.05). Since amorphous Fe is more readily reduced by microbes than crystalline Fe, these results suggested that the roots provide a good substrate for iron-reducing bacteria. To determine how differences in reducible Fe(III) might limit Fe reduction potential, we performed 12-day anaerobic incubations of roots and soil with Geobacter metallireducans, a common FeRB isolated from aquatic environments. Although Fe(III) reduction rates peaked at between 48 and 72 hours in both the roots and soils, the total amount of Fe(II) production in the root samples was significantly higher than that in the soil samples (350 μ moles g dry weight-1 vs. 153 μ moles g dry weight-1; p<0.05). All of these

Genomic analyses of bacterial porin-cytochrome gene clusters

DOE PAGES

Shi, Liang; Fredrickson, James K.; Zachara, John M.

2014-11-26

In this study, 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 bacteriamore » 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.« less

Comparative proteomic analysis of Desulfotomaculum reducens MI-1: Insights into the metabolic versatility of a gram-positive sulfate- and metal-reducing bacterium

DOE PAGES

Otwell, Anne E.; Callister, Stephen J.; Zink, Erika M.; ...

2016-02-19

In this study, the proteomes of the metabolically versatile and poorly characterized Gram-positive bacterium Desulfotomaculum reducens MI-1 were compared across four cultivation conditions including sulfate reduction, soluble Fe(III) reduction, insoluble Fe(III) reduction, and pyruvate fermentation. Collectively across conditions, we observed at high confidence ~38% of genome-encoded proteins. Here, we focus on proteins that display significant differential abundance on conditions tested. To the best of our knowledge, this is the first full-proteome study focused on a Gram-positive organism cultivated either on sulfate or metal-reducing conditions. Several proteins with uncharacterized function encoded within heterodisulfide reductase ( hdr)-containing loci were upregulated on eithermore » sulfate (Dred_0633-4, Dred_0689-90, and Dred_1325-30) or Fe(III)-citrate-reducing conditions (Dred_0432-3 and Dred_1778-84). Two of these hdr-containing loci display homology to recently described flavin-based electron bifurcation (FBEB) pathways (Dred_1325-30 and Dred_1778-84). Additionally, we propose that a cluster of proteins, which is homologous to a described FBEB lactate dehydrogenase (LDH) complex, is performing lactate oxidation in D. reducens (Dred_0367-9). Analysis of the putative sulfate reduction machinery in D. reducens revealed that most of these proteins are constitutively expressed across cultivation conditions tested. In addition, peptides from the single multiheme c-type cytochrome (MHC) in the genome were exclusively observed on the insoluble Fe(III) condition, suggesting that this MHC may play a role in reduction of insoluble metals.« less

Comparative proteomic analysis of Desulfotomaculum reducens MI-1: Insights into the metabolic versatility of a gram-positive sulfate- and metal-reducing bacterium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Otwell, Anne E.; Callister, Stephen J.; Zink, Erika M.

In this study, the proteomes of the metabolically versatile and poorly characterized Gram-positive bacterium Desulfotomaculum reducens MI-1 were compared across four cultivation conditions including sulfate reduction, soluble Fe(III) reduction, insoluble Fe(III) reduction, and pyruvate fermentation. Collectively across conditions, we observed at high confidence ~38% of genome-encoded proteins. Here, we focus on proteins that display significant differential abundance on conditions tested. To the best of our knowledge, this is the first full-proteome study focused on a Gram-positive organism cultivated either on sulfate or metal-reducing conditions. Several proteins with uncharacterized function encoded within heterodisulfide reductase ( hdr)-containing loci were upregulated on eithermore » sulfate (Dred_0633-4, Dred_0689-90, and Dred_1325-30) or Fe(III)-citrate-reducing conditions (Dred_0432-3 and Dred_1778-84). Two of these hdr-containing loci display homology to recently described flavin-based electron bifurcation (FBEB) pathways (Dred_1325-30 and Dred_1778-84). Additionally, we propose that a cluster of proteins, which is homologous to a described FBEB lactate dehydrogenase (LDH) complex, is performing lactate oxidation in D. reducens (Dred_0367-9). Analysis of the putative sulfate reduction machinery in D. reducens revealed that most of these proteins are constitutively expressed across cultivation conditions tested. In addition, peptides from the single multiheme c-type cytochrome (MHC) in the genome were exclusively observed on the insoluble Fe(III) condition, suggesting that this MHC may play a role in reduction of insoluble metals.« less

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem.

PubMed

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.

Production of gold nanoparticles by electrode-respiring Geobacter sulfurreducens biofilms

PubMed Central

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

2017-01-01

The goal of this work was to synthesize gold nanoparticles (AuNPs) using electrode-respiring Geobacter sulfurreducens biofilms. We found that AuNPs are generated in the extracellular matrix of Geobacter biofilms and have 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 reduce Au3+ to AuNPs. From FTIR spectra, it appears that reduced sugars were involved in the bioreduction and synthesis of AuNPs and that amine groups acted as the major biomolecules involved in binding. PMID:27866628

Dissimilatory Fe(III) and Mn(IV) reduction.

PubMed Central

Lovley, D R

1991-01-01

The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater. This process, which may have been the first globally significant mechanism for the oxidation of organic matter to carbon dioxide, plays an important role in the oxidation of natural and contaminant organic compounds in a variety of environments and contributes to other phenomena of widespread significance such as the release of metals and nutrients into water supplies, the magnetization of sediments, and the corrosion of metal. Until recently, much of the Fe(III) and Mn(IV) reduction in sedimentary environments was considered to be the result of nonenzymatic processes. However, microorganisms which can effectively couple the oxidation of organic compounds to the reduction of Fe(III) or Mn(IV) have recently been discovered. With Fe(III) or Mn(IV) as the sole electron acceptor, these organisms can completely oxidize fatty acids, hydrogen, or a variety of monoaromatic compounds. This metabolism provides energy to support growth. Sugars and amino acids can be completely oxidized by the cooperative activity of fermentative microorganisms and hydrogen- and fatty-acid-oxidizing Fe(III) and Mn(IV) reducers. This provides a microbial mechanism for the oxidation of the complex assemblage of sedimentary organic matter in Fe(III)- or Mn(IV)-reducing environments. The available evidence indicates that this enzymatic reduction of Fe(III) or Mn(IV) accounts for most of the oxidation of organic matter coupled to reduction of Fe(III) and Mn(IV) in sedimentary environments. Little is known about the diversity and ecology of the microorganisms responsible for Fe(III) and Mn(IV) reduction, and only preliminary studies have been conducted on the physiology and biochemistry of this process. PMID:1886521

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

PubMed Central

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

2015-01-01

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 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. PMID:25083935

Vertical distribution of Fe and Fe(III)-reducing bacteria in the sediments of Lake Donghu, China.

PubMed

Tian, Cuicui; Wang, Chunbo; Tian, Yingying; Wu, Xingqiang; Xiao, Bangding

2015-08-01

In lake sediments, iron (Fe) is the most versatile element, and the redox cycling of Fe has a wide influence on the biogeochemical cycling of organic and inorganic substances. The aim of the present study was to analyze the vertical distribution of Fe and Fe(III)-reducing bacteria (FeRB) in the surface sediment (30 cm) of Lake Donghu, China. At the 3 sites we surveyed, FeRB and Fe(II)-oxidizing bacteria (FeOB) coexisted in anoxic sediments. Geobacter-related FeRB accounted for 5%-31% of the total Bacteria, while Gallionella-related FeOB accounted for only 0.1%-1.3%. A significant correlation between the relative abundance of poorly crystalline Fe and Geobacter spp. suggested that poorly crystalline Fe favored microbial Fe(III) reduction. Poorly crystalline Fe and Geobacter spp. were significantly associated with solid-phase Fe(II) and total inorganic phosphorus levels. Pore water Fe(II) concentrations negatively correlated with NO3(-) at all sites. We concluded that Geobacter spp. were abundant in the sediments of Lake Donghu, and the redox of Fe might participate in the cycling of nitrogen and phosphorus in sediments. These observations provided insight into the roles of microbial Fe cycling in lake sediments.

Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium

PubMed Central

Hong, Kar Wai; Thinagaran, Dinaiz a/l; Gan, Han Ming; Yin, Wai-Fong

2012-01-01

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome. PMID:23115161

Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium.

PubMed

Hong, Kar Wai; Thinagaran, Dinaiz al; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2012-11-01

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine.

PubMed

Bao, Yanping; Guo, Chuling; Lu, Guining; Yi, Xiaoyun; Wang, Han; Dang, Zhi

2018-03-01

Fe(III) hydroxysulfate minerals are secondary minerals commonly found in acid mine drainage (AMD) sites and have a major impact on water and soil quality in these environments. While previous studies showed that the Fe(III) hydroxysulfate mineral transformation could be mediated by some bacterial strains under laboratory conditions, the role of indigenous microbial activity in Fe(III) hydroxysulfate mineral transformation in natural environment has received little attention. In this study, microcosms were constructed with AMD-affected river water and sediment from the Dabaoshan Mine that was either left unamended or enriched with nutrients (lactate, nitrogen, and phosphorus (LNP)) and biosynthetic minerals (schwertmannite or jarosite). The results show that microbial activity played a decisive role in the mineralogical transformation of schwertmannite/jarosite in the AMD-contaminated site when organic carbon was available. The accumulation of Fe(II) and sulfide in microcosms amended with LNP indicates that schwertmannite/jarosite transformation is mediated by microbial reduction. XRD, SEM and FTIR analyses suggest that schwertmannite was completely transformed to goethite in the Sch-LNP microcosms at the end of their incubation. Jarosite in the Jar-LNP microcosms was also transformed to goethite, but at a much slower rate than schwertmannite. Bacterial community analysis reveals that the stimulated indigenous bacteria promote the mineralogical transformation of schwertmannite/jarosite. Most of these bacteria, including Geobacter, Desulfosporosinus, Geothrix, Desulfurispora, Desulfovibrio, and Anaeromyxobacter, are known to reduce iron and/or sulfate. The mineralogical transformation of schwertmannite and jarosite exerts significant control on the geochemistry of AMD-contaminated systems. Copyright © 2018 Elsevier B.V. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aklujkar, Muktak; Krushkal, Julia; DiBartolo, Genevieve

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 recentlymore » 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

Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luef, Birgit; Fakra, Sirine C.; Csencsits, Roseann

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 sitemore » 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.« less

Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium

USGS Publications Warehouse

Liu, D.; Dong, H.; Bishop, M.E.; Zhang, Jiahua; Wang, Hongfang; Xie, S.; Wang, Shaoming; Huang, L.; Eberl, D.D.

2012-01-01

Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals. ?? 2011 Blackwell Publishing Ltd.

Rapid electron exchange between surface-exposed bacterial cytochromes and Fe(III) minerals

PubMed Central

White, Gaye F.; Shi, Zhi; Shi, Liang; Wang, Zheming; Dohnalkova, Alice C.; Marshall, Matthew J.; Fredrickson, James K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas A.

2013-01-01

The mineral-respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes, MtrC and MtrA, brought together inside a transmembrane porin, MtrB, to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system containing a pool of internalized electron carriers was used to investigate how the topology of the MtrCAB complex relates to its ability to transport electrons across a lipid bilayer to externally located Fe(III) oxides. With MtrA facing the interior and MtrC exposed on the outer surface of the phospholipid bilayer, the established in vivo orientation, electron transfer from the interior electron carrier pool through MtrCAB to solid-phase Fe(III) oxides was demonstrated. The rates were 103 times higher than those reported for reduction of goethite, hematite, and lepidocrocite by S. oneidensis, and the order of the reaction rates was consistent with those observed in S. oneidensis cultures. In contrast, established rates for single turnover reactions between purified MtrC and Fe(III) oxides were 103 times lower. By providing a continuous flow of electrons, the proteoliposome experiments demonstrate that conduction through MtrCAB directly to Fe(III) oxides is sufficient to support in vivo, anaerobic, solid-phase iron respiration. PMID:23538304

Microbial reduction of structural iron in interstratified illite-smectite minerals by a sulfate-reducing bacterium.

PubMed

Liu, D; Dong, H; Bishop, M E; Zhang, J; Wang, H; Xie, S; Wang, S; Huang, L; Eberl, D D

2012-03-01

Clay minerals are ubiquitous in soils, sediments, and sedimentary rocks and could coexist with sulfate-reducing bacteria (SRB) in anoxic environments, however, the interactions of clay minerals and SRB are not well understood. The objective of this study was to understand the reduction rate and capacity of structural Fe(III) in dioctahedral clay minerals by a mesophilic SRB, Desulfovibrio vulgaris and the potential role in catalyzing smectite illitization. Bioreduction experiments were performed in batch systems, where four different clay minerals (nontronite NAu-2, mixed-layer illite-smectite RAr-1 and ISCz-1, and illite IMt-1) were exposed to D. vulgaris in a non-growth medium with and without anthraquinone-2,6-disulfonate (AQDS) and sulfate. Our results demonstrated that D. vulgaris was able to reduce structural Fe(III) in these clay minerals, and AQDS enhanced the reduction rate and extent. In the presence of AQDS, sulfate had little effect on Fe(III) bioreduction. In the absence of AQDS, sulfate increased the reduction rate and capacity, suggesting that sulfide produced during sulfate reduction reacted with the phyllosilicate Fe(III). The extent of bioreduction of structural Fe(III) in the clay minerals was positively correlated with the percentage of smectite and mineral surface area of these minerals. X-ray diffraction, and scanning and transmission electron microscopy results confirmed formation of illite after bioreduction. These data collectively showed that D. vulgaris could promote smectite illitization through reduction of structural Fe(III) in clay minerals. © 2011 Blackwell Publishing Ltd.

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

USGS Publications Warehouse

Holmes, Dawn E.; O'Neil, Regina A.; Vrionis, Helen A.; N'Guessan, Lucie A.; Ortiz-Bernad, Irene; Larrahondo, Maria J.; Adams, Lorrie A.; Ward, Joy A.; Nicoll , Julie S.; Nevin, Kelly P.; Chavan, Milind A.; Johnson, Jessica P.; Long, Philip E.; Lovely, Derek R.

2007-01-01

There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.

A hydrogen-oxidizing, Fe(III)-reducing microorganism from the Great Bay estuary, New Hampshire

USGS Publications Warehouse

Caccavo, F.; Blakemore, R.P.; Lovley, D.R.

1992-01-01

A dissimilatory Fe(III)- and Mn(IV)-reducing bacterium was isolated from bottom sediments of the Great Bay estuary, New Hampshire. The isolate was a facultatively anaerobic gram-negative rod which did not appear to fit into any previously described genus. It was temporarily designated strain BrY. BrY grew anaerobically in a defined medium with hydrogen or lactate as the electron donor and Fe(III) as the electron acceptor. BrY required citrate, fumarate, or malate as a carbon source for growth on H2 and Fe(III). With Fe(III) as the sole electron acceptor, BrY metabolized hydrogen to a minimum threshold at least 60-fold lower than the threshold reported for pure cultures of sulfate reducers. This finding supports the hypothesis that when Fe(III) is available, Fe(III) reducers can outcompete sulfate reducers for electron donors. Lactate was incompletely oxidized to acetate and carbon dioxide with Fe(III) as the electron acceptor. Lactate oxidation was also coupled to the reduction of Mn(IV), U(VI), fumarate, thiosulfate, or trimethylamine n-oxide under anaerobic conditions. BrY provides a model for how enzymatic metal reduction by respiratory metal-reducing microorganisms has the potential to contribute to the mobilization of iron and trace metals and to the immobilization of uranium in sediments of Great Bay Estuary.

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

PubMed

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.

Two Isoforms of Geobacter sulfurreducens PilA Have Distinct Roles in Pilus Biogenesis, Cytochrome Localization, Extracellular Electron Transfer, and Biofilm Formation

PubMed Central

Richter, Lubna V.; Sandler, Steven J.

2012-01-01

Type IV pili of Geobacter sulfurreducens are composed of PilA monomers and are essential for long-range extracellular electron transfer to insoluble Fe(III) oxides and graphite anodes. A previous analysis of pilA expression indicated that transcription was initiated at two positions, with two predicted ribosome-binding sites and translation start codons, potentially producing two PilA preprotein isoforms. The present study supports the existence of two functional translation start codons for pilA and identifies two isoforms (short and long) of the PilA preprotein. The short PilA isoform is found predominantly in an intracellular fraction. It seems to stabilize the long isoform and to influence the secretion of several outer-surface c-type cytochromes. The long PilA isoform is required for secretion of PilA to the outer cell surface, a process that requires coexpression of pilA with nine downstream genes. The long isoform was determined to be essential for biofilm formation on certain surfaces, for optimum current production in microbial fuel cells, and for growth on insoluble Fe(III) oxides. PMID:22408162

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

PubMed Central

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

2011-01-01

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. PMID:20668487

Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface

USGS Publications Warehouse

Lovely, Derek R.; Anderson, Robert T.

2000-01-01

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.

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

USGS Publications Warehouse

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.

Novel processes for anaerobic sulfate production from elemental sulfur by sulfate-reducing bacteria

USGS Publications Warehouse

Lovley, D.R.; Phillips, E.J.P.

1994-01-01

Sulfate reducers and related organisms which had previously been found to reduce Fe(III) with H2 or organic electron donors oxidized S0 to sulfate when Mn(IV) was provided as an electron acceptor. Organisms catalyzing this reaction in washed cell suspensions included Desulfovibrio desulfuricans, Desulfomicrobium baculatum. Desulfobacterium autotrophicum, Desulfuromonas acetoxidans, and Geobacter metallireducens. These organisms produced little or no sulfate from S0 with Fe(III) as a potential electron acceptor or in the absence of an electron acceptor. In detailed studies with Desulfovibrio desulfuricans, the stoichiometry of sulfate and Mn(II) production was consistent with the reaction S0 + 3 MnO2 + 4H+ ???SO42- + 3Mn(II) + 2H2O. None of the organisms evaluated could be grown with S0 as the sole electron donor and Mn(IV) as the electron acceptor. In contrast to the other sulfate reducers evaluated, Desulfobulbus propionicus produced sulfate from S0 in the absence of an electron acceptor and Fe(III) oxide stimulated sulfate production. Sulfide also accumulated in the absence of Mn(IV) or Fe(III). The stoichiometry of sulfate and sulfide production indicated that Desulfobulbus propionicus disproportionates S0 as follows: 4S0 + 4H2O???SO42- + 3HS- + 5 H+. Growth of Desulfobulbus propionicus with S0 as the electron donor and Fe(III) as a sulfide sink and/or electron acceptor was very slow. The S0 oxidation coupled to Mn(IV) reduction described here provides a potential explanation for the Mn(IV)-dependent sulfate production that previous studies have observed in anoxic marine sediments. Desulfobulbus propionicus is the first example of a pure culture known to disproportionate S0.

Carboxydocella manganica sp. nov., a thermophilic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium from a Kamchatka hot spring.

PubMed

Slobodkina, G B; Panteleeva, A N; Sokolova, T G; Bonch-Osmolovskaya, E A; Slobodkin, A I

2012-04-01

A thermophilic, anaerobic, dissimilatory Mn(IV)- and Fe(III)-reducing bacterium (strain SLM 61T) was isolated from a terrestrial hot spring on the Kamchatka peninsula. The cells were straight rods, 0.5-0.6 µm in diameter and 1.0-6.0 µm long, and exhibited tumbling motility by means of peritrichous flagellation. The strain grew at 26-70 °C, with an optimum at 58-60 °C, and at pH 5.5-8.0, with an optimum at pH 6.5. Growth of SLM 61T was observed at 0-2.0 % (w/v) NaCl, with an optimum at 0.5 % (w/v). The generation time under optimal growth conditions was 40 min. Strain SLM 61T grew and reduced Mn(IV), Fe(III) or nitrate with a number of organic acids and complex proteinaceous compounds as electron donors. It was capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor, Fe(III) but not Mn(IV) or nitrate as an electron acceptor and CO2 as a carbon source. It also was able to ferment pyruvate, yeast extract, glucose, fructose, sucrose and maltose. The G+C content of DNA of strain SLM 61T was 50.9 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Carboxydocella thermautotrophica 41T (96.9 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Carboxydocella manganica sp. nov. is proposed. The type strain is SLM 61T (=DSM 23132T=VKM B-2609T). C. manganica is the first described representative of the genus Carboxydocella that possesses the ability to reduce metals and does not utilize CO.

Protection of Nitrate-Reducing Fe(II)-Oxidizing Bacteria from UV Radiation by Biogenic Fe(III) Minerals

NASA Astrophysics Data System (ADS)

Gauger, Tina; Konhauser, Kurt; Kappler, Andreas

2016-04-01

Due to the lack of an ozone layer in the Archean, ultraviolet radiation (UVR) reached early Earth's surface almost unattenuated; as a consequence, a terrestrial biosphere in the form of biological soil crusts would have been highly susceptible to lethal doses of irradiation. However, a self-produced external screen in the form of nanoparticular Fe(III) minerals could have effectively protected those early microorganisms. In this study, we use viability studies by quantifying colony-forming units (CFUs), as well as Fe(II) oxidation and nitrate reduction rates, to show that encrustation in biogenic and abiogenic Fe(III) minerals can protect a common soil bacteria such as the nitrate-reducing Fe(II)-oxidizing microorganisms Acidovorax sp. strain BoFeN1 and strain 2AN from harmful UVC radiation. Analysis of DNA damage by quantifying cyclobutane pyrimidine dimers (CPD) confirmed the protecting effect by Fe(III) minerals. This study suggests that Fe(II)-oxidizing microorganisms, as would have grown in association with mafic and ultramafic soils/outcrops, would have been able to produce their own UV screen, enabling them to live in terrestrial habitats on early Earth.

Protection of Nitrate-Reducing Fe(II)-Oxidizing Bacteria from UV Radiation by Biogenic Fe(III) Minerals.

PubMed

Gauger, Tina; Konhauser, Kurt; Kappler, Andreas

2016-04-01

Due to the lack of an ozone layer in the Archean, ultraviolet radiation (UVR) reached early Earth's surface almost unattenuated; as a consequence, a terrestrial biosphere in the form of biological soil crusts would have been highly susceptible to lethal doses of irradiation. However, a self-produced external screen in the form of nanoparticular Fe(III) minerals could have effectively protected those early microorganisms. In this study, we use viability studies by quantifying colony-forming units (CFUs), as well as Fe(II) oxidation and nitrate reduction rates, to show that encrustation in biogenic and abiogenic Fe(III) minerals can protect a common soil bacteria such as the nitrate-reducing Fe(II)-oxidizing microorganisms Acidovorax sp. strain BoFeN1 and strain 2AN from harmful UVC radiation. Analysis of DNA damage by quantifying cyclobutane pyrimidine dimers (CPD) confirmed the protecting effect by Fe(III) minerals. This study suggests that Fe(II)-oxidizing microorganisms, as would have grown in association with mafic and ultramafic soils/outcrops, would have been able to produce their own UV screen, enabling them to live in terrestrial habitats on early Earth.

Fe Isotope Fractionation During Fe(III) Reduction to Fe(II)

NASA Astrophysics Data System (ADS)

Baker, E. A.; Greene, S.; Hardin, E. E.; Hodierne, C. E.; Rosenberg, A.; John, S.

2014-12-01

The redox chemistry of Fe(III) and Fe(II) is tied to a variety of earth processes, including biological, chemical, or photochemical reduction of Fe(III) to Fe(II). Each process may fractionate Fe isotopes, but the magnitudes of the kinetic isotope effects have not been greatly explored in laboratory conditions. Here, we present the isotopic fractionation of Fe during reduction experiments under a variety of experimental conditions including photochemical reduction of Fe(III) bound to EDTA or glucaric acid, and chemical reduction of Fe-EDTA by sodium dithionite, hydroxylamine hydrochloride, Mn(II), and ascorbic acid. A variety of temperatures and pHs were tested. In all experiments, Fe(III) bound to an organic ligand was reduced in the presence of ferrozine. Ferrozine binds with Fe(II), forming a purple complex which allows us to measure the extent of reaction. The absorbance of the experimental solutions was measured over time to determine the Fe(II)-ferrozine concentration and thus the reduction rate. After about 5% of the Fe(III) was reduced, Fe(III)-EDTA and Fe(II)-ferrozine were separated using a C-18 column to which Fe(II)-ferrozine binds. The Fe(II) was eluted and purified through anion exchange chromatography for analysis of δ56Fe by MC-ICPMS. Preliminary results show that temperature and pH both affect reduction rate. All chemical reductants tested reduce Fe(III) at a greater rate as temperature increases. The photochemical reductant EDTA reduces Fe(III) at a greater rate under more acidic conditions. Comparison of the two photochemical reductants shows that glucaric acid reduces Fe(III) significantly faster than EDTA. For chemical reduction, the magnitude of isotopic fractionation depends on the reductant used. Temperature and pH also affect the isotopic fractionation of Fe. Experiments using chemical reductants show that an increase in temperature at low temperatures produces lighter 56Fe ratios, while at high temperatures some reductants produce heavier

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

USGS Publications Warehouse

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.

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

PubMed Central

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 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. PMID:19473543

Reduction of Cr(VI) under acidic conditions by the facultative Fe(III)-reducing bacterium Acidiphilium cryptum

DOE Office of Scientific and Technical Information (OSTI.GOV)

David E. Cummings; Scott Fendorf; Rajesh K. Sani

2007-01-01

The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 M Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and wasmore » inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.« less

Lack of electricity production by Pelobacter carbinolicus indicates that the capacity for Fe(III) oxide reduction does not necessarily confer electron transfer ability to fuel cell anodes.

PubMed

Richter, Hanno; Lanthier, Martin; Nevin, Kelly P; Lovley, Derek R

2007-08-01

The ability of Pelobacter carbinolicus to oxidize electron donors with electron transfer to the anodes of microbial fuel cells was evaluated because microorganisms closely related to Pelobacter species are generally abundant on the anodes of microbial fuel cells harvesting electricity from aquatic sediments. P. carbinolicus could not produce current in a microbial fuel cell with electron donors which support Fe(III) oxide reduction by this organism. Current was produced using a coculture of P. carbinolicus and Geobacter sulfurreducens with ethanol as the fuel. Ethanol consumption was associated with the transitory accumulation of acetate and hydrogen. G. sulfurreducens alone could not metabolize ethanol, suggesting that P. carbinolicus grew in the fuel cell by converting ethanol to hydrogen and acetate, which G. sulfurreducens oxidized with electron transfer to the anode. Up to 83% of the electrons available in ethanol were recovered as electricity and in the metabolic intermediate acetate. Hydrogen consumption by G. sulfurreducens was important for ethanol metabolism by P. carbinolicus. Confocal microscopy and analysis of 16S rRNA genes revealed that half of the cells growing on the anode surface were P. carbinolicus, but there was a nearly equal number of planktonic cells of P. carbinolicus. In contrast, G. sulfurreducens was primarily attached to the anode. P. carbinolicus represents the first Fe(III) oxide-reducing microorganism found to be unable to produce current in a microbial fuel cell, providing the first suggestion that the mechanisms for extracellular electron transfer to Fe(III) oxides and fuel cell anodes may be different.

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem

DOE PAGES

Lu, Xia; Liu, Yurong; Johs, Alexander; ...

2016-03-28

Two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems are microbial methylation and demethylation. Though 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 bemidjensis Bem. Here we report, for the first time, that the strain G. bemidjensis Bem can methylate inorganic Hg and degrade MeHg concurrently under anoxic conditions. Our results suggest that G. bemidjensis cells utilize a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) asmore » the major reaction product, possibly due to the presence of homologs encoding both organo-mercurial lyase (MerB) and mercuric reductase (MerA) in this organism. In addition, the cells can mediate multiple reactions including Hg/MeHg sorption, Hg reduction and oxidation, resulting in both time and concentration dependent Hg species transformations. Moderate concentrations (10 500 M) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of methylation and demethylation among anaerobic bacteria and suggest that mer-mediated demethylation may play a role in the net balance of MeHg production in anoxic water and sediments.« less

Alkaliphilus namsaraevii sp. nov., an alkaliphilic iron- and sulfur-reducing bacterium isolated from a steppe soda lake.

PubMed

Zakharyuk, Anastasiya; Kozyreva, Lyudmila; Ariskina, Elena; Troshina, Olga; Kopitsyn, Dmitry; Shcherbakova, Viktoria

2017-06-01

A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated Х-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain Х-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6-10.3). Growth was observed at 25-47 °C (optimum 30 °C) and at an NaCl concentration from 5 to 150 g l-1 with an optimum at 40 g l-1. Strain Х-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor. It used tryptone, peptone and trypticase with Fe(III) citrate as the electron acceptor. The predominant fatty acids in cell walls were C16:1ω8, iso-C15:0, C14 : 0 3-OH and C16 : 0. The DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis revealed that strain Х-07-2T was related most closely to members of the genus Alkaliphilus within the family Clostridiaceae. The closest relative was Alkaliphilus peptidifermentans Z-7036T (96.4 % similarity). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Х-07-2T represents a novel species in the genus Alkaliphilus, for which the name Alkaliphilus namsaraevii sp. nov. is proposed. The type strain is Х-07-2T (=VKM В-2746Т=DSM 26418Т).

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

PubMed

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.

Anaerobic biodegradation of BTEX using Mn(IV) and Fe(III) as alternative electron acceptors.

PubMed

Villatoro-Monzón, W R; Mesta-Howard, A M; Razo-Flores, E

2003-01-01

Anaerobic BTEX biodegradation was tested in batch experiments using an anaerobic sediment as inoculum under Fe(III) and Mn(IV) reducing conditions. All BTEX were degraded under the conditions tested, specially under Mn(IV) reducing conditions, where benzene was degraded at a rate of 0.8 micromol l(-1) d(-1), significantly much faster than Fe(III) reducing conditions. Under Fe(III) reducing conditions, ethylbenzene was the compound that degraded at the faster rate of 0.19 micromol l(-1) d(-1). Mn(IV) reducing conditions are energetically more favourable than Fe(III), therefore, BTEX were more rapidly degraded under Mn(IV) reducing conditions. These results represent the first report of the degradation of benzene with Mn(IV) as the final electron acceptor. Amorphous manganese oxide is a natural widely distributed metal in groundwater, where it can be microbiologically reduced, leading to the degradation of monoaromatic compounds.

Contrasting Effects of Dissolved Organic Matter on Mercury Methylation by Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132.

PubMed

Zhao, Linduo; Chen, Hongmei; Lu, Xia; Lin, Hui; Christensen, Geoff A; Pierce, Eric M; Gu, Baohua

2017-09-19

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. In this study, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under nonsulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hg via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting microbial Hg uptake and methylation. Additionally, DOM and glutathione greatly decreased Hg sorption by G. sulfurreducens PCA but showed little effect on D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. These observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.

Importance of clay size minerals for Fe(III) respiration in a petroleum-contaminated aquifer

USGS Publications Warehouse

Shelobolina, Evgenya S.; Anderson, Robert T.; Vodyanitskii, Yury N.; Sivtsov, Anatolii V.; Yuretich, Richard; Lovely, Derek R.

2004-01-01

The availability of Fe(III)-bearing minerals for dissimilatory Fe(III) reduction was evaluated in sediments from a petroleum-contaminated sandy aquifer near Bemidji, Minnesota (USA). First, the sediments from a contaminated area of the aquifer, in which Fe(III) reduction was the predominant terminal electron accepting process, were compared with sediments from a nearby, uncontaminated site. Data from 0.5 m HCl extraction of different size fractions of the sediments revealed that the clay size fraction contributed a significant portion of the ‘bio-available’ Fe(III) in the background sediment and was the most depleted in ‘bio-available’ Fe(III) in the iron-reducing sediment. Analytical transmission electron microscopy (TEM) revealed the disappearance of thermodynamically unstable Fe(III) and Mn(IV) hydroxides (ferrihydrite and Fe vernadite), as well as a decrease in the abundance of goethite and lepidocrocite in the clay size fraction from the contaminated sediment. TEM observations and X-ray diffraction examination did not provide strong evidence of Fe(III)-reduction-related changes within another potential source of ‘bio-available’ Fe(III) in the clay size fraction – ferruginous phyllosilicates. However, further testing in the laboratory with sediments from the methanogenic portion of the aquifer that were depleted in microbially reducible Fe(III) revealed the potential for microbial reduction of Fe(III) associated with phyllosilicates. Addition of a clay size fraction from the uncontaminated sediment, as well as Fe(III)-coated kaolin and ferruginous nontronite SWa-1, as sources of poorly crystalline Fe(III) hydroxides and structural iron of phyllosilicates respectively, lowered steady-state hydrogen concentrations consistent with a stimulation of Fe(III) reduction in laboratory incubations of methanogenic sediments. There was no change in hydrogen concentration when non-ferruginous clays or no minerals were added. This demonstrated that Fe

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

PubMed

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. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Reduction of Fe(III) colloids by Shewanella putrefaciens: A kinetic model

NASA Astrophysics Data System (ADS)

Bonneville, Steeve; Behrends, Thilo; van Cappellen, Philippe; Hyacinthe, Christelle; Röling, Wilfred F. M.

2006-12-01

A kinetic model for the microbial reduction of Fe(III) oxyhydroxide colloids in the presence of excess electron donor is presented. The model assumes a two-step mechanism: (1) attachment of Fe(III) colloids to the cell surface and (2) reduction of Fe(III) centers at the surface of attached colloids. The validity of the model is tested using Shewanella putrefaciens and nanohematite as model dissimilatory iron reducing bacteria and Fe(III) colloidal particles, respectively. Attachment of nanohematite to the bacteria is formally described by a Langmuir isotherm. Initial iron reduction rates are shown to correlate linearly with the relative coverage of the cell surface by nanohematite particles, hence supporting a direct electron transfer from membrane-bound reductases to mineral particles attached to the cells. Using internally consistent parameter values for the maximum attachment capacity of Fe(III) colloids to the cells, Mmax, the attachment constant, KP, and the first-order Fe(III) reduction rate constant, k, the model reproduces the initial reduction rates of a variety of fine-grained Fe(III) oxyhydroxides by S. putrefaciens. The model explains the observed dependency of the apparent Fe(III) half-saturation constant, Km∗, on the solid to cell ratio, and it predicts that initial iron reduction rates exhibit saturation with respect to both the cell density and the abundance of the Fe(III) oxyhydroxide substrate.

Control of Fe(III) site occupancy on the rate and extent of microbial reduction of Fe(III) in nontronite

USGS Publications Warehouse

Jaisi, Deb P.; Kukkadapu, R.K.; Eberl, D.D.; Dong, H.

2005-01-01

average nontronite particle thickness remained nearly the same (from 2.1 to 2.5 nm) for NAu-1, but decreased significantly from 6 to 3.5 nm for NAu-2 with a concomitant change in crystal size distribution. The decrease in crystal size suggests reductive dissolution of nontronite NAu-2, which was supported by aqueous solution chemistry (i.e., aqueous Si). These data suggest that the more extensive Fe(III) bioreduction in NAu-2 was due to the presence of the tetrahedral and the trans-octahedral Fe(III), which was presumed to be more reducible. The biogenic Fe(II) was not associated with biogenic solids or in the aqueous solution. We infer that it may be either adsorbed onto surfaces of nontronite particles/bacteria or in the structure of nontronite. Furthermore, we have demonstrated that natural nontronite clays were capable of supporting cell growth even in medium without added nutrients, possibly due to presence of naturally existing nutrients in the nontronite clays. These results suggest that crystal chemical environment of Fe(III) is an important determinant in controlling the rate and extent of microbial reduction of Fe(III) in nontronite. Copyright ?? 2005 Elsevier Ltd.

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

PubMed

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.

Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth

PubMed Central

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

2013-01-01

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 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. PMID:23038172

Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth.

PubMed

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.

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

PubMed

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.

Particle Aggregation During Fe(III) Bioreduction in Nontronite

NASA Astrophysics Data System (ADS)

Jaisi, D. P.; Dong, H.; Hi, Z.; Kim, J.

2005-12-01

the particles size of 0.12-0.22 and 1.42-1.8 mm, respectively. The particle aggregation was limited in control experiment to the factor of 2.8 and 2.1 for these two size fractions, respectively. The measured electrophoretic mobility decreased with increase in the extent of bioreduction and aggregation, but the rate of decrease was greatest in the finest size fraction. The EPS measurements showed the increase in the carbohydrate and protein fractions as a result of bioreduction. Separate experiments were performed to understand the relative contribution of Fe(III) reduction and EPS production in controlling nontronite particle aggregation The rate of particle aggregation was measured for nontronite that was chemically pre-reduced by dithionite to various extents, both with and without addition of dextran, a neutral and pure EPS. The aggregation rate was greater in the nontronite that were pre-reduced to a higher extent than those with a lower extent of reduction. The relative contribution to particle aggregation due to Fe(III) reduction and polysaccharide bridging was about 4:1. However, in the real system where bacterial cells are involved, and amount of EPS production and extent of Fe(III) bioreduction increase with time, the relative contribution may be different than in this simple system. In summary, we conclude that both Fe(III) reduction and microbial production of EPS contribute to the observed nontronite particle aggregation with Fe(III) reduction playing more dominant role.

Molecular Analysis of the In Situ Growth Rates of Subsurface Geobacter Species

PubMed Central

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

2013-01-01

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 (r2 = 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. PMID:23275510

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

PubMed Central

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

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

PubMed

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.

Fe(III) and Fe(II) induced photodegradation of nonylphenol polyethoxylate (NPEO) oligomer in aqueous solution and toxicity evaluation of the irradiated solution.

PubMed

Wang, Lei; Zhang, Junjie; Duan, Zhenghua; Sun, Hongwen

2017-06-01

Photodegradation of nonylphenol tri-ethoxylate (NPEO 3 ) in aqueous solution, and the effects of Fe(III) or Fe(II) were studied. The increasing degradation kinetics of NPEO 3 were observed when 500µM Fe(III) or Fe(II) was present in the solutions. Altered formation of NPEO oligomers with shorter EO chains, including nonyphenol (NP), NPEO 1 and NPEO 2 , was observed in water and in solutions containing Fe(III) or Fe(II). The molar percentage yields of NP and NPEO 1,2 production from NPEO 3 photodegradation were approximately 20% in NPEO 3 solution, while NPEO 3 solution with Fe(III), this percentage increased to approximately 50%. In solution with Fe(II), the molar balance between the photodegradation of NPEO 3 and the production of NP and NPEO 1,2 was observed. A luminescent bacterium, Vibrio fischeri, was used to identify changes in the toxicity of NPEO 3 solutions during the photodegradation process under different conditions, while dose addition (DA) model was used to estimate the toxicity of products. Toxicity of NPEO 3 /water solution increased significantly following the irradiation of UVA/UVB mixture. In contrast, obviously decreasing toxicity was observed when NPEO 3 underwent photodegradation in the presence of Fe(III). Copyright © 2017. Published by Elsevier Inc.

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

PubMed Central

Kimura, Zen-ichiro; Okabe, Satoshi

2013-01-01

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. PMID:23486252

Microbial reduction of Fe(III) in acidic sediments: isolation of Acidiphilium cryptum JF-5 capable of coupling the reduction of Fe(III) to the oxidation of glucose.

PubMed

Küsel, K; Dorsch, T; Acker, G; Stackebrandt, E

1999-08-01

To evaluate the microbial populations involved in the reduction of Fe(III) in an acidic, iron-rich sediment, the anaerobic flow of supplemental carbon and reductant was evaluated in sediment microcosms at the in situ temperature of 12 degrees C. Supplemental glucose and cellobiose stimulated the formation of Fe(II); 42 and 21% of the reducing equivalents that were theoretically obtained from glucose and cellobiose, respectively, were recovered in Fe(II). Likewise, supplemental H(2) was consumed by acidic sediments and yielded additional amounts of Fe(II) in a ratio of approximately 1:2. In contrast, supplemental lactate did not stimulate the formation of Fe(II). Supplemental acetate was not consumed and inhibited the formation of Fe(II). Most-probable-number estimates demonstrated that glucose-utilizing acidophilic Fe(III)-reducing bacteria approximated to 1% of the total direct counts of 4', 6-diamidino-2-phenylindole-stained bacteria. From the highest growth-positive dilution of the most-probable-number series at pH 2. 3 supplemented with glucose, an isolate, JF-5, that could dissimilate Fe(III) was obtained. JF-5 was an acidophilic, gram-negative, facultative anaerobe that completely oxidized the following substrates via the dissimilation of Fe(III): glucose, fructose, xylose, ethanol, glycerol, malate, glutamate, fumarate, citrate, succinate, and H(2). Growth and the reduction of Fe(III) did not occur in the presence of acetate. Cells of JF-5 grown under Fe(III)-reducing conditions formed blebs, i.e., protrusions that were still in contact with the cytoplasmic membrane. Analysis of the 16S rRNA gene sequence of JF-5 demonstrated that it was closely related to an Australian isolate of Acidiphilium cryptum (99.6% sequence similarity), an organism not previously shown to couple the complete oxidation of sugars to the reduction of Fe(III). These collective results indicate that the in situ reduction of Fe(III) in acidic sediments can be mediated by heterotrophic

Reduction of structural Fe(III) in nontronite by methanogen Methanosarcina barkeri

USGS Publications Warehouse

Liu, D.; Dong, Hailiang H.; Bishop, M.E.; Wang, Hongfang; Agrawal, A.; Tritschler, S.; Eberl, D.D.; Xie, S.

2011-01-01

Clay minerals and methanogens are ubiquitous and co-exist in anoxic environments, yet it is unclear whether methanogens are able to reduce structural Fe(III) in clay minerals. In this study, the ability of methanogen Methanosarcina barkeri to reduce structural Fe(III) in iron-rich smectite (nontronite NAu-2) and the relationship between iron reduction and methanogenesis were investigated. Bioreduction experiments were conducted in growth medium using three types of substrate: H2/CO2, methanol, and acetate. Time course methane production and hydrogen consumption were measured by gas chromatography. M. barkeri was able to reduce structural Fe(III) in NAu-2 with H2/CO2 and methanol as substrate, but not with acetate. The extent of bioreduction, as measured by the 1,10-phenanthroline method, was 7-13% with H2/CO2 as substrate, depending on nontronite concentration (5-10g/L). The extent was higher when methanol was used as a substrate, reaching 25-33%. Methanogenesis was inhibited by Fe(III) reduction in the H2/CO2 culture, but enhanced when methanol was used. High charge smectite and biogenic silica formed as a result of bioreduction. Our results suggest that methanogens may play an important role in biogeochemical cycling of iron in clay minerals and may have important implications for the global methane budget. ?? 2010 Elsevier Ltd.

MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens.

PubMed

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J; Einsle, Oliver

2012-04-03

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS(-2) as an electron donor. The observed K(M) was 38.5 ± 3.7 μM H(2)O(2) and v(max) was 0.78 ± 0.03 μmol of H(2)O(2)·min(-1)·mg(-1), resulting in a turnover number k(cat) = 0.46 · s(-1). In contrast, no Fe(III) reductase activity was observed. MacA was found to display electrochemical properties similar to other bacterial diheme peroxidases, in addition to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergoes conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein, the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation.

MacA is a Second Cytochrome c Peroxidase of Geobacter sulfurreducens

PubMed Central

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E.; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J.

2012-01-01

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS2– as an electron donor. The observed KM was 38.5 ± 3.7 μM H2O2 and vmax was 0.78 ± 0.03 μmol H2O2·min–1·mg–1, resulting in a turnover number kcat = 0.46 · s–1. In contrast, no Fe(III) reductase activity was observed. MacA was found to display similar electrochemical properties to other bacterial diheme peroxidases, in additional to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergo conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation. PMID:22417533

Production of gold nanoparticles by electrode-respiring Geobacter sulfurreducens biofilms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tanzil, Abid H.; Sultana, Sujala T.; Saunders, Steven R.

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 nanoparticlesmore » (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.« less

Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

NASA Astrophysics Data System (ADS)

Cooper, Rebecca Elizabeth; Eusterhues, Karin; Wegner, Carl-Eric; Totsche, Kai Uwe; Küsel, Kirsten

2017-11-01

The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron

Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

PubMed

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

2010-10-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

Humic substances as a mediator for microbially catalyzed metal reduction

USGS Publications Warehouse

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.

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

PubMed Central

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

2010-01-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

Microbial reduction of Fe(III) and turnover of acetate in Hawaiian soils.

PubMed

Küsel, Kirsten; Wagner, Christine; Trinkwalter, Tanja; Gössner, Anita S; Bäumler, Rupert; Drake, Harold L

2002-04-01

Soils contain anoxic microzones, and acetate is an intermediate during the turnover of soil organic carbon. Due to negligible methanogenic activities in well-drained soils, acetate accumulates under experimentally imposed short-term anoxic conditions. In contrast to forest, agricultural, and prairie soils, grassland soils from Hawaii rapidly consumed rather than formed acetate when incubated under anoxic conditions. Thus, alternative electron acceptors that might be linked to the anaerobic oxidation of soil organic carbon in Hawaiian soils were assessed. Under anoxic conditions, high amounts of Fe(II) were formed by Hawaiian soils as soon as soils were depleted of nitrate. Rates of Fe(II) formation for different soils ranged from 0.01 to 0.31 micromol (g dry weight soil)(-1) h(-1), but were not positively correlated to increasing amounts of poorly crystallized iron oxides. In general, sulfate-reducing and methanogenic activities were negligible. Supplemental acetate was rapidly oxidized to CO2 via the sequential reduction of nitrate and Fe(III) in grassland soil (obtained near Kaena State Park). Supplemental H2 stimulated the formation of Fe(II), but H2-utilizing acetogens appeared to also be involved in the consumption of H2. Approximately 270 micromol Fe(III) (g dry weight soil)(-1) was available for Fe(III)-reducing bacteria, and acetate became a stable end product when Fe(III) was depleted in long-term incubations. Most-probable-number estimates of H2- and acetate-utilizing Fe(III) reducers and of H2-utilizing acetogens were similar. These results indicate that (i) the microbial reduction of Fe(III) is an important electron-accepting process for the anaerobic oxidation of organic matter in Fe(III)-rich Hawaiian soils of volcanic origin, and (ii) acetate, formed by the combined activity of fermentative and acetogenic bacteria, is an important trophic link in anoxic microsites of these soils.

Influence of Oxygen and Nitrate on Fe (Hydr)oxide Mineral Transformation and Soil Microbial Communities during Redox Cycling.

PubMed

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.

Carbohydrate oxidation coupled to Fe(III) reduction, a novel form of anaerobic metabolism

USGS Publications Warehouse

Coates, J.D.; Councell, T.; Ellis, D.J.; Lovley, D.R.

1998-01-01

An isolate, designated GC-29, that could incompletely oxidize glucose to acetate and carbon dioxide with Fe(III) serving as the electron acceptor was recovered from freshwater sediments of the Potomac River, Maryland. This metabolism yielded energy to support cell growth. Strain GC-29 is a facultatively anaerobic, Gram-negative motile rod which, in addition to glucose, also used sucrose, lactate, pyruvate, yeast extract, casamino acids or H2 as alternative electron donors for Fe(III) reduction. Stain GC-29 could reduce NO-3, Mn(IV), U(VI), fumarate, malate, S2O32-, and colloidal S0 as well as the humics analog, 2,6-anthraquinone disulfonate. Analysis of the almost complete 16S rRNA sequence indicated that strain GC-29 belongs in the Shewanella genus in the epsilon subdivision of the Proteobacteria. The name Shewanella saccharophilia is proposed. Shewanella saccharophilia differs from previously described fermentative microorganisms that metabolize glucose with the reduction of Fe(III) because it transfers significantly more electron equivalents to Fe(III); acetate and carbon dioxide are the only products of glucose metabolism; energy is conserved from Fe(III) reduction; and glucose is not metabolized in the absence of Fe(III). The metabolism of organisms like S. saccharophilia may account for the fact that glucose is metabolized primarily to acetate and carbon dioxide in a variety of sediments in which Fe(III) reduction is the terminal electron accepting process.

Kinetics of DCE and VC mineralization under methanogenic and Fe(III)- reducing conditions

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

1997-01-01

The kinetics of anaerobic mineralization of DCE and VC under mathanogenic and Fe(III)-reducing conditions as a function of dissolved contaminant concentration were evaluated. Microorganisms indigenous to creek bed sediments, where groundwater contaminated with chlorinated ethenes continuously discharges, demonstrated significant mineralization of DCE and VC under methanogenic and Fe(III)- reducing conditions. Over 37 days, the recovery of [1,214C]VC radioactivity as 14CO2 ranged from 5% to 44% and from 8% to 100% under methanogenic and Fe(III)-reducing conditions, respectively. The recovery of [1,2-14C]DCE radioactivity as 14CO2 ranged from 4% to 14% and did not vary significantly between methanogenic and Fe(III)reducing conditions. VC mineralization was described by Michaelis- Menten kinetics. Under methanogenic conditions, V(max) was 0.19 ?? 0.01 ??mol L-1 d-1 and the half-saturation constant, k(m), was 7.6 ?? 1.7 ??M. Under Fe(III)-reducing conditions, V(max) was 0.76 ?? 0.07 ??mol L-1 d-1 and k(m) was 1.3 ?? 0.5 ??M. In contrast, DCE mineralization could be described by first-order kinetics. The first-order degradation rate constant for DCE mineralization was 0.6 ?? 0.2% d-1 under methanogenic and Fe(III)-reducing conditions. The results indicate that the kinetics of chlorinated ethane mineralization can vary significantly with the specific contaminant and the predominant redox conditions under which mineralization occurs.

Enhanced reduction of Fe(III) oxides and methyl orange by Klebsiella oxytoca in presence of anthraquinone-2-disulfonate.

PubMed

Yu, Lei; Wang, Shi; Tang, Qing-Wen; Cao, Ming-Yue; Li, Jia; Yuan, Kun; Wang, Ping; Li, Wen-Wei

2016-05-01

Klebsiella oxytoca GS-4-08 is capable of azo dye reduction, but its quinone respiration and Fe(III) reduction abilities have not been reported so far. In this study, the abilities of this strain were reported in detail for the first time. As the biotic reduction of Fe(III) plays an important role in the biogeochemical cycles, two amorphous Fe(III) oxides were tested as the sole electron acceptor during the anaerobic respiration of strain GS-4-08. For the reduction of goethite and hematite, the biogenic Fe(II) concentrations reached 0.06 and 0.15 mM, respectively. Humic acid analog anthraquinone-2-disulfonate (AQS) was found to serve as an electron shuttle to increase the reduction of both methyl orange (MO) and amorphous Fe(III) oxides, and improve the dye tolerance of the strain. However, the formation of Fe(II) was not accelerated by biologically reduced AQS (B-AH2QS) because of the high bioavailability of soluble Fe(III). For the K. oxytoca strain, high soluble Fe(III) concentrations (above 1 mM) limit its growth and decolorization ability, while lower soluble Fe(III) concentrations produce an electron competition with MO initially, and then stimulate the decolorization after the electron couples of Fe(III)/Fe(II) are formed. With the ability to respire both soluble Fe(III) and insoluble Fe(III) oxides, this formerly known azo-reducer may be used as a promising model organism for the study of the interaction of these potentially competing processes in contaminated environments.

Role of microbial iron reduction in the dissolution of iron hydroxysulfate minerals

USGS Publications Warehouse

Jones, E.J.P.; Nadeau, T.-L.; Voytek, M.A.; Landa, E.R.

2006-01-01

Iron-hydroxysulfate minerals can be important hosts for metals such as lead, mercury, copper, zinc, silver, chromium, arsenic, and selenium and for radionuclides such as 226Ra. These mineral-bound contaminants are considered immobilized under oxic conditions. However, when anoxic conditions develop, the activities of sulfate- or iron-reducing bacteria could result in mineral dissolution, releasing these bound contaminants. Reduction of structural sulfate in the iron-hydroxysulfate mineral jarosite by sulfate-reducing bacteria has previously been demonstrated. The primary objective of this work was to evaluate the potential for anaerobic dissolution of the iron-hydroxysulfate minerals jarosite and schwertmannite at neutral PH by iron-reducing bacteria. Mineral dissolution was tested using a long-term cultivar, Geobacter metallireducens strain GS-15, and a fresh isolate Geobacter sp. strain ENN1, previously undescribed. ENN1 was isolated from the discharge site of Shadle Mine, in the southern anthracite coalfield of Pennsylvania, where schwertmannite was the predominant iron-hydroxysulfate mineral. When jarosite from Elizabeth Mine (Vermont) was provided as the sole terminal electron acceptor, resting cells of both G. metallireducens and ENN1 were able to reduce structural Fe(III), releasing Fe+2, SO4-2, and K+ ions. A lithified jarosite sample from Utah was more resistant to microbial attack, but slow release of Fe+2 was observed. Neither bacterium released Fe+2 from poorly crystalline synthetic schwertmannite. Our results indicate that exposure of jarosite to iron-reducing conditions at neutral pH is likely to promote the mobility of hazardous constituents and should therefore be considered in evaluating waste disposal and/or reclamation options involving jarosite-bearing materials.

Intracellular versus extracellular accumulation of Hexavalent chromium reduction products by Geobacter sulfurreducens PCA.

PubMed

Gong, Yufeng; Werth, Charles J; He, Yaxue; Su, Yiming; Zhang, Yalei; Zhou, Xuefei

2018-05-10

Hexavalent chromium (Cr(VI)) reduction by Geobacter sulfurreducens PCA was evaluated in batch experiments, and the form and amounts of intracellular and extra-cellular Cr(VI) reduction products were determined over time. The first-order Cr(VI) reduction rate per unit mass of cells was consistent for different initial cell concentrations, and approximately equal to (2.065 ± 0.389) x 10 -9  mL CFU -1 h -1 . A portion of the reduced Cr(VI) products precipitated on Geobacter cell walls as Cr(III) and was bound via carboxylate functional groups, a portion accumulated inside Geobacter cells, and another portion existed as soluble Cr(III) or organo-Cr(III) released to solution. A mass balance analysis of total chromium in aqueous media, on cell walls, and inside cells was determined as a function of time, and with different initial cell concentrations. Mass balances were between 92% and 98%, and indicated Cr(VI) reduction products accumulate more on cell walls and inside cells with time and with increasing initial cell concentration, as opposed to particulates in aqueous solution. Reduced Cr(VI) products both in solution and on cell surfaces appear to form organo-Cr(III) complexes, and our results suggest that such complexes are more stable to reoxidation than aqueous Cr(III) or Cr(OH) 3 . Chromium inside cells is also likely more stable to reoxidation, both because it can form organic complexes, and it is separated by the cell membrane from solution conditions. Hence, Cr(VI) reduction products in groundwater during bioremediation may become more stable against re-oxidation, and may pose a lower risk to human health, over time and with greater initial biomass densities. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkley, Eric D.; Wrighton, Kelly C.; Castelle, Cindy

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 inmore » 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.« less

Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33

DOE PAGES

Bhattacharya, Pamela; Barnebey, Adam; Zemla, Marcin; ...

2015-10-05

Thermoanaerobacter thermohydrosulfuricus BSB-33 is a thermophilic gram positive obligate anaerobe isolated from a hot spring in West Bengal, India. Unlike other T. thermohydrosulfuricus strains, BSB-33 is able to anaerobically reduce Fe(III) and Cr(VI) optimally at 60 °C. BSB-33 is the first Cr(VI) reducing T. thermohydrosulfuricus genome sequenced and of particular interest for bioremediation of environmental chromium contaminations. Here we discuss features of T. thermohydrosulfuricus BSB-33 and the unique genetic elements that may account for the peculiar metal reducing properties of this organism. The T. thermohydrosulfuricus BSB-33 genome comprises 2597606 bp encoding 2581 protein genes, 12 rRNA, 193 pseudogenes and hasmore » a G + C content of 34.20 %. Lastly, putative chromate reductases were identified by comparative analyses with other Thermoanaerobacter and chromate-reducing bacteria.« less

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

PubMed

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. Copyright © 2015. Published by Elsevier B.V.

Enzymatic iron and uranium reduction by sulfate-reducing bacteria

USGS Publications Warehouse

Lovley, D.R.; Roden, E.E.; Phillips, E.J.P.; Woodward, J.C.

1993-01-01

The potential for sulfate-reducing bacteria (SRB) to enzymatically reduce Fe(III) and U(VI) was investigated. Five species of Desulfovibrio as well as Desulfobacterium autotrophicum and Desulfobulbus propionicus reduced Fe(III) chelated with nitrilotriacetic acid as well as insoluble Fe(III) oxide. Fe(III) oxide reduction resulted in the accumulation of magnetite and siderite. Desulfobacter postgatei reduced the chelated Fe(III) but not Fe(III) oxide. Desulfobacter curvatus, Desulfomonile tiedjei, and Desulfotomaculum acetoxidans did not reduce Fe(III). Only Desulfovibrio species reduced U(VI). U(VI) reduction resulted in the precipitation of uraninite. None of the SRB that reduced Fe(III) or U(VI) appeared to conserve enough energy to support growth from this reaction. However, Desulfovibrio desulfuricans metabolized H2 down to lower concentrations with Fe(III) or U(VI) as the electron acceptor than with sulfate, suggesting that these metals may be preferred electron acceptors at the low H2 concentrations present in most marine sediments. Molybdate did not inhibit Fe(III) reduction by D. desulfuricans. This indicates that the inability of molybdate to inhibit Fe(III) reduction in marine sediments does not rule out the possibility that SRB are important catalysts for Fe(III) reduction. The results demonstrate that although SRB were previously considered to reduce Fe(III) and U(VI) indirectly through the production of sulfide, they may also directly reduce Fe(III) and U(VI) through enzymatic mechanisms. These findings, as well as our recent discovery that the So-reducing microorganism Desulfuromonas acetoxidans can reduce Fe(III), demonstrate that there are close links between the microbial sulfur, iron, and uranium cycles in anaerobic marine sediments. ?? 1993.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, T.; Griffin, A. M.; Gorski, C. A.

Dissimilatory microbial reduction of solid-phase Fe(III)-oxides and Fe(III)-bearing phyllosilicates (Fe(III)-phyllosilicates) is an important process in anoxic soils, sediments, and subsurface materials. Although various studies have documented the relative extent of microbial reduction of single-phase Fe(III)-oxides and Fe(III)-phyllosilicates, detailed information is not available on interaction between these two processes in situations where both phases are available for microbial reduction. The goal of this research was to use the model dissimilatory iron-reducing bacterium (DIRB) Geobacter sulfurreducens to study Fe(III)-oxide vs. Fe(III)-phyllosilicate reduction in a range of subsurface materials and Fe(III)-oxide stripped versions of the materials. Low temperature (12K) Mossbauer spectroscopy was usedmore » to infer changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate). A Fe partitioning model was employed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The results showed that in most cases Fe(III)- oxide utilization dominated (70-100 %) bulk Fe(III) reduction activity, and that electron transfer from oxide-derived Fe(II) played only a minor role (ca. 10-20 %) in Fe partitioning. In addition, the extent of Fe(III)-oxide reduction was positively correlated to surface area-normalized cation exchange capacity and the phyllosilicate-Fe(III)/total Fe(III) ratio, which suggests that the phyllosilicates in the natural sediments promoted Fe(III)-oxide reduction by binding of oxide-derived Fe(II), thereby enhancing Fe(III)-oxide reduction by reducing or delaying the inhibitory effect that Fe(II) accumulation on oxide and DIRB cell surfaces has on Fe(III)-oxide reduction. In general our results suggest that although Fe(III)-oxide reduction is likely to dominate bulk Fe(III) reduction in most subsurface

Microbial reduction of Fe(III) in the Fifthian and Muloorina illites: Contrasting extents and rates of bioreduction

USGS Publications Warehouse

Seabaugh, Jennifer L.; Dong, Hailiang; Kukkadapu, Ravi K.; Eberl, Dennis D.; Morton, John P.; Kim, J.

2006-01-01

Shewanella putrefaciens CN32 reduces Fe(III) within two illites which have different properties: the Fithian bulk fraction and the <0.2 m fraction of Muloorina. The Fithian illite contained 4.6% (w/w) total Fe, 81% of which was Fe(III). It was dominated by illite with some jarosite (∼32% of the total Fe(III)) and goethite (11% of the total Fe(III)). The Muloorina illite was pure and contained 9.2% Fe, 93% of which was Fe(III). Illite suspensions were buffered at pH 7 and were inoculated with CN32 cells with lactate as the electron donor. Select treatments included anthraquinone-2,6-disulfonate (AQDS) as an electron shuttle. Bioproduction of Fe(II) was determined by ferrozine analysis. The unreduced and bioreduced solids were characterized by Mössbauer spectroscopy, X-ray diffraction and transmission electron microscopy. The extent of Fe(III) reduction in the bulk Fithian illite was enhanced by the presence of AQDS (73%) with complete reduction of jarosite and goethite and partial reduction of illite. Mössbauer spectroscopy and chemical extraction determined that 21–25% of illite-associated Fe(III) was bioreduced. The extent of bioreduction was less in the absence of AQDS (63%) and only jarosite was completely reduced with partial reduction of goethite and illite. The XRD and TEM data revealed no significant illite dissolution or biogenic minerals, suggesting that illite was reduced in the solid state and biogenic Fe(II) from jarosite and goethite was either released to aqueous solution or adsorbed onto residual solid surfaces. In contrast, only 1% of the structural Fe(III) in Muloorina illite was bioreduced. The difference in the extent and rate of bioreduction between the two illites was probably due to the difference in layer charge and the total structural Fe content between the Fithian illite (0.56 per formula) and Muloorina illite (0.87). There may be other factors contributing to the observed differences, such as expandability, surface area and the

Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions.

PubMed

Pearce, Carolyn I; Wilkins, Michael J; Zhang, Changyong; Heald, Steve M; Fredrickson, Jim K; Zachara, John M

2012-08-07

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.

Pore-Scale Characterization of Biogeochemical Controls on Iron and Uranium Speciation under Flow Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearce, Carolyn I.; Wilkins, Michael J.; Zhang, Changyong

2012-09-17

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray Microprobe and X-ray Absorption Spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced inmore » the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting re-oxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.« less

Metabolic spatial variability in electrode-respiring Geobacter sulfurreducens biofilms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renslow, Ryan S.; Babauta, Jerome T.; Dohnalkova, Alice

2013-06-01

Certain bacteria are capable of transferring electrons derived from respiratory metabolism to solid extracellular electron-accepting materials1-4. This ability allows the organisms to use conductive substrata as their sole electron sink, generating electricity that is available for practical applications5-7. Geobacter is a biofilm-forming genus capable of this extracellular electron transfer8-11. Evidence in the literature suggests that Geobacter cells produce a conductive matrix to gain access to electron-accepting surfaces12,13. It has been hypothesized that cells that are more than tens of microns from the electron-accepting surface cannot respire because of electrical resistance in the matrix and thus remain metabolically inactive14-16. To testmore » this hypothesis, we sought to determine whether the entire biofilm remains metabolically active and able to respire on an electron-accepting surface as the biofilm thickness increases. We developed and used a novel electrochemical-nuclear magnetic resonance (EC-NMR) microimaging system capable of sustaining an electrochemically active biofilm on a polarized electrode inside a superconducting magnet, allowing for simultaneous NMR and electrochemical investigation of a biofilm for the first time. Here, we show that Geobacter biofilms can grow to several hundred microns thick while respiring on an electrode and that the top of the biofilm remains metabolically active. This is only possible if the cells near the top are able to transfer electrons through the initial biofilm matrix to the electrode. We used X-ray absorption spectroscopy to verify electron transfer to uranium ions by metabolically active cells near the top of the biofilm. Our results reveal that extracellular electron transfer is not prevented by electrical resistance, even when the biofilm is hundreds of microns thick. Furthermore, the electron donor may be the limiting factor for respiration and the base of the biofilm may be less active despite

Effect of dissimilatory Fe(III) reducers on bio-reduction and nickel-cobalt recovery from Sukinda chromite-overburden.

PubMed

Esther, Jacintha; Panda, Sandeep; Behera, Sunil K; Sukla, Lala B; Pradhan, Nilotpala; Mishra, Barada K

2013-10-01

The effect of an adapted dissimilatory iron reducing bacterial consortium (DIRB) towards bio-reduction of Sukinda chromite overburden (COB) with enhanced recovery of nickel and cobalt is being reported for the first time. The remarkable ability of DIRB to utilize Fe(III) as terminal electron acceptor reducing it to Fe(II) proved beneficial for treatment of COB as compared to previous reports for nickel leaching. XRD studies showed goethite as the major iron-bearing phase in COB. Under facultative anaerobic conditions, goethite was reduced to hematite and magnetite with the exposure of nickel oxide. FESEM studies showed DIRB to be associated with COB through biofilm formation with secondary mineral precipitates of magnetite deposited as tiny globular clusters on the extra polymeric substances. The morphological and mineralogical changes in COB, post DIRB application, yielded a maximum of 68.5% nickel and 80.98% cobalt in 10 days using 8M H2SO4. Copyright © 2013 Elsevier Ltd. All rights reserved.

(Per)chlorate Reduction by the Thermophilic Bacterium Moorella perchloratireducens sp. nov., Isolated from Underground Gas Storage▿

PubMed Central

Balk, Melike; van Gelder, Ton; Weelink, Sander A.; Stams, Alfons J. M.

2008-01-01

A thermophilic bacterium, strain An10, was isolated from underground gas storage with methanol as a substrate and perchlorate as an electron acceptor. Cells were gram-positive straight rods, 0.4 to 0.6 μm in diameter and 2 to 8 μm in length, growing as single cells or in pairs. Spores were terminal with a bulged sporangium. The temperature range for growth was 40 to 70°C, with an optimum at 55 to 60°C. The pH optimum was around 7. The salinity range for growth was between 0 and 40 g NaCl liter−1 with an optimum at 10 g liter−1. Strain An10 was able to grow on CO, methanol, pyruvate, glucose, fructose, cellobiose, mannose, xylose, and pectin. The isolate was able to respire with (per)chlorate, nitrate, thiosulfate, neutralized Fe(III) complexes, and anthraquinone-2,6-disulfonate. The G+C content of the DNA was 57.6 mol%. On the basis of 16S rRNA analysis, strain An10 was most closely related to Moorella thermoacetica and Moorella thermoautotrophica. The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell extracts. Strain An10 is the first thermophilic and gram-positive bacterium with the ability to use (per)chlorate as a terminal electron acceptor. PMID:17981952

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

PubMed

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. Copyright © 2015 Elsevier B.V. All rights reserved.

IN SITU RT-PCR WITH A SULFATE-REDUCING BACTERIUM ISOLATED FROM SEAGRASS ROOTS

EPA Science Inventory

Bacteria considered to be obligate anaerobes internally colonize roots of the submerged macrophyte Halodule wrightii. A sulfate reducing bacterium, Summer lac 1, was isolated on lactate from H. wrightii roots. The isolate has physiological characteristics typical of Desulfovibri...

An Inner Membrane Cytochrome Required Only for Reduction of High Redox Potential Extracellular Electron Acceptors

PubMed Central

Levar, Caleb E.; Chan, Chi Ho; Mehta-Kolte, Misha G.

2014-01-01

ABSTRACT Dissimilatory metal-reducing bacteria, such as Geobacter sulfurreducens, transfer electrons beyond their outer membranes to Fe(III) and Mn(IV) oxides, heavy metals, and electrodes in electrochemical devices. In the environment, metal acceptors exist in multiple chelated and insoluble forms that span a range of redox potentials and offer different amounts of available energy. Despite this, metal-reducing bacteria have not been shown to alter their electron transfer strategies to take advantage of these energy differences. Disruption of imcH, encoding an inner membrane c-type cytochrome, eliminated the ability of G. sulfurreducens to reduce Fe(III) citrate, Fe(III)-EDTA, and insoluble Mn(IV) oxides, electron acceptors with potentials greater than 0.1 V versus the standard hydrogen electrode (SHE), but the imcH mutant retained the ability to reduce Fe(III) oxides with potentials of ≤−0.1 V versus SHE. The imcH mutant failed to grow on electrodes poised at +0.24 V versus SHE, but switching electrodes to −0.1 V versus SHE triggered exponential growth. At potentials of ≤−0.1 V versus SHE, both the wild type and the imcH mutant doubled 60% slower than at higher potentials. Electrodes poised even 100 mV higher (0.0 V versus SHE) could not trigger imcH mutant growth. These results demonstrate that G. sulfurreducens possesses multiple respiratory pathways, that some of these pathways are in operation only after exposure to low redox potentials, and that electron flow can be coupled to generation of different amounts of energy for growth. The redox potentials that trigger these behaviors mirror those of metal acceptors common in subsurface environments where Geobacter is found. PMID:25425235

An inner membrane cytochrome required only for reduction of high redox potential extracellular electron acceptors

DOE PAGES

Levar, Caleb E.; Chan, Chi Ho; Mehta-Kolte, Misha G.; ...

2014-10-28

Dissimilatory metal-reducing bacteria, such as Geobacter sulfurreducens, transfer electrons beyond their outer membranes to Fe(III) and Mn(IV) oxides, heavy metals, and electrodes in electrochemical devices. In the environment, metal acceptors exist in multiple chelated and insoluble forms that span a range of redox potentials and offer different amounts of available energy. Despite this, metal-reducing bacteria have not been shown to alter their electron transfer strategies to take advantage of these energy differences. Disruption of imcH, encoding an inner membrane c-type cytochrome, eliminated the ability of G. sulfurreducens to reduce Fe(III) citrate, Fe(III)-EDTA, and insoluble Mn(IV) oxides, electron acceptors with potentialsmore » greater than 0.1 V versus the standard hydrogen electrode (SHE), but the imcH mutant retained the ability to reduce Fe(III) oxides with potentials of ≤–0.1 V versus SHE. The imcH mutant failed to grow on electrodes poised at +0.24 V versus SHE, but switching electrodes to –0.1 V versus SHE triggered exponential growth. At potentials of ≤–0.1 V versus SHE, both the wild type and the imcH mutant doubled 60% slower than at higher potentials. Electrodes poised even 100 mV higher (0.0 V versus SHE) could not trigger imcH mutant growth. These results demonstrate that G. sulfurreducens possesses multiple respiratory pathways, that some of these pathways are in operation only after exposure to low redox potentials, and that electron flow can be coupled to generation of different amounts of energy for growth. Redox potentials that trigger these behaviors mirror those of metal acceptors common in subsurface environments where Geobacter is found.« less

Reduction And Immobilization Of Hexavalent Chromium By Microbially Reduced Fe-bearing Clay Minerals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bishop, Michael E.; Glasser, Paul; Dong, Hailiang

Hexavalent chromium (Cr6+) is a major contaminant in the environment. As a redox-sensitive element, the fate and toxicity of chromium is controlled by reduction-oxidation (redox) reactions. Previous research has shown the ability of structural Fe(II) in naturally present and chemically reduced clay minerals to reduce Cr6+ to Cr(III) as a way of immobilization and detoxification. However, it is still poorly known whether or not structural Fe(II) in biologically reduced clay minerals exhibits a similar reactivity and if so, what the kinetics and mechanisms of Cr6+ reduction are. The objective of this study was to determine the kinetics and possible mechanismsmore » of Cr6+ reduction by structural Fe(II) in microbially reduced clay minerals and the nature of reduced Cr(III). Structural Fe(III) in nontronite (NAu-2), montmorillonite (SWy-2), chlorite (CCa-2), and clay-rich sediments from the Ringold Formation of the Hanford site of Washington State, USA was first bioreduced to Fe(II) by an iron-reducing bacterium Geobacter sulfurreducens with acetate as the sole electron donor and anthraquinone-2,6-disulfate (AQDS) as electron shuttle in synthetic groundwater (pH 7). Biogenic Fe(II) was then used to reduce aqueous Cr6+ at three different temperatures, 10°, 20°, and 30°C, in order to determine the temperature dependence of the redox reaction between Cr6+ and clay-Fe(II). The results showed that nontronite and montmorillonite were most effective in reducing aqueous Cr6+ at all three temperatures. In contrast, most Fe(II) in chlorite was not reactive towards Cr6+ reduction at 10°C, though at 30°C there was some reduction. For all the clay minerals, the ratio of total Fe(II) oxidized to Cr6+ reduced was close to the expected stoichiometric value of 3. Characterization of the Cr-clay reaction product with scanning electron microscopy with focused ion beam and transmission electron microscopy with electron energy loss spectroscopy revealed that reduced chromium was

Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1

PubMed Central

Fredrickson, J. K.; Kostandarithes, H. M.; Li, S. W.; Plymale, A. E.; Daly, M. J.

2000-01-01

Deinococcus radiodurans is an exceptionally radiation-resistant microorganism capable of surviving acute exposures to ionizing radiation doses of 15,000 Gy and previously described as having a strictly aerobic respiratory metabolism. Under strict anaerobic conditions, D. radiodurans R1 reduced Fe(III)-nitrilotriacetic acid coupled to the oxidation of lactate to CO2 and acetate but was unable to link this process to growth. D. radiodurans reduced the humic acid analog anthraquinone-2,6-disulfonate (AQDS) to its dihydroquinone form, AH2DS, which subsequently transferred electrons to the Fe(III) oxides hydrous ferric oxide and goethite via a previously described electron shuttle mechanism. D. radiodurans reduced the solid-phase Fe(III) oxides in the presence of either 0.1 mM AQDS or leonardite humic acids (2 mg ml−1) but not in their absence. D. radiodurans also reduced U(VI) and Tc(VII) in the presence of AQDS. In contrast, Cr(VI) was directly reduced in anaerobic cultures with lactate although the rate of reduction was higher in the presence of AQDS. The results are the first evidence that D. radiodurans can reduce Fe(III) coupled to the oxidation of lactate or other organic compounds. Also, D. radiodurans, in combination with humic acids or synthetic electron shuttle agents, can reduce U and Tc and thus has potential applications for remediation of metal- and radionuclide-contaminated sites where ionizing radiation or other DNA-damaging agents may restrict the activity of more sensitive organisms. PMID:10788374

Humic substance-mediated Fe(III) reduction by a fermenting Bacillus strain from the alkaline gut of a humus-feeding scarab beetle larva.

PubMed

Hobbie, Sven N; Li, Xiangzhen; Basen, Mirko; Stingl, Ulrich; Brune, Andreas

2012-06-01

Humus-feeding macroinvertebrates play an important role in the transformation of soil organic matter. Their diet contains significant amounts of redox-active components such as iron minerals and humic substances. In soil-feeding termites, acid-soluble Fe(III) and humic acids are almost completely reduced during gut passage. Here, we show that the reduction of Fe(III) and humic acids takes place also in the alkaline guts of scarab beetle larvae. Sterilized gut homogenates of Pachnoda ephippiata no longer converted Fe(III) to Fe(II), indicating an essential role of the gut microbiota in the process. From Fe(III)-reducing enrichment cultures inoculated with highly diluted gut homogenates, we isolated several facultatively anaerobic, alkali-tolerant bacteria that were closely related to metal-reducing isolates in the Bacillus thioparans group. Strain PeC11 showed a remarkable capacity for dissimilatory Fe(III) reduction, both at pH 7 and 10. Rates were strongly stimulated by the addition of the redox mediator 2,6-antraquinone disulfonate and by redox-active components in the fulvic-acid fraction of humus. Although the contribution of strain PeC11 to intestinal Fe(III) reduction in P. ephippiata remains to be further elucidated, our results corroborate the hypothesis that the lack of oxygen and the solubilization of humic substances in the extremely alkaline guts of humivorous soil fauna provide favorable conditions for the efficient reduction of Fe(III) and humic substances by a primarily fermentative microbiota. Copyright © 2012 Elsevier GmbH. All rights reserved.

A novel bioaugmentation strategy to accelerate methanogenesis via adding Geobacter sulfurreducens PCA in anaerobic digestion system.

PubMed

Zhang, Shuo; Chang, Jiali; Liu, Wei; Pan, Yiran; Cui, Kangping; Chen, Xi; Liang, Peng; Zhang, Xiaoyuan; Wu, Qing; Qiu, Yong; Huang, Xia

2018-06-12

Based on the new syntrophic methanogenesis route via direct interspecies electron transfer (DIET), a novel bioaugmentation method by adding exoelectrogenic Geobacter species to accelerate methanogenesis was developed in this study. Geobacter sulfurreducens PCA, type exoelectrogenic strain of Geobacter species was chosen for the research. To clarify the effect of G. sulfurreducens on methanogenesis, batch tests of CH 4 production were carried out. Acetate, the most typical precursor of methanogenesis was chosen as the substrate of batch tests. Amendment of G. sulfurreducens accelerated CH 4 production remarkably. The lag phase of CH 4 production was shortened, and the maximum CH 4 production rate was increased by 78%. Fluorescence in situ hybridization showed that G. sulfurreducens closely gathered with methanogens. For the archaeal communities, the high-throughput sequencing results demonstrated that Methanosaetaceae and Methanobacteriaceae were potential bioaugmented methanogens. We speculated that the accelerated methanogenesis by adding G. sulfurreducens may result from the syntrophic association between G. sulfurreducens and methanogens affiliated with Methanosaetaceae and Methanobacteriaceae. This research provides a new route to enhance methanogenesis through the utilization of G. sulfurreducens. Through this study, the role of Geobacter in the anaerobic engineering and carbon cycling of nature should be paid more attention. Copyright © 2018. Published by Elsevier B.V.

A new influence on iron dissolution in Bangladesh aquifers: electron shuttling by groundwater fulvic acids

NASA Astrophysics Data System (ADS)

Mladenov, N.; Kulkarni, H. V.; McKnight, D. M.; Zheng, Y.; Kirk, M. F.

2016-12-01

It was demonstrated more than two decades ago that the electron shuttling ability of fulvic acids (FA) accelerates iron (Fe) reduction. However, the environmental relevance of this mechanism for arsenic-laden groundwater environments has thus far only been hypothesized. Here we show that FAs isolated from high and low arsenic groundwater aquifers in the Bengal Basin can act to shuttle electrons between bacteria and Fe(III). Bangladesh groundwater FAs were reduced by Geobacter metallireducens and were subsequently capable of abiotically reducing Fe(III) to Fe(II). Moreover, all four Bangladesh groundwater FAs investigated in the study had higher Fe(III) to Fe(II) conversion rates compared to anthraquinone disulfonate, an oxidized quinone, and Suwannee River Fulvic Acid, a commercially-available FA isolated from a terrestrially-dominated surface water source. Until now, microbially-mediated reductive dissolution of Fe (oxy)hydroxides, driven by the availability of labile organic matter, was widely accepted as the main control on arsenic mobilization in reducing aquifers. Our evidence for the electron shuttling ability of Bangladesh FAs implicates electron shuttling as another important control on elevated As concentrations in groundwater of the Bengal Basin.

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

PubMed

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.

Rapid anaerobic benzene oxidation with a variety of chelated Fe(III) forms

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.; Chapelle, F.H.

1996-01-01

Fe(III) chelated to such compounds as EDTA, N-methyliminodiacetie acid, ethanol diglycine, humic acids, and phosphates stimulated benzene oxidation coupled to Fe(III) reduction in anaerobic sediments from a petroleum- contaminated aquifer as effectively as or more effectively than nitrilotriacetic acid did in a previously demonstrated stimulation experiment. These results indicate that many forms of chelated Fe(III) might be applicable to aquifer remediation.

Analysis of long-term bacterial vs. chemical Fe(III) oxide reduction kinetics

NASA Astrophysics Data System (ADS)

Roden, Eric E.

2004-08-01

Data from studies of dissimilatory bacterial (10 8 cells mL -1 of Shewanella putrefaciens strain CN32, pH 6.8) and ascorbate (10 mM, pH 3.0) reduction of two synthetic Fe(III) oxide coated sands and three natural Fe(III) oxide-bearing subsurface materials (all at ca. 10 mmol Fe(III) L -1) were analyzed in relation to a generalized rate law for mineral dissolution (J t/m 0 = k'(m/m 0) γ, where J t is the rate of dissolution and/or reduction at time t, m 0 is the initial mass of oxide, and m/m 0 is the unreduced or undissolved mineral fraction) in order to evaluate changes in the apparent reactivity of Fe(III) oxides during long-term biological vs. chemical reduction. The natural Fe(III) oxide assemblages demonstrated larger changes in reactivity (higher γ values in the generalized rate law) compared to the synthetic oxides during long-term abiotic reductive dissolution. No such relationship was evident in the bacterial reduction experiments, in which temporal changes in the apparent reactivity of the natural and synthetic oxides were far greater (5-10 fold higher γ values) than in the abiotic reduction experiments. Kinetic and thermodynamic considerations indicated that neither the abundance of electron donor (lactate) nor the accumulation of aqueous end-products of oxide reduction (Fe(II), acetate, dissolved inorganic carbon) are likely to have posed significant limitations on the long-term kinetics of oxide reduction. Rather, accumulation of biogenic Fe(II) on residual oxide surfaces appeared to play a dominant role in governing the long-term kinetics of bacterial crystalline Fe(III) oxide reduction. The experimental findings together with numerical simulations support a conceptual model of bacterial Fe(III) oxide reduction kinetics that differs fundamentally from established models of abiotic Fe(III) oxide reductive dissolution, and indicate that information on Fe(III) oxide reactivity gained through abiotic reductive dissolution techniques cannot be used to

Raw hematite based Fe(III) bio-reduction process for humified landfill leachate treatment.

PubMed

Li, Rui; Jiang, Yu; Xi, Beidou; Li, Mingxiao; Meng, Xiaoguang; Feng, Chuanping; Mao, Xuhui; Liu, Hongliang; Jiang, Yonghai

2018-05-03

Microorganisms from paddy soils and raw hematite are used for enhancing natural Fe(III) bio-reduction, in order to remove macromolecular organic pollutants from humified landfill leachate. Based on batch experiments, 60% of refractory organics can be adsorbed by hematite in 12 days. In the presence of Fe(III)-reducing bacteria, 489.60 ± 0.14 mg L -1 of dissolved organic matters can be degraded to 51.90 ± 3.96 mg L -1 within 50 days; twelve types of semi volatile organic compounds can be degraded; hereby, the reaction follows a first-order kinetics. Crystalline Fe(III) is transformed into the amorphous form and reduced to Fe(II), hydroquinone functional groups in the humic acid (HA) are transformed to quinone ones, and the formation of HA-hematite ligands is promoted. Comparing with most of the studies about electron shuttling of HA, the transformation of quinone in the HA to hydroquinone could not be observed in the present bio-system. Based on column evaluations, more than 93% of chemical oxygen demand (influent concentration of 658 ± 19 mg L -1 ) could be removed microbially under flow conditions, when the hydraulic retention time was 45 h. Raw hematite-based Fe(III) bio-reduction has a promising potential for the removal of humic and benzene series in humified landfill leachate. Copyright © 2018. Published by Elsevier B.V.

Anaerobic Redox Cycling of Iron by Freshwater Sediment Microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weber, Karrie A.; Urrutia, Matilde M.; Churchill, Perry F.

2006-01-01

The potential for microbially-mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. MPN enumerations revealed the presence of significant populations of Fe(III)-reducing (ca. 108 cells mL-1) and Fe(II)-oxidizing, nitrate-reducing organisms (ca. 105 cells mL-1) in the sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (ca. 1 mM) medium with a small quantity (1% vol/vol) of wetland sediment, and resulted in the transient accumulation of NO2- and production of a mixture of end-products including NH4+. Fe(III) oxide (high surface area goethite) reduction took placemore » - after NO3- was depleted and continued until all the acetate was utilized. Addition of NO3 after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of + NO3-to NH4 . No significant NO2- accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by DGGE analysis of PCR amplified 16s rDNA and RT-PCR amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (= 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both + dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3-reduction to NH4 . Our findings suggest that microbially-catalyzed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic

Influence of humic acid imposed changes of ferrihydrite aggregation on microbial Fe(III) reduction

NASA Astrophysics Data System (ADS)

Amstaetter, Katja; Borch, Thomas; Kappler, Andreas

2012-05-01

Microbial reduction of Fe(III) minerals at neutral pH is faced by the problem of electron transfer from the cells to the solid-phase electron acceptor and is thought to require either direct cell-mineral contact, the presence of Fe(III)-chelators or the presence of electron shuttles, e.g. dissolved or solid-phase humic substances (HS). In this study we investigated to which extent the ratio of Pahokee Peat Humic Acids (HA) to ferrihydrite in the presence and absence of phosphate influences rates of Fe(III) reduction by Shewanella oneidensis MR-1 and the identity of the minerals formed. We found that phosphate generally decreased reduction rates by sorption to the ferrihydrite and surface site blocking. In the presence of low ferrihydrite concentrations (5 mM), the addition of HA helped to overcome this inhibiting effect by functioning as electron shuttle between cells and the ferrihydrite. In contrast, at high ferrihydrite concentrations (30 mM), the addition of HA did not lead to an increase but rather to a decrease in reduction rates. Confocal laser scanning microscopy images and ferrihydrite sedimentation behaviour suggest that the extent of ferrihydrite surface coating by HA influences the aggregation of the ferrihydrite particles and thereby their accessibility for Fe(III)-reducing bacteria. We further conclude that in presence of dissolved HA, iron reduction is stimulated through electron shuttling while in the presence of only sorbed HA, no stimulation by electron shuttling takes place. In presence of phosphate the stimulation effect did not occur until a minimum concentration of 10 mg/l of dissolved HA was reached followed by increasing Fe(III) reduction rates up to dissolved HA concentrations of approximately 240 mg/l above which the electron shuttling effect ceased. Not only Fe(III) reduction rates but also the mineral products changed in the presence of HA. Sequential extraction, XRD and 57Fe-Mössbauer spectroscopy showed that crystallinity and grain

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

DOE PAGES

Liu, Yimo; Wang, Zheming; Liu, Juan; ...

2014-09-24

The multiheme, 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 Pccmore » 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. Finally, complementation with the ombB-omaB-omcB gene cluster restored the ability of G. sulfurreducens PCA to reduce Fe(III)-citrate and ferrihydrite.« less

Stimulated anoxic biodegradation of aromatic hydrocarbons using Fe(III) ligands

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.; Chapelle, F.H.

1994-01-01

Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing the bioavailability of Fe(III) by adding suitable ligands provides a potential alternative to oxygen addition for the bioremediation of petroleum-contaminated aquifers.Contamination of ground waters with water-soluble aromatic hydrocarbons, common components of petroleum pollution, often produces anoxic conditions under which microbial degradation of the aromatics is slow. Oxygen is often added to contaminated ground water to stimulate biodegradation, but this can be technically difficult and expensive. Insoluble Fe(III) oxides, which are generally abundant in shallow aquifers, are alternative potential oxidants, but are difficult for microorganisms to access. Here we report that adding organic ligands that bind to Fe(III) dramatically increases its bioavailability, and that in the presence of these ligands, rates of degradation of aromatic hydrocarbons in anoxic aquifer sediments are comparable to those in oxic sediments. We find that even benzene, which is notoriously refractory in the absence of oxygen, can be rapidly degraded. Our results suggest that increasing

Fine Tuning of Redox Networks on Multiheme Cytochromes from Geobacter sulfurreducens Drives Physiological Electron/Proton Energy Transduction

PubMed Central

Morgado, Leonor; Dantas, Joana M.; Bruix, Marta; Londer, Yuri Y.; Salgueiro, Carlos A.

2012-01-01

The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e−/H+ coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e−/H+ transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e−/H+ transfer at the physiological pH range for cellular growth. PMID:22899897

Anaerobic hydrocarbon degradation in petroleum-contaminated harbor sediments under sulfate-reducing and artificially imposed iron-reducing conditions

USGS Publications Warehouse

Coates, J.D.; Anderson, R.T.; Woodward, J.C.; Phillips, E.J.P.; Lovley, D.R.

1996-01-01

The potential use of iron(III) oxide to stimulate in-situ hydrocarbon degradation in anaerobic petroleum-contaminated harbor sediments was investigated. Previous studies have indicated that Fe(III)-reducing bacteria (FeRB) can oxidize some electron donors more effectively than sulfate- reducing bacteria (SRB). In contrast to previous results in freshwater sediments, the addition of Fe(III) to marine sediments from San Diego Bay, CA did not switch the terminal electron-accepting process (TEAP) from sulfate reduction to Fe-(III) reduction. Addition of Fe(III) also did not stimulate anaerobic hydrocarbon oxidation. Exposure of the sediment to air [to reoxidize Fe(II) to Fe(III)] followed by anaerobic incubation of the sediments, resulted in Fe-(III) reduction as the TEAP, but contaminant degradation was not stimulated and in some instances was inhibited. The difference in the ability of FeRB to compete with the SRB in the different sediment treatments was related to relative population sizes. Although the addition of Fe(III) did not stimulate hydrocarbon degradation, the results presented here as well as other recent studies demonstrate that there may be significant anaerobic hydrocarbon degradation under sulfate-reducing conditions in harbor sediments.

Sulfate-Reducing Bacterium with Unusual Morphology and Pigment Content

PubMed Central

Jones, H. E.

1971-01-01

A dissimilatory sulfate-reducing bacterium was isolated which differed in morphology and pigment content from previously described species. The organism was mesophilic, obligately anaerobic, gram-negative, nonsporulating, long, and slender with one polar flagellum. Whole cells fluoresced red at neutral pH when excited with light at 365 nm owing to the presence of a pink pigment. Desulfoviridin was present. Reduced minus oxidized spectra of whole cells showed peaks in the position of a c-type cytochrome characteristic of Desulfovibrio species and peaks at about 629 and 603 nm. CO difference spectra showed the presence of a CO-binding pigment with a peak at 593 nm. Lactate and pyruvate supported growth in the presence of sulfate but not in its absence. Sulfate, sulfite, and thiosulfate served as electron acceptors for growth. Hydrogenase was present. The deoxyribonucleic acid had a buoyant density of 1.722 g/cm3 and a guanosine plus cystosine molar percentage of total bases calculated by two different methods of 61.2 or 63.2. Images PMID:4929856

Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium.

PubMed

Watts, Mathew P; Khijniak, Tatiana V; Boothman, Christopher; Lloyd, Jonathan R

2015-08-15

Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. Copyright © 2015, Watts et al.

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

USGS Publications Warehouse

Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

1990-01-01

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. ?? 1990.

Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov.

PubMed

Kashefi, Kazem; Holmes, Dawn E; Reysenbach, Anna-Louise; Lovley, Derek R

2002-04-01

It has recently been recognized that the ability to use Fe(III) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. This suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if Fe(III) is used as an electron acceptor. As part of a study of the microbial diversity of the Obsidian Pool area in Yellowstone National Park, Wyo., hot sediment samples were used as the inoculum for enrichment cultures in media containing hydrogen as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. A pure culture was recovered on solidified, Fe(III) oxide medium. The isolate, designated FW-1a, is a hyperthermophilic anaerobe that grows exclusively by coupling hydrogen oxidation to the reduction of poorly crystalline Fe(III) oxide. Organic carbon is not required for growth. Magnetite is the end product of Fe(III) oxide reduction under the culture conditions evaluated. The cells are rod shaped, about 0.5 microm by 1.0 to 1.2 microm, and motile and have a single flagellum. Strain FW-1a grows at circumneutral pH, at freshwater salinities, and at temperatures of between 65 and 100 degrees C with an optimum of 85 to 90 degrees C. To our knowledge this is the highest temperature optimum of any organism in the Bacteria. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain FW-1a places it within the Bacteria, most closely related to abundant but uncultured microorganisms whose 16S rDNA sequences have been previously recovered from Obsidian Pool and a terrestrial hot spring in Iceland. While previous studies inferred that the uncultured microorganisms with these 16S rDNA sequences were sulfate-reducing organisms, the physiology of the strain FW-1a, which does not reduce sulfate, indicates that these organisms are just as likely to be Fe(III) reducers. These results further demonstrate that Fe(III) may be helpful for recovering as-yet-uncultured microorganisms

Oxidation of tetracycline antibiotics induced by Fe(III) ions without light irradiation.

PubMed

Wang, Hui; Yao, Hong; Sun, Peizhe; Pei, Jin; Li, Desheng; Huang, Ching-Hua

2015-01-01

The presence of Fe(III) ions was found to induce degradation of three tetracycline antibiotics (TCs), tetracycline (TTC), oxytetracycline (OTC) and chlorotetracycline (CTC), in aqueous solutions without light. The presence of Fe(III) promoted the degradation of TCs in most experimental pH (5.0, 7.0 and 9.0) except at pH 9.0 for CTC. Degradation rate constants of TTC, OTC and CTC reached maximum ((6.2±0.5)×10(-3) h(-1), (10.6±0.1)×10(-3) h(-1) and (15.9±0.5)×10(-3) h(-1) at pH 7.0, 20 °C) when Fe(III):TC molar ratio was 1:1, 1:1 and 2:1, respectively. Such metal-to-ligand ratios agreed well with the most favorable complexation between Fe(III) and each TC. Compared to without metals, Fe(III) enhanced the degradation rate of TTC, OTC and CTC by up to 20.67, 7.07 and 2.30 times, respectively, in clean water matrix, and also promoted degradation of TCs in real surface water and wastewater matrices. The promoted degradation likely occurred via complexation of TCs and subsequent oxidation by Fe(III). Degradation results of CTC versus 4-epi-CTC suggested Fe(III) likely binds to TCs' C4 dimethylamino group. Toxicity of the complexes evaluated using Photobacterium phosphoreum T3 was increased after several hours of reaction, suggesting the transformation products may exert a stronger toxicity than parent TCs. This study identifies new oxidative transformation of TCs induced by Fe(III) ions without light irradiation, further supporting the important role of iron species in the environmental fate of TCs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Selective transport of Fe(III) using ionic imprinted polymer (IIP) membrane particle

NASA Astrophysics Data System (ADS)

Djunaidi, Muhammad Cholid; Jumina, Siswanta, Dwi; Ulbricht, Mathias

2015-12-01

The membrane particles was prepared from polyvinyl alcohol (PVA) and polymer IIP with weight ratios of 1: 2 and 1: 1 using different adsorbent templates and casting thickness. The permeability of membrane towards Fe(III) and also mecanism of transport were studied. The selectivity of the membrane for Fe(III) was studied by performing adsorption experiments also with Cr(III) separately. In this study, the preparation of Ionic Imprinted Polymer (IIP) membrane particles for selective transport of Fe (III) had been done using polyeugenol as functional polymer. Polyeugenol was then imprinted with Fe (III) and then crosslinked with PEGDE under alkaline condition to produce polyeugenol-Fe-PEGDE polymer aggregates. The agrregates was then crushed and sieved using mesh size of 80 and the powder was then used to prepare the membrane particles by mixing it with PVA (Mr 125,000) solution in 1-Methyl-2-pyrrolidone (NMP) solvent. The membrane was obtained after casting at a speed of 25 m/s and soaking in NaOH solution overnight. The membrane sheet was then cut and Fe(III) was removed by acid to produce IIP membrane particles. Analysis of the membrane and its constituent was done by XRD, SEM and size selectivity test. Experimental results showed the transport of Fe(III) was faster with the decrease of membrane thickness, while the higher concentration of template ion correlates with higher Fe(III) being transported. However, the transport of Fe(III) was slower for higher concentration of PVA in the membrane. IImparticles works through retarded permeation mechanism, where Fe(III) was bind to the active side of IIP. The active side of IIP membrane was dominated by the -OH groups. The selectivity of all IIP membranes was confirmed as they were all unable to transport Cr (III), while NIP (Non-imprinted Polymer) membrane was able transport Cr (III).

Isolation of an arsenate-respiring bacterium from a redox front in an arsenic-polluted aquifer in West Bengal, Bengal Basin.

PubMed

Osborne, Thomas H; McArthur, John M; Sikdar, Pradip K; Santini, Joanne M

2015-04-07

Natural pollution of groundwater by arsenic adversely affects the health of tens of millions of people worldwide, with the deltaic aquifers of SE Asia being particularly polluted. The pollution is caused primarily by, or as a side reaction of, the microbial reduction of sedimentary Fe(III)-oxyhydroxides, but the organism(s) responsible for As release have not been isolated. Here we report the first isolation of a dissimilatory arsenate reducer from sediments of the Bengal Basin in West Bengal. The bacterium, here designated WB3, respires soluble arsenate and couples its reduction to the oxidation of acetate; WB3 is therefore implicated in the process of arsenic pollution of groundwater, which is largely by arsenite. The bacterium WB3 is also capable of reducing dissolved Fe(III) citrate, solid Fe(III)-oxyhydroxide, and elemental sulfur, using acetate as the electron donor. It is a member of the Desulfuromonas genus and possesses a dissimilatory arsenate reductase that was identified using degenerate polymerase chain reaction primers. The sediment from which WB3 was isolated was brown, Pleistocene sand at a depth of 35.2 m below ground level (mbgl). This level was some 3 cm below the boundary between the brown sands and overlying reduced, gray, Holocene aquifer sands. The color boundary is interpreted to be a reduction front that releases As for resorption downflow, yielding a high load of labile As sorbed to the sediment at a depth of 35.8 mbgl and concentrations of As in groundwater that reach >1000 μg/L.

Mechanistic investigation of Fe(III) oxide reduction by low molecular weight organic sulfur species

NASA Astrophysics Data System (ADS)

Eitel, Eryn M.; Taillefert, Martial

2017-10-01

Low molecular weight organic sulfur species, often referred to as thiols, are known to be ubiquitous in aquatic environments and represent important chemical reductants of Fe(III) oxides. Thiols are excellent electron shuttles used during dissimilatory iron reduction, and in this capacity could indirectly affect the redox state of sediments, release adsorbed contaminants via reductive dissolution, and influence the carbon cycle through alteration of bacterial respiration processes. Interestingly, the reduction of Fe(III) oxides by thiols has not been previously investigated in environmentally relevant conditions, likely due to analytical limitations associated with the detection of thiols and their oxidized products. In this study, a novel electrochemical method was developed to simultaneously determine thiol/disulfide pair concentrations in situ during the reduction of ferrihydrite in batch reactors. First order rate laws with respect to initial thiol concentration were confirmed for Fe(III) oxyhydroxide reduction by four common thiols: cysteine, homocysteine, cysteamine, and glutathione. Zero order was determined for both Fe(III) oxyhydroxide and proton concentration at circumneutral pH. A kinetic model detailing the molecular mechanism of the reaction was optimized with proposed intermediate surface structures. Although metal oxide overall reduction rate constants were inversely proportional to the complexity of the thiol structure, the extent of metal reduction increased with structure complexity, indicating that surface complexes play a significant role in the ability of these thiols to reduce iron. Taken together, these results demonstrate the importance of considering the molecular reaction mechanism at the iron oxide surface when investigating the potential for thiols to act as electron shuttles during dissimilatory iron reduction in natural environments.

High Biofilm Conductivity Maintained Despite Anode Potential Changes in a Geobacter-Enriched Biofilm

EPA Science Inventory

This study systematically assessed intracellular electron transfer (IET) and extracellular electron transfer (EET) kinetics with respect to anode potential (Eanode) in a mixed-culture biofilm anode enriched with Geobacter spp. High biofilm conductivity (0.96–1.24 mScm^-1) was mai...

Porphyromonas endodontalis binds, reduces and grows on human hemoglobin.

PubMed

Zerr, M; Drake, D; Johnson, W; Cox, C D

2001-08-01

Porphyromonas endodontalis is a black-pigmented, obligate anaerobic rod-shaped bacterium implicated as playing a major role in endodontic infections. We have previously shown that P. endodontalis requires the porphyrin nucleus, preferably supplied as hemoglobin, as a growth supplement. The bacteria also actively transport free iron, although this activity does not support growth in the absence of a porphyrin source. The purpose of this study was to further investigate the binding and subsequent utilization of human hemoglobin by P. endodontalis. P. endodontalis binds hemoglobin and reduces the Fe(III) porphyrin, resulting in a steady accumulation of ferrous hemoglobin. Reduction of methemoglobin was similar to the extracellular reduction of nitrobluetetrazolium in the presence of oxidizable substrate. Turbidimetric and viable cell determinations showed that P. endodontalis grew when supplied only hemoglobin. Therefore, we conclude that hemoglobin appears to serve as a sole carbon and nitrogen source, and that these bacteria reduce extracellular compounds at the expense of oxidized substrates.

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems

PubMed Central

Venkidusamy, Krishnaveni; Hari, Ananda Rao; Megharaj, Mallavarapu

2018-01-01

Exoelectrogenic biofilms capable of extracellular electron transfer are important in advanced technologies such as those used in microbial electrochemical remediation systems (MERS) Few bacterial strains have been, nevertheless, obtained from MERS exoelectrogenic biofilms and characterized for bioremediation potential. Here we report the identification of one such bacterial strain, Citrobacter sp. KVM11, a petrophilic, iron reducing bacterial strain isolated from hydrocarbon fed MERS, producing anodic currents in microbial electrochemical systems. Fe(III) reduction of 90.01 ± 0.43% was observed during 5 weeks of incubation with Fe(III) supplemented liquid cultures. Biodegradation screening assays showed that the hydrocarbon degradation had been carried out by metabolically active cells accompanied by growth. The characteristic feature of diazo dye decolorization was used as a simple criterion for evaluating the electrochemical activity in the candidate microbe. The electrochemical activities of the strain KVM11 were characterized in a single chamber fuel cell and three electrode electrochemical cells. The inoculation of strain KVM11 amended with acetate and citrate as the sole carbon and energy sources has resulted in an increase in anodic currents (maximum current density) of 212 ± 3 and 359 ± mA/m2 with respective coulombic efficiencies of 19.5 and 34.9% in a single chamber fuel cells. Cyclic voltammetry studies showed that anaerobically grown cells of strain KVM11 are electrochemically active whereas aerobically grown cells lacked the electrochemical activity. Electrobioremediation potential of the strain KVM11 was investigated in hydrocarbonoclastic and dye detoxification conditions using MERS. About 89.60% of 400 mg l-1 azo dye was removed during the first 24 h of operation and it reached below detection limits by the end of the batch operation (60 h). Current generation and biodegradation capabilities of strain KVM11 were examined using an initial

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems.

PubMed

Venkidusamy, Krishnaveni; Hari, Ananda Rao; Megharaj, Mallavarapu

2018-01-01

Exoelectrogenic biofilms capable of extracellular electron transfer are important in advanced technologies such as those used in microbial electrochemical remediation systems (MERS) Few bacterial strains have been, nevertheless, obtained from MERS exoelectrogenic biofilms and characterized for bioremediation potential. Here we report the identification of one such bacterial strain, Citrobacter sp. KVM11, a petrophilic, iron reducing bacterial strain isolated from hydrocarbon fed MERS, producing anodic currents in microbial electrochemical systems. Fe(III) reduction of 90.01 ± 0.43% was observed during 5 weeks of incubation with Fe(III) supplemented liquid cultures. Biodegradation screening assays showed that the hydrocarbon degradation had been carried out by metabolically active cells accompanied by growth. The characteristic feature of diazo dye decolorization was used as a simple criterion for evaluating the electrochemical activity in the candidate microbe. The electrochemical activities of the strain KVM11 were characterized in a single chamber fuel cell and three electrode electrochemical cells. The inoculation of strain KVM11 amended with acetate and citrate as the sole carbon and energy sources has resulted in an increase in anodic currents (maximum current density) of 212 ± 3 and 359 ± mA/m 2 with respective coulombic efficiencies of 19.5 and 34.9% in a single chamber fuel cells. Cyclic voltammetry studies showed that anaerobically grown cells of strain KVM11 are electrochemically active whereas aerobically grown cells lacked the electrochemical activity. Electrobioremediation potential of the strain KVM11 was investigated in hydrocarbonoclastic and dye detoxification conditions using MERS. About 89.60% of 400 mg l -1 azo dye was removed during the first 24 h of operation and it reached below detection limits by the end of the batch operation (60 h). Current generation and biodegradation capabilities of strain KVM11 were examined using an initial

Biochemical capacitance of Geobacter sulfurreducens biofilms.

PubMed

Bueno, Paulo R; Schrott, Germán D; Bonanni, Pablo S; Simison, Silvia N; Busalmen, Juan P

2015-08-10

An electrical model able to decouple the electron pathway from microbial cell machinery impedance terms is introduced. In this context, capacitance characteristics of the biofilm are clearly resolved. In other words, the model allows separating, according to the advantage of frequency and spectroscopic response approach, the different terms controlling the performance of the microbial biofilm respiratory process and thus the directly related electricity production process. The model can be accurately fitted to voltammetry measurements obtained under steady-state conditions and also to biofilm discharge amperometric measurements. The implications of biological aspects of the electrochemical or redox capacitance are discussed theoretically in the context of current knowledge with regard to structure and physiological activity of microbial Geobacter biofilms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Degradation of Nitrobenzene Using Bio-Reduced Fe-Clays: Progress Towards the Development of an in-situ Groundwater Remediation Technology

NASA Astrophysics Data System (ADS)

White, M. L.; Fialips, C. I.

2008-12-01

Clay minerals are widely used in agricultural, industrial and environmental engineering applications due to their specific physical and chemical properties and their high abundance in soils in sediments. Currently however, Fe-bearing clays are not widely exploited in these applied fields. Fe-rich smectites, such as nontronite, can contain up to 20wt% of Fe2O3 as structural Fe(III) and if a suitable electron donor is available, this Fe(III) can be utilized by Fe-reducing bacteria as a terminal electron acceptor. When reduced, the overall reactivity of Fe-smectites changes, particularly where interactions with water and various organic compounds are involved. For instance, the presence of reduced Fe-smectites has been found to induce the degradation of certain organic contaminants found in groundwaters and the subsurface, e.g. chlorinated aliphatics and nitroaromatic compounds. The goal of this study is to develop an in-situ groundwater remediation technology that targets redox- sensitive organics, in the form of a permeable Bio Fe-clay barrier. To achieve this, the iron-reducing bacterium Shewanella algae BrY was first used to reduce structural FeIII in <2micron fractions of the Fe- rich smectite nontronite (NAu-2, 41.74wt% Fe2O3) and a Fe-bearing montmorrillonite (Speeton Clay, Yorkshire, UK, ~8wt% Fe2O3). S. algae BrY was able to reduce structural FeIII within these clays to maximum Fe(II)/Fe(II)+Fe(III) ratios 0.34 and 0.19 for the nontronite and Speeton Clay, respectively, in the presence and absence of the electron shuttle, AQDS (9, 10-anthraquinone-2, 6-disulfonic acid). These results are novel because the capability of S. algae BrY to reduce structural Fe(III) in smectite clays has not previously been tested. Nitrobenzene was selected as the test redox-sensitive organic compound as it is a common subsurface contaminant and is of global ecotoxicological concern. To test the capability of bio- reduced Fe-clays to transform nitrobenzene to aniline (the less

Growth of thermophilic and hyperthermophilic Fe(III)-reducing microorganisms on a ferruginous smectite as the sole electron acceptor.

PubMed

Kashefi, Kazem; Shelobolina, Evgenya S; Elliott, W Crawford; Lovley, Derek R

2008-01-01

Recent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilic Archaea and Bacteria from marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested, Geoglobus ahangari and Geothermobacterium ferrireducens, were not able to conserve energy to support growth by reduction of Fe(III) in SWa-1 despite the fact that both organisms were originally isolated with solid-phase Fe(III) as the electron acceptor. The other organisms tested were able to grow on SWa-1 and reduced 6.3 to 15.1% of the Fe(III). This is 20 to 50% less than the reported amounts of Fe(III) reduced in the same smectite (SWa-1) by mesophilic Fe(III) reducers. Two organisms, Geothermobacter ehrlichii and archaeal strain 140, produced copious amounts of an exopolysaccharide material, which may have played an active role in the dissolution of the structural iron in SWa-1 smectite. The reduction of structural Fe(III) in SWa-1 by archaeal strain 140 was studied in detail. Microbial Fe(III) reduction was accompanied by an increase in interlayer and octahedral charges and some incorporation of potassium and magnesium into the smectite structure. However, these changes in the major element chemistry of SWa-1 smectite did not result in the formation of an illite-like structure, as reported for a mesophilic Fe(III) reducer. These results suggest that thermophilic Fe(III)-reducing organisms differ in their ability to reduce and solubilize structural Fe(III) in SWa-1 smectite and that SWa-1

Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor▿

PubMed Central

Kashefi, Kazem; Shelobolina, Evgenya S.; Elliott, W. Crawford; Lovley, Derek R.

2008-01-01

Recent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilic Archaea and Bacteria from marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested, Geoglobus ahangari and Geothermobacterium ferrireducens, were not able to conserve energy to support growth by reduction of Fe(III) in SWa-1 despite the fact that both organisms were originally isolated with solid-phase Fe(III) as the electron acceptor. The other organisms tested were able to grow on SWa-1 and reduced 6.3 to 15.1% of the Fe(III). This is 20 to 50% less than the reported amounts of Fe(III) reduced in the same smectite (SWa-1) by mesophilic Fe(III) reducers. Two organisms, Geothermobacter ehrlichii and archaeal strain 140, produced copious amounts of an exopolysaccharide material, which may have played an active role in the dissolution of the structural iron in SWa-1 smectite. The reduction of structural Fe(III) in SWa-1 by archaeal strain 140 was studied in detail. Microbial Fe(III) reduction was accompanied by an increase in interlayer and octahedral charges and some incorporation of potassium and magnesium into the smectite structure. However, these changes in the major element chemistry of SWa-1 smectite did not result in the formation of an illite-like structure, as reported for a mesophilic Fe(III) reducer. These results suggest that thermophilic Fe(III)-reducing organisms differ in their ability to reduce and solubilize structural Fe(III) in SWa-1 smectite and that SWa-1

New method for the direct determination of dissolved Fe(III) concentration in acid mine waters

USGS Publications Warehouse

To, T.B.; Nordstrom, D. Kirk; Cunningham, K.M.; Ball, J.W.; McCleskey, R. Blaine

1999-01-01

A new method for direct determination of dissolved Fe(III) in acid mine water has been developed. In most present methods, Fe(III) is determined by computing the difference between total dissolved Fe and dissolved Fe(II). For acid mine waters, frequently Fe(II) >> Fe(III); thus, accuracy and precision are considerably improved by determining Fe(III) concentration directly. The new method utilizes two selective ligands to stabilize Fe(III) and Fe(II), thereby preventing changes in Fe reduction-oxidation distribution. Complexed Fe(II) is cleanly removed using a silica-based, reversed-phase adsorbent, yielding excellent isolation of the Fe(III) complex. Iron(III) concentration is measured colorimetrically or by graphite furnace atomic absorption spectrometry (GFAAS). The method requires inexpensive commercial reagents and simple procedures that can be used in the field. Calcium(II), Ni(II), Pb(II), AI(III), Zn(II), and Cd(II) cause insignificant colorimetric interferences for most acid mine waters. Waters containing >20 mg of Cu/L could cause a colorimetric interference and should be measured by GFAAS. Cobalt(II) and Cr(III) interfere if their molar ratios to Fe(III) exceed 24 and 5, respectively. Iron(II) interferes when its concentration exceeds the capacity of the complexing ligand (14 mg/L). Because of the GFAAS elemental specificity, only Fe(II) is a potential interferent in the GFAAS technique. The method detection limit is 2 ??g/L (40 nM) using GFAAS and 20 ??g/L (0.4 ??M) by colorimetry.A new method for direct determination of dissolved Fe(III) in acid mine water has been developed. In most present methods, Fe(III) is determined by computing the difference between total dissolved Fe and dissolved Fe(II). For acid mine waters, frequently Fe(II)???Fe(III); thus, accuracy and precision are considerably improved by determining Fe(III) concentration directly. The new method utilizes two selective ligands to stabilize Fe(III) and Fe(II), thereby preventing changes

Investigation of complexes tannic acid and myricetin with Fe(III)

NASA Astrophysics Data System (ADS)

Sungur, Şana; Uzar, Atike

2008-01-01

The pH dependence of the complexes was determined by both potentiometric and spectrophotometric studies. Stability constants and stoichiometries of the formed complexes were determined using slope ratio method. Fe(III) was formed complexes with tannic acid of various stoichiometries, which in the 1:1 molar ratio at pH < 3, in the 2:1 molar ratio at pH 3-7 and in the 4:1 molar ratio at pH > 7. Fe(III) was formed complexes with myricetin in the 1:2 molar ratio at pH 4 and 5 and in the 1:1 molar ratio at pH 6. Stability constant values were found to be 10 5 to 10 17 and 10 5 to 10 9 for Fe(III)-tannic acid complexes and Fe(III)-myricetin complexes. Both tannic acid and myricetin were possessed minimum affinities to Cu(II) and Zn(II). They had less affinity for Al(III) than for Fe(III).

Geothrix fermentans Secretes Two Different Redox-Active Compounds To Utilize Electron Acceptors across a Wide Range of Redox Potentials

PubMed Central

Mehta-Kolte, Misha G.

2012-01-01

The current understanding of dissimilatory metal reduction is based primarily on isolates from the proteobacterial genera Geobacter and Shewanella. However, environments undergoing active Fe(III) reduction often harbor less-well-studied phyla that are equally abundant. In this work, electrochemical techniques were used to analyze respiratory electron transfer by the only known Fe(III)-reducing representative of the Acidobacteria, Geothrix fermentans. In contrast to previously characterized metal-reducing bacteria, which typically reach maximal rates of respiration at electron acceptor potentials of 0 V versus standard hydrogen electrode (SHE), G. fermentans required potentials as high as 0.55 V to respire at its maximum rate. In addition, G. fermentans secreted two different soluble redox-active electron shuttles with separate redox potentials (−0.2 V and 0.3 V). The compound with the lower midpoint potential, responsible for 20 to 30% of electron transfer activity, was riboflavin. The behavior of the higher-potential compound was consistent with hydrophilic UV-fluorescent molecules previously found in G. fermentans supernatants. Both electron shuttles were also produced when cultures were grown with Fe(III), but not when fumarate was the electron acceptor. This study reveals that Geothrix is able to take advantage of higher-redox-potential environments, demonstrates that secretion of flavin-based shuttles is not confined to Shewanella, and points to the existence of high-potential-redox-active compounds involved in extracellular electron transfer. Based on differences between the respiratory strategies of Geothrix and Geobacter, these two groups of bacteria could exist in distinctive environmental niches defined by redox potential. PMID:22843516

Complete Genome Sequence of Alkaliphilus metalliredigens QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-contaminated Leachate Ponds

DOE PAGES

Hwang, C.; Copeland, A.; Lucas, Susan; ...

2016-11-03

Alkaliphilus metalliredigens QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

Complete Genome Sequence of Alkaliphilus metalliredigens QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-contaminated Leachate Ponds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hwang, C.; Copeland, A.; Lucas, Susan

Alkaliphilus metalliredigens QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2015-09-05

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 poisedmore » 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 ΔcbcL 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.« less

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

PubMed

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. Copyright © 2015. Published by Elsevier B.V.

Hexanuclear Fe(III) wheels functionalized by amino-acetonitrile derivatives

NASA Astrophysics Data System (ADS)

Kravtsov, Victor Ch.; Malaestean, Iurie; Stingach, Eugenia P.; Duca, Gheorghe G.; Macaev, Fliur Z.; van Leusen, Jan; Kögerler, Paul; Hauser, Jürg; Krämer, Karl; Decurtins, Silvio; Liu, Shi-Xia; Ghosh, Ashta C.; Garcia, Yann; Baca, Svetlana G.

2018-04-01

Three new hexanuclear Fe(III) coordination wheels [Fe6Cl6(L1)6]·5(MeCN) (1), [Na0.5Fe6Cl6(L1)6](N3)0.5·4.5(MeCN) (2), and [Fe6Cl6(L2)6]·2(MeCN) (3) have been synthesized with new prepared amino-acetonitrile derivatives 2-[bis(2-hydroxyethyl)amino]acetonitrile hydrochloride (H2L1) and 3-[bis(2-hydroxyethyl)amino]propanenitrile hydrochloride (H2L2). They were structurally characterized by single-crystal X-ray diffraction. Mößbauer spectroscopy and magnetic susceptibility measurements indicate dominant antiferromagnetic behavior between the Fe(III) centers.

Functional Role of Infective Viral Particles on Metal Reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 andmore » 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.« less

Stepping stones in the electron transport from cells to electrodes in Geobacter sulfurreducens biofilms.

PubMed

Bonanni, Pablo Sebastián; Massazza, Diego; Busalmen, Juan Pablo

2013-07-07

Geobacter sulfurreducens bacteria grow on biofilms and have the particular ability of using polarized electrodes as the final electron acceptor of their respiratory chain. In these biofilms, electrons are transported through distances of more than 50 μm before reaching the electrode. The way in which electrons are transported across the biofilm matrix through such large distances remains under intense discussion. None of the two mechanisms proposed for explaining the process, electron hopping through outer membrane cytochromes and metallic like conduction through conductive PilA filaments, can account for all the experimental evidence collected so far. Aiming at providing new elements for understanding the basis for electron transport, in this perspective article we present a modelled structure of Geobacter pilus. Its analysis in combination with already existing experimental evidence gives support to the proposal of the "stepping stone" mechanism, in which the combined action of pili and cytochromes allows long range electron transport through the biofilm.

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, Yilin; Wilkins, Michael J.; Yabusaki, Steven B.

2012-12-12

Biomass and shotgun global proteomics data that reflected relative protein abundances from samples collected during the 2008 experiment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge site in Rifle, Colorado, provided an unprecedented opportunity to validate a genome-scale metabolic model of Geobacter metallireducens and assess its performance with respect to prediction of metal reduction, biomass yield, and growth rate under dynamic field conditions. Reconstructed from annotated genomic sequence, biochemical, and physiological data, 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.more » 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 fluxes through 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.« less

Rapid photooxidation of Sb(III) in the presence of different Fe(III) species

NASA Astrophysics Data System (ADS)

Kong, Linghao; He, Mengchang; Hu, Xingyun

2016-05-01

The toxicity and mobility of antimony (Sb) are strongly influenced by the redox processes associated with Sb. Dissolved iron (Fe) is widely distributed in the environment as different species and plays a significant role in Sb speciation. However, the mechanisms of Sb(III) oxidation in the presence of Fe have remained unclear because of the complexity of Fe and Sb speciation. In this study, the mechanisms of Sb(III) photooxidation in the presence of different Fe species were investigated systematically. The photooxidation of Sb(III) occurred over a wide pH range, from 1 to 10. Oxygen was not a predominant or crucial factor in the Sb(III) oxidation process. The mechanism of Sb(III) photooxidation varied depending on the Fe(III) species. In acidic solution (pH 1-3), dichloro radicals (radCl2-) and hydroxyl radicals (radOH) generated by the photocatalysis of FeCl2+ and FeOH2+ were the main oxidants for Sb(III) oxidation. Fe(III) gradually transformed into the colloid ferric hydroxide (CFH) and ferrihydrite in circumneutral and alkaline solutions (pH 4-10). Photooxidation of Sb(III) occurred through electron transfer from Sb(III) to Fe(III) along with the reduction of Fe(III) to Fe(II) through a ligand-to-metal charge-transfer (LMCT) process. The photocatalysis of different Fe(III) species may play an important role in the geochemical cycle of Sb(III) in surface soil and aquatic environments.

Intercalation of Coordinatively Unsaturated Fe(III) Ion within Interpenetrated Metal-Organic Framework MOF-5.

PubMed

Holmberg, Rebecca J; Burns, Thomas; Greer, Samuel M; Kobera, Libor; Stoian, Sebastian A; Korobkov, Ilia; Hill, Stephen; Bryce, David L; Woo, Tom K; Murugesu, Muralee

2016-06-01

Coordinatively unsaturated Fe(III) metal sites were successfully incorporated into the iconic MOF-5 framework. This new structure, Fe(III) -iMOF-5, is the first example of an interpenetrated MOF linked through intercalated metal ions. Structural characterization was performed with single-crystal and powder XRD, followed by extensive analysis by spectroscopic methods and solid-state NMR, which reveals the paramagnetic ion through its interaction with the framework. EPR and Mössbauer spectroscopy confirmed that the intercalated ions were indeed Fe(III) , whereas DFT calculations were employed to ascertain the unique pentacoordinate architecture around the Fe(III) ion. Interestingly, this is also the first crystallographic evidence of pentacoordinate Zn(II) within the MOF-5 SBU. This new MOF structure displays the potential for metal-site addition as a framework connector, thus creating further opportunity for the innovative development of new MOF materials. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aluminum affects heterogeneous Fe(III) (Hydr)oxide nucleation, growth, and ostwald ripening.

PubMed

Hu, Yandi; Li, Qingyun; Lee, Byeongdu; Jun, Young-Shin

2014-01-01

Heterogeneous coprecipitation of iron and aluminum oxides is an important process for pollutant immobilization and removal in natural and engineered aqueous environments. Here, using a synchrotron-based small-angle X-ray scattering technique, we studied heterogeneous nucleation and growth of Fe(III) (hydr)oxide on quartz under conditions found in acid mine drainage (at pH = 3.7 ± 0.2, [Fe(3+)] = 10(-4) M) with different initial aqueous Al/Fe ratios (0:1, 1:1, and 5:1). Interestingly, although the atomic ratios of Al/Fe in the newly formed Fe(III) (hydr)oxide precipitates were less than 1%, the in situ particle size and volume evolutions of the precipitates on quartz were significantly influenced by aqueous Al/Fe ratios. At the end of the 3 h experiments, with aqueous Al/Fe ratios of 0:1, 1:1, and 5:1, the average radii of gyration of particles on quartz were 5.7 ± 0.3, 4.6 ± 0.1, and 3.7 ± 0.3 nm, respectively, and the ratio of total particle volumes on quartz was 1.7:3.4:1.0. The Fe(III) (hydr)oxide precipitates were poorly crystallized, and were positively charged in all solutions. In the presence of Al(3+), Al(3+) adsorption onto quartz changed the surface charge of quartz from negative to positive, which caused the slower heterogeneous growth of Fe(III) (hydr)oxide on quartz. Furthermore, Al affected the amount of water included in the Fe(III) (hydr)oxides, which can influence their adsorption capacity. This study yielded important information usable for pollutant removal not only in natural environments, but also in engineered water treatment processes.

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds

PubMed Central

Copeland, A.; Lucas, S.; Lapidus, A.; Barry, K.; Detter, J. C.; Glavina del Rio, T.; Hammon, N.; Israni, S.; Dalin, E.; Tice, H.; Pitluck, S.; Chertkov, O.; Brettin, T.; Bruce, D.; Han, C.; Schmutz, J.; Larimer, F.; Land, M. L.; Hauser, L.; Kyrpides, N.; Mikhailova, N.; Ye, Q.; Zhou, J.; Richardson, P.; Fields, M. W.

2016-01-01

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes. QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms. PMID:27811105

Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Haiyan; Lin, Hui; Zheng, Wang

2013-08-04

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 methylmercury1-4. One strain of sulphate-reducing bacteria (Desulfovibrio desulfuricans ND132) can also methylate elemental mercury5. 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 oxidise 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 ofmore » elemental mercury. We report differences in the ability of these organisms to oxidise and methylate elemental mercury. In line with recent findings5, we show that Desulfovibrio desulfuricans ND132 can both oxidise and methylate elemental mercury. However, the rate of methylation of elemental mercury is only about one third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidise, but not methylate, elemental mercury. Geobacter sulfurreducens PCA is able to oxidise 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.« less

Role of an organic carbon-rich soil and Fe(III) reduction in reducing the toxicity and environmental mobility of chromium(VI) at a COPR disposal site.

PubMed

Ding, Weixuan; Stewart, Douglas I; Humphreys, Paul N; Rout, Simon P; Burke, Ian T

2016-01-15

Cr(VI) is an important contaminant found at sites where chromium ore processing residue (COPR) is deposited. No low cost treatment exists for Cr(VI) leaching from such sites. This study investigated the mechanism of interaction of alkaline Cr(VI)-containing leachate with an Fe(II)-containing organic matter rich soil beneath the waste. The soil currently contains 0.8% Cr, shown to be present as Cr(III)(OH)3 in EXAFS analysis. Lab tests confirmed that the reaction of Cr(VI) in site leachate with Fe(II) present in the soil was stoichiometrically correct for a reductive mechanism of Cr accumulation. However, the amount of Fe(II) present in the soil was insufficient to maintain long term Cr(VI) reduction at historic infiltration rates. The soil contains a population of bacteria dominated by a Mangroviflexus-like species, that is closely related to known fermentative bacteria, and a community capable of sustaining Fe(III) reduction in alkaline culture. It is therefore likely that in situ fermentative metabolism supported by organic matter in the soil produces more labile organic substrates (lactate was detected) that support microbial Fe(III) reduction. It is therefore suggested that addition of solid phase organic matter to soils adjacent to COPR may reduce the long term spread of Cr(VI) in the environment. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

PubMed

Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

2012-08-02

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Environmental Factors Affecting Ammonium Oxidation Under Iron Reducing Conditions

NASA Astrophysics Data System (ADS)

Jaffe, P. R.; Huang, S.; Ruiz-Urigüen, M.

2014-12-01

Ammonium (NH4+) oxidation coupled to iron (Fe) reduction in the absence of oxygen and nitrate/nitrite (NO3-/NO2-) has been reported by several investigators and referred to as Feammox. Feammox is a biological reaction, where Fe(III) is the electron acceptor, which is reduced to Fe(II), and NH4+ is the electron donor, which is oxidized to NO2-. Through a 180-day anaerobic incubation experiment, and using PCR-DGGE, 454-pyosequecing and qPCR analysis, we have shown that an Acidimicrobiaceae bacterium A6, a previously unreported species in the Acidimicrobiaceae family, might be either responsible or plays a key role in the Feammox process, We have enriched these Feammox bacteria (65.8% in terms of cell numbers) in a membrane reactor, and isolated the pure Acidimicrobiaceae bacterium A6 strain in an autotrophic medium. In samples collected and then incubated from a series of local wetland-, upland-, as well as storm-water detention pond-sediments, Feammox activity was only detected in acidic soil environments that contain Fe oxides. Using primers we developed for this purpose, Acidimicrobiaceae bacterium A6 was detected in all incubations where Feammox was observed. Anaerobic incubations of Feammox enrichment cultures adjusted to different pH, revealed that the optimal pH for Feammox is 4 ~ 5, and the reaction does not proceed when pH > 7. Feammox was still proceeding at pH as low as 2. In Feammox culture amended with different Fe(III) sources, Feammox reaction proceeded only when Fe oxides (ferrihydrite or goethite ) were supplied, whereas samples incubated with ferric chloride or ferric citrate showed no measurable NH4+ oxidation. Furthermore, we have also determined from incubation experiments conducted with a temperature gradient (10 ~ 35℃), that the Feammox process was active when the temperature is above 15℃, and the optimal temperature is 20℃. Incubations of enrichment culture with 79% Feammox bacteria appeared to remove circa 8% more NH4+ at 20ºC than at

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

[Research on mercury methylation by Geobacter sulfurreducens and its influencing factors].

PubMed

Zou, Yan; Si, You-Bin; Yan, Xue; Chen, Yan

2012-09-01

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 x L(-1) HgCl2 and 0.9% salinity at 35 degrees C, 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 degrees C. Weakly acidic environment was more beneficial to mercury methylation than acidic, neutral or alkaline conditions. In addition, the efficiency of mercury methylation was also affected by humic acid and cysteine. Humic acid inhibited mercury methyaltion, whereas cysteine could improve the efficiency of mercury methylation. This study provided a direct evidence for mercury methylation mediated by iron-reducing bacteria in the natural aquatic ecosystem.

Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage

PubMed Central

Brantner, Justin S.; Haake, Zachary J.; Burwick, John E.; Menge, Christopher M.; Hotchkiss, Shane T.; Senko, John M.

2014-01-01

We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O2 at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O2. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O2 and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O2. PMID:24860562

Loihichelins A-F, a Suite of Amphiphilic Siderophores Produced by the Marine Bacterium Halomonas LOB-5

PubMed Central

Homann, Vanessa V; Sandy, Moriah; Tincu, J. Andy; Templeton, Alexis S.; Tebo, Bradley M.; Butler, Alison

2009-01-01

A suite of amphiphilic siderophores, loihichelins A-F, were isolated from cultures of the marine bacterium Halomonas sp. LOB-5. This heterotrophic Mn(II)-oxidizing bacterium was recently isolated from the partially weathered surfaces of submarine glassy pillow basalts and associated hydrothermal flocs of iron oxides collected from the southern rift zone of Loihi Seamount east of Hawai’i. The loihichelins contain a hydrophilic head group consisting of an octapeptide comprised of D-threo-β-hydroxyaspartic acid, D-serine, L-glutamine, L-serine, L-N(δ)-acetyl-N(δ)-hydroxy ornithine, dehydroamino-2-butyric acid, D-serine and cyclic N(δ)-hydroxy-D-ornithine, appended by one of a series of fatty acids ranging from decanoic acid to tetradecanoic acid. The structure of loihichelin C was determined by a combination of amino acid and fatty acid analyses, tandem mass spectrometry and NMR spectroscopy. The structures of the other loihichelins were inferred from the amino acid and fatty acid analyses, and tandem mass spectrometry. The role of these siderophores in sequestering Fe(III) released during basaltic rock weathering, as well as their potential role in the promotion of Mn(II) and Fe(II) oxidation, is of considerable interest. PMID:19320498

Using proteomic data to assess a genome-scale "in silico" model of metal reducing bacteria in the simulation of field-scale uranium bioremediation

NASA Astrophysics Data System (ADS)

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

Biogeochemical transformation of Fe minerals in a petroleum-contaminated aquifer

USGS Publications Warehouse

Zachara, John M.; Kukkadapu, Ravi K.; Glassman, Paul L.; Dohnalkova, Alice; Fredrickson, Jim K.; Anderson, Todd

2004-01-01

The Bemidji aquifer in Minnesota, USA is a well-studied site of subsurface petroleum contamination. The site contains an anoxic groundwater plume where soluble petroleum constituents serve as an energy source for a region of methanogenesis near the source and bacterial Fe(III) reduction further down gradient. Methanogenesis apparently begins when bioavailable Fe(III) is exhausted within the sediment. Past studies indicate that Geobacter species and Geothrix fermentens-like organisms are the primary dissimilatory Fe-reducing bacteria at this site. The Fe mineralogy of the pristine aquifer sediments and samples from the methanogenic (source) and Fe(III) reducing zones were characterized in this study to identify microbiologic changes to Fe valence and mineral distribution, and to identify whether new biogenic mineral phases had formed. Methods applied included X-ray diffraction; X-ray fluorescence (XRF); and chemical extraction; optical, transmission, and scanning electron microscopy; and Mössbauer spectroscopy.All of the sediments were low in total Fe content (≈ 1%) and exhibited complex Fe-mineralogy. The bulk pristine sediment and its sand, silt, and clay-sized fractions were studied in detail. The pristine sediments contained Fe(II) and Fe(III) mineral phases. Ferrous iron represented approximately 50% of FeTOT. The relative Fe(II) concentration increased in the sand fraction, and its primary mineralogic residence was clinochlore with minor concentrations found as a ferroan calcite grain cement in carbonate lithic fragments. Fe(III) existed in silicates (epidote, clinochlore, muscovite) and Fe(III) oxides of detrital and authigenic origin. The detrital Fe(III) oxides included hematite and goethite in the form of mm-sized nodular concretions and smaller-sized dispersed crystallites, and euhedral magnetite grains. Authigenic Fe(III) oxides increased in concentration with decreasing particle size through the silt and clay fraction. Chemical extraction and M�

Online spectrophotometric determination of Fe(II) and Fe(III) by flow injection combined with low pressure ion chromatography

NASA Astrophysics Data System (ADS)

Chen, Shujuan; Li, Nan; Zhang, Xinshen; Yang, Dongjing; Jiang, Heimei

2015-03-01

A simple and new low pressure ion chromatography combined with flow injection spectrophotometric procedure for determining Fe(II) and Fe(III) was established. It is based on the selective adsorption of low pressure ion chromatography column to Fe(II) and Fe(III), the online reduction reaction of Fe(III) and the reaction of Fe(II) in sodium acetate with phenanthroline, resulting in an intense orange complex with a suitable absorption at 515 nm. Various chemical (such as the concentration of colour reagent, eluant and reductive agent) and instrumental parameters (reaction coil length, reductive coil length and wavelength) were studied and were optimized. Under the optimum conditions calibration graph of Fe(II)/Fe(III) was linear in the Fe(II)/Fe(III) range of 0.040-1.0 mg/L. The detection limit of Fe(III) and Fe(II) was respectively 3.09 and 1.55 μg/L, the relative standard deviation (n = 10) of Fe(II) and Fe(III) 1.89% and 1.90% for 0.5 mg/L of Fe(II) and Fe(III) respectively. About 2.5 samples in 1 h can be analyzed. The interfering effects of various chemical species were studied. The method was successfully applied in the determination of water samples.

Electron transfer capacity dependence of quinone-mediated Fe(III) reduction and current generation by Klebsiella pneumoniae L17.

PubMed

Li, Xiaomin; Liu, Liang; Liu, Tongxu; Yuan, Tian; Zhang, Wei; Li, Fangbai; Zhou, Shungui; Li, Yongtao

2013-06-01

Quinone groups in exogenous electron shuttles can accelerate extracellular electron transfer (EET) from bacteria to insoluble terminal electron acceptors, such as Fe(III) oxides and electrodes, which are important in biogeochemical redox processes and microbial electricity generation. However, the relationship between quinone-mediated EET performance and electron-shuttling properties of the quinones remains incompletely characterized. This study investigates the effects of a series of synthetic quinones (SQs) on goethite reduction and current generation by a fermenting bacterium Klebsiella pneumoniae L17. In addition, the voltammetric behavior and electron transfer capacities (ETCs) of SQ, including electron accepting (EAC) and donating (EDC) capacities, is also examined using electrochemical methods. The results showed that SQ can significantly increase both the Fe(III) reduction rates and current outputs of L17. Each tested SQ reversibly accepted and donated electrons as indicated by the cyclic voltammograms. The EAC and EDC results showed that Carmine and Alizarin had low relative capacities of electron transfer, whereas 9,10-anthraquinone-2,6-disulfonic acid (AQDS), 2-hydroxy-1,4-naphthoquinone (2-HNQ), and 5-hydroxy-1,4-naphthoquinone (5-HNQ) showed stronger relative ETC, and 9,10-anthraquinone-2-carboxylic acid (AQC) and 9,10-anthraquinone-2-sulfonic acid (AQS) had high relative ETC. Enhancement of microbial goethite reduction kinetics and current outputs by SQ had a good linear relationship with their ETC, indicating that the effectiveness of quinone-mediated EET may be strongly dependent on the ETC of the quinones. Therefore, the presence of quinone compounds and fermenting microorganisms may increase the diversity of microbial populations that contribute to element transformation in natural environments. Moreover, ETC determination of different SQ would help to evaluate their performance for microbial EET under anoxic conditions. Copyright © 2013 Elsevier

Ferric iron amendment increases Fe(III)-reducing microbial diversity and carbon oxidation in on-site wastewater systems.

PubMed

Azam, Hossain M; Finneran, Kevin T

2013-01-01

Onsite wastewater systems, or septic tanks, serve approximately 25% of the United States population; they are therefore a critical component of the total carbon balance for natural water bodies. Septic tanks operate under strictly anaerobic conditions, and fermentation is the dominant process driving carbon transformation. Nitrate, Fe(III), and sulfate reduction may be operating to a limited extent in any given septic tank. Electron acceptor amendments will increase carbon oxidation, but nitrate is toxic and sulfate generates corrosive sulfides, which may damage septic system infrastructure. Fe(III) reducing microorganisms transform all major classes of organic carbon that are dominant in septic wastewater: low molecular weight organic acids, carbohydrate monomers and polymers, and lipids. Fe(III) is not toxic, and the reduction product Fe(II) is minimally disruptive if the starting Fe(III) is added at 50-150 mg L(-1). We used (14)C radiolabeled acetate, lactate, propionate, butyrate, glucose, starch, and oleic acid to demonstrate that short and long-term carbon oxidation is increased when different forms of Fe(III) are amended to septic wastewater. The rates of carbon mineralization to (14)CO(2) increased 2-5 times (relative to unamended systems) in the presence of Fe(III). The extent of mineralization reached 90% for some carbon compounds when Fe(III) was present, compared to levels of 50-60% in the absence of Fe(III). (14)CH(4) was not generated when Fe(III) was added, demonstrating that this strategy can limit methane emissions from septic systems. Amplified 16S rDNA restriction analysis indicated that unique Fe(III)-reducing microbial communities increased significantly in Fe(III)-amended incubations, with Fe(III)-reducers becoming the dominant microbial community in several incubations. The form of Fe(III) added had a significant impact on the rate and extent of mineralization; ferrihydrite and lepidocrocite were favored as solid phase Fe(III) and chelated Fe(III

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

DOE PAGES

Dantas, Joana M.; Morgado, Leonor; Aklujkar, Muktak; ...

2015-07-30

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. Throughout 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. Inmore » 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

Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater

PubMed Central

Ortiz-Bernad, Irene; Anderson, Robert T.; Vrionis, Helen A.; Lovley, Derek R.

2004-01-01

Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments. PMID:15128571

Oxidation of aromatic contaminants coupled to microbial iron reduction

USGS Publications Warehouse

Lovley, D.R.; Baedecker, M.J.; Lonergan, D.J.; Cozzarelli, I.M.; Phillips, E.J.P.; Siegel, D.I.

1989-01-01

THE contamination of sub-surface water supplies with aromatic compounds is a significant environmental concern1,2. As these contaminated sub-surface environments are generally anaerobic, the microbial oxidation of aromatic compounds coupled to nitrate reduction, sulphate reduction and methane production has been studied intensively1-7. In addition, geochemical evidence suggests that Fe(III) can be an important electron acceptor for the oxidation of aromatic compounds in anaerobic groundwater. Until now, only abiological mechanisms for the oxidation of aromatic compounds with Fe(III) have been reported8-12. Here we show that in aquatic sediments, microbial activity is necessary for the oxidation of model aromatic compounds coupled to Fe(III) reduction. Furthermore, a pure culture of the Fe(III)-reducing bacterium GS-15 can obtain energy for growth by oxidizing benzoate, toluene, phenol or p-cresol with Fe(III) as the sole electron acceptor. These results extend the known physiological capabilities of Fe(III)-reducing organisms and provide the first example of an organism of any type which can oxidize an aromatic hydrocarbon anaerobically. ?? 1989 Nature Publishing Group.

Geobacter Dominates the Inner Layers of a Stratified Biofilm on a Fluidized Anode During Brewery Wastewater Treatment

PubMed Central

Tejedor-Sanz, Sara; Fernández-Labrador, Patricia; Hart, Steven; Torres, Cesar I.; Esteve-Núñez, Abraham

2018-01-01

In this study, we designed a microbial electrochemical fluidized bed reactor (ME-FBR), with an electroconductive anodic bed made of activated carbon particles for treating a brewery wastewater. Under a batch operating mode, acetate and propionate consumption rates were 13-fold and 2.4-fold higher, respectively, when the fluidized anode was polarized (0.2 V) with respect to open circuit conditions. Operating in a continuous mode, this system could effectively treat the brewery effluent at organic loading rates (OLR) over 1.7 kg m-3NRV d-1 and with removal efficiencies of 95 ± 1.4% (hydraulic retention time of 1 day and an influent of 1.7 g-COD L-1). The coulombic efficiency values highly depended upon the OLR applied, and varied from a 56 ± 15% to 10 ± 1%. Fluorescence in situ hybridization (FISH) analysis revealed a relative high abundance of Geobacter species (ca. 20%), and clearly showed a natural microbial stratification. Interestingly, the Geobacter cluster was highly enriched in the innermost layers of the biofilm (thickness of 10 μm), which were in contact with the electroconductive particles of bed, whereas the rest of bacteria were located in the outermost layers. To our knowledge, this is the first time that such a clear microbial stratification has been observed on an anode-respiring biofilm. Our results revealed the relevant role of Geobacter in switching between the electrode and other microbial communities performing metabolic reactions in the outermost environment of the biofilm. PMID:29568284

Fe(III) reduction and U(VI) immobilization by Paenibacillus sp. strain 300A, isolated from Hanford 300A subsurface sediments.

PubMed

Ahmed, Bulbul; Cao, Bin; McLean, Jeffrey S; Ica, Tuba; Dohnalkova, Alice; Istanbullu, Ozlem; Paksoy, Akin; Fredrickson, Jim K; Beyenal, Haluk

2012-11-01

A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes [Fe(III)-nitrilotriacetic acid and Fe(III)-citrate] but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 μM) of either of the electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6-disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 μM) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We also found that Paenibacillus sp. 300A could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ∼7:3 in PIPES [piperazine-N,N'-bis(2-ethanesulfonic acid)] and ∼1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments.

Fe(III) Reduction and U(VI) Immobilization by Paenibacillus sp. Strain 300A, Isolated from Hanford 300A Subsurface Sediments

PubMed Central

Ahmed, Bulbul; Cao, Bin; McLean, Jeffrey S.; Ica, Tuba; Dohnalkova, Alice; Istanbullu, Ozlem; Paksoy, Akin; Fredrickson, Jim K.

2012-01-01

A facultative iron-reducing [Fe(III)-reducing] Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes [Fe(III)-nitrilotriacetic acid and Fe(III)-citrate] but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 μM) of either of the electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6-disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 μM) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We also found that Paenibacillus sp. 300A could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ∼7:3 in PIPES [piperazine-N,N′-bis(2-ethanesulfonic acid)] and ∼1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments. PMID:22961903

Fe(III) Reduction and U(VI) Immobilization by Paenibacillus sp. Strain 300A, Isolated from Hanford 300A Subsurface Sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, B.; Cao, B.; McLean, Jeffrey S.

2012-11-07

A facultative iron-reducing (Fe(III)-reducing) Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable of reducing soluble Fe(III) complexes (Fe(III)-NTA and Fe(III)-citrate) but unable to reduce poorly crystalline ferrihydrite (Fh). However, Paenibacillus sp. 300A was capable of reducing Fh in the presence of low concentrations (2 µM) of either of electron transfer mediators (ETMs) flavin mononucleotide (FMN) or anthraquinone-2,6-disulfonate (AQDS). Maximum initial Fh reduction rates were observed at catalytic concentrations (<10 µM) of either FMN or AQDS. Higher FMN concentrations inhibited Fh reduction, while increased AQDS concentrations did not. We found that Paenibacillus sp. 300A alsomore » could reduce Fh in the presence of natural ETMs from Hanford 300A subsurface sediments. In the absence of ETMs, Paenibacillus sp. 300A was capable of immobilizing U(VI) through both reduction and adsorption. The relative contributions of adsorption and microbial reduction to U(VI) removal from the aqueous phase were ~7:3 in PIPES and ~1:4 in bicarbonate buffer. Our study demonstrated that Paenibacillus sp. 300A catalyzes Fe(III) reduction and U(VI) immobilization and that these reactions benefit from externally added or naturally existing ETMs in 300A subsurface sediments.« less

Role of U(VI) Reduction by Geobacter species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovely, Derrick

2008-12-23

Previous work had suggested that Acholeplasma palmae has a higher capacity for uranium sorption than other bacteria studied. Sorption studies were performed with cells in suspension in various solutions containing uranium, and results were used to generate uranium-biosorption isotherms. Results from this study showed that the U(VI) sorption capacity of G. uraniireducens was relatively similar in simple solutions, such as sodium chloride or bicarbonate. However, this ability to sorb uranium significantly decreased in groundwater. This suggested that certain chemicals present in the groundwater were inhibiting the ability of cell components of Geobacter to adsorb uranium. It was hypothesized that uraniummore » removal would also be diminished in the bicarbonate solution. However, this did not seem to be the case, as uranium was as easily removed in the bicarbonate solution as in the sodium chloride solution.« less

Single Upconversion Nanoparticle-Bacterium Cotrapping for Single-Bacterium Labeling and Analysis.

PubMed

Xin, Hongbao; Li, Yuchao; Xu, Dekang; Zhang, Yueli; Chen, Chia-Hung; Li, Baojun

2017-04-01

Detecting and analyzing pathogenic bacteria in an effective and reliable manner is crucial for the diagnosis of acute bacterial infection and initial antibiotic therapy. However, the precise labeling and analysis of bacteria at the single-bacterium level are a technical challenge but very important to reveal important details about the heterogeneity of cells and responds to environment. This study demonstrates an optical strategy for single-bacterium labeling and analysis by the cotrapping of single upconversion nanoparticles (UCNPs) and bacteria together. A single UCNP with an average size of ≈120 nm is first optically trapped. Both ends of a single bacterium are then trapped and labeled with single UCNPs emitting green light. The labeled bacterium can be flexibly moved to designated locations for further analysis. Signals from bacteria of different sizes are detected in real time for single-bacterium analysis. This cotrapping method provides a new approach for single-pathogenic-bacterium labeling, detection, and real-time analysis at the single-particle and single-bacterium level. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

USGS Publications Warehouse

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.

Promoted reduction of tellurite and formation of extracellular tellurium nanorods by concerted reaction between iron and Shewanella oneidensis MR-1.

PubMed

Kim, Dong-Hun; Kim, Min-Gyu; Jiang, Shenghua; Lee, Ji-Hoon; Hur, Hor-Gil

2013-08-06

The reduction of tellurite (Te(IV)) by dissimilatory metal reducing bacterium, Shewanella oneidensis MR-1, was promoted in the presence of Fe(III) in comparison with Te(IV) bioreduction in the absence of Fe(III). Electron microscopic analyses revealed that iron promoted Te(IV) reduction led to form exclusively extracellular crystalline Te(0) nanorods, as compared to the mostly intracellular formation of Te(0) nanorods in the absence of Fe(III). The Te K-edge X-ray absorption spectrometric analyses demonstrated that S. oneidensis MR-1 in the presence of Fe(III) reduced Te(IV) to less harmful metallic Te(0) nanorods through the precipitation of tellurite (Te(IV)Ox) complex by the bacterial respiration of Fe(III) to Fe(II) under anaerobic conditions. However, Fe(II) ion itself was only able to precipitate the solid tellurite (Te(IV)Ox) complex from the Te(IV) solution, which was not further reduced to Te(0). The results clearly indicated that bacterial S. oneidensis MR-1 plays important roles in the reduction and crystallization of Te(0) nanorods by as yet undetermined biochemical mechanisms. As compared to the slow bacterial Te(IV) reduction in the absence of Fe(III), the rapid reduction of Te(IV) to Te(0) by the concerted biogeochemical reaction between Fe(II) and S. oneidensis MR-1 could be applied for the sequestration and detoxification of Te(IV) in the environments as well as for the preparation of extracellular Te(0) nanorod structures.

Single peak parameters technique for simultaneous measurements: Spectrophotometric sequential injection determination of Fe(II) and Fe(III).

PubMed

Kozak, J; Paluch, J; Węgrzecka, A; Kozak, M; Wieczorek, M; Kochana, J; Kościelniak, P

2016-02-01

Spectrophotometric sequential injection system (SI) is proposed to automate the method of simultaneous determination of Fe(II) and Fe(III) on the basis of parameters of a single peak. In the developed SI system, sample and mixture of reagents (1,10-phenanthroline and sulfosalicylic acid) are introduced into a vessel, where in an acid environment (pH≅3) appropriate compounds of Fe(II) and Fe(III) with 1,10-phenanthroline and sulfosalicylic acid are formed, respectively. Then, in turn, air, sample, EDTA and sample again, are introduced into a holding coil. After the flow reversal, a segment of air is removed from the system by an additional valve and as EDTA replaces sulfosalicylic acid forming a more stable colorless compound with Fe(III), a complex signal is registered. Measurements are performed at wavelength 530 nm. The absorbance measured at minimum of the negative peak and the area or the absorbance measured at maximum of the signal can be used as measures corresponding to Fe(II) and Fe(III) concentrations, respectively. The time of the peak registration is about 2 min. Two-component calibration has been applied to analysis. Fe(II) and Fe(III) can be determined within the concentration ranges of 0.04-4.00 and 0.1-5.00 mg L(-1), with precision less than 2.8% and 1.7% (RSD), respectively and accuracy better than 7% (RE). The detection limit is 0.04 and 0.09 mg L(-1) for Fe(II) and Fe(III), respectively. The method was applied to analysis of artesian water samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

PubMed Central

Han, Ruyang; Karaoz, Ulas; Lim, HsiaoChien; Brodie, Eoin L.

2013-01-01

Pelosinus spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H2 cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments. PMID:23064329

Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment.

PubMed

Finster, K; Coates, J D; Liesack, W; Pfennig, N

1997-07-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27T, was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27T is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27T belongs to the Desulfuromonas cluster in the recently proposed family "Geobacteracea" in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27T represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publication, is the name proposed for strain NZ27T in this paper.

Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

USGS Publications Warehouse

Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

1997-01-01

A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

Mixed-valent [FeIV(mu-O)(mu-carboxylato)2FeIII]3+ core.

PubMed

Slep, Leonardo D; Mijovilovich, Ana; Meyer-Klaucke, Wolfram; Weyhermüller, Thomas; Bill, Eckhard; Bothe, Eberhard; Neese, Frank; Wieghardt, Karl

2003-12-17

The symmetrically ligated complexes 1, 2, and 3 with a (mu-oxo)bis(mu-acetato)diferric core can be one-electron oxidized electrochemically or chemically with aminyl radical cations [*NR3][SbCl6] in acetonitrile yielding complexes which contain the mixed-valent [(mu-oxo)bis(mu-acetato)iron(IV)iron(III)]3+ core: [([9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](ClO4)2 (1(ClO4)2), [(Me3[9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](PF6)2 (2(PF6)(2)), and [(tpb)(2FeIII2)(mu-O)(mu-CH3CO2)2] (3) where ([9]aneN3) is the neutral triamine 1,4,7-triazacyclononane and (Me3[9]aneN3) is its tris-N-methylated derivative, and (tpb)(-) is the monoanion trispyrazolylborate. The asymmetrically ligated complex [(Me3[9]aneN3)FeIII(mu-O)(mu-CH3CO2)2FeIII(tpb)](PF6) (4(PF6)) and its one-electron oxidized form [4ox]2+ have also been prepared. Finally, the known heterodinuclear species [(Me3[9]aneN3)CrIII(mu-O)(mu-CH3CO2)2Fe([9]aneN3)](PF6)2 (5(PF6)(2)) can also be one-electron oxidized yielding [5ox]3+ containing an iron(IV) ion. The structure of 4(PF6).0.5CH3CN.0.25(C2H5)2O has been determined by X-ray crystallography and that of [5ox]2+ by Fe K-edge EXAFS-spectroscopy (Fe(IV)-O(oxo): 1.69(1) A; Fe(IV)-O(carboxylato) 1.93(3) A, Fe(IV)-N 2.00(2) A) contrasting the data for 5 (Fe(III)-O(oxo) 1.80 A; Fe(III)-O(carboxylato) 2.05 A, Fe-N 2.20 A). [5ox]2+ has an St = 1/2 ground state whereas all complexes containing the mixed-valent [FeIV(mu-O)(mu-CH3CO2)2FeIII]3+ core have an St = 3/2 ground state. Mössbauer spectra of the oxidized forms of complexes clearly show the presence of low spin FeIV ions (isomer shift approximately 0.02 mm s(-1), quadrupole splitting approximately 1.4 mm s(-1) at 80 K), whereas the high spin FeIII ion exhibits delta approximately 0.46 mm s(-1) and DeltaE(Q) approximately 0.5 mm s(-1). Mössbauer, EPR spectral and structural parameters have been calculated by density functional theoretical methods at the BP86 and B3LYP levels. The exchange coupling constant, J, for diiron complexes

Formation of Fe(III) oxyhydroxide colloids in freshwater and brackish seawater, with incorporation of phosphate and calcium

NASA Astrophysics Data System (ADS)

Gunnars, Anneli; Blomqvist, Sven; Johansson, Peter; Andersson, Christian

2002-03-01

The formation of Fe(III) oxyhydroxide colloids by oxidation of Fe(II) and their subsequent aggregation to larger particles were studied in laboratory experiments with natural water from a freshwater lake and a brackish coastal sea. Phosphate was incorporated in the solid phase during the course of hydrolysis of iron. The resulting precipitated amorphous Fe(III) oxyhydroxide phases were of varying composition, depending primarily on the initial dissolved Fe/P molar ratio, but with little influence by salinity or concentration of calcium ions. The lower limiting Fe/P ratio found for the solid phase suggests the formation of a basic Fe(III) phosphate compound with a stoichiometric Fe/P ratio of close to two. This implies that an Fe/P stoichiometry of ≈2 ultimately limits the capacity of precipitating Fe(III) to fix dissolved phosphate at oxic/anoxic boundaries in natural waters. In contrast to phosphorus, the uptake of calcium seemed to be controlled by sorption processes at the surface of the iron-rich particles formed. This uptake was more efficient in freshwater than in brackish water, suggesting that salinity restrains the uptake of calcium by newly formed Fe(III) oxyhydroxides in natural waters. Moreover, salinity enhanced the aggregation rate of the colloids formed. The suspensions were stabilised by the presence of organic matter, although this effect was less pronounced in seawater than in freshwater. Thus, in seawater of 6 to 33 ‰S, the removal of particles was fast (removal half time < 200 h), whereas the colloidal suspensions formed in freshwater were stable (removal half time > 900 h). Overall, oxidation of Fe(II) and removal of Fe(III) oxyhydroxide particles were much faster in seawater than in freshwater. This more rapid turnover results in lower iron availability in coastal seawater than in freshwater, making iron more likely to become a limiting element for chemical scavenging and biologic production.

Microbial Anaerobic Ammonium Oxidation Under Iron Reducing Conditions, Alternative Electron Acceptors

NASA Astrophysics Data System (ADS)

Ruiz-Urigüen, M.; Jaffe, P. R.

2015-12-01

Autotrophic Acidimicrobiaceae-bacterium named A6 (A6), part of the Actinobacteria phylum have been linked to anaerobic ammonium (NH4+) oxidation under iron reducing conditions. These organisms obtain their energy by oxidizing NH4+ and transferring the electrons to a terminal electron acceptor (TEA). Under environmental conditions, the TEAs are iron oxides [Fe(III)], which are reduced to Fe(II), this process is known as Feammox. Our studies indicate that alternative forms of TEAs can be used by A6, e.g. iron rich clays (i.e. nontronite) and electrodes in bioelectrochemical systems such as Microbial Electrolysis Cells (MECs), which can sustain NH4+removal and A6 biomass production. Our results show that nontronite can support Feammox and promote bacterial cell production. A6 biomass increased from 4.7 x 104 to 3.9 x 105 cells/ml in 10 days. Incubations of A6 in nontronite resulted in up to 10 times more NH4+ removal and 3 times more biomass production than when ferrihydrite is used as the Fe(III) source. Additionally, Fe in nontronite can be reoxidized by aeration and A6 can reutilize it; however, Fe is still finite in the clay. In contrast, in MECs, A6 harvest electrons from NH4+ and use an anode as an unlimited TEA, as a result current is produced. We operated multiple MECs in parallel using a single external power source, as described by Call & Logan (2011). MECs were run with an applied voltage of 0.7V and different growing mediums always containing initial 5mM NH4+. Results show that current production is favored when anthraquinone-2,6-disulfonate (AQDS), an electron shuttled, is present in the medium as it facilitates the transfer of electrons from the bacterial cell to the anode. Additionally, A6 biomass increased from 1 x 104 to 9.77 x 105cells/ml in 14 days of operation. Due to Acidimicrobiaceae-bacterium A6's ability to use various TEAs, MECs represent an alternative, iron-free form, for optimized biomass production of A6 and its application in NH4

Effect of ferrihydrite biomineralization on methanogenesis in an anaerobic incubation from paddy soil

NASA Astrophysics Data System (ADS)

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.

Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea.

PubMed

Pérez-Rodríguez, Ileana; Rawls, Matthew; Coykendall, D Katharine; Foustoukos, Dionysis I

2016-02-01

A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30-70 °C (optimum 60 °C), 0-50 g NaCl l- 1 (optimum 15-20 g l- 1) and pH 5.5-8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( - )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).

Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment.

PubMed

Liu, Hongyan; Wang, Hongyu

2016-07-01

To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

Amino group in Leptothrix sheath skeleton is responsible for direct deposition of Fe(III) minerals onto the sheaths.

PubMed

Kunoh, Tatsuki; Matsumoto, Syuji; Nagaoka, Noriyuki; Kanashima, Shoko; Hino, Katsuhiko; Uchida, Tetsuya; Tamura, Katsunori; Kunoh, Hitoshi; Takada, Jun

2017-07-26

Leptothrix species produce microtubular organic-inorganic materials that encase the bacterial cells. The skeleton of an immature sheath, consisting of organic exopolymer fibrils of bacterial origin, is formed first, then the sheath becomes encrusted with inorganic material. Functional carboxyl groups of polysaccharides in these fibrils are considered to attract and bind metal cations, including Fe(III) and Fe(III)-mineral phases onto the fibrils, but the detailed mechanism remains elusive. Here we show that NH 2 of the amino-sugar-enriched exopolymer fibrils is involved in interactions with abiotically generated Fe(III) minerals. NH 2 -specific staining of L. cholodnii OUMS1 detected a terminal NH 2 on its sheath skeleton. Masking NH 2 with specific reagents abrogated deposition of Fe(III) minerals onto fibrils. Fe(III) minerals were adsorbed on chitosan and NH 2 -coated polystyrene beads but not on cellulose and beads coated with an acetamide group. X-ray photoelectron spectroscopy at the N1s edge revealed that the terminal NH 2 of OUMS1 sheaths, chitosan and NH 2 -coated beads binds to Fe(III)-mineral phases, indicating interaction between the Fe(III) minerals and terminal NH 2 . Thus, the terminal NH 2 in the exopolymer fibrils seems critical for Fe encrustation of Leptothrix sheaths. These insights should inform artificial synthesis of highly reactive NH 2 -rich polymers for use as absorbents, catalysts and so on.

Characterization of the cellulose-degrading bacterium NCIMB 10462

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dees, C.; Scott, T.C.; Phelps, T.J.

The gram-negative cellulase-producing bacterium NCIMB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulose. Because of renewed interest in cellulose-degrading bacteria for use in the bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its true metabolic potential. Metabolic and physical characterization of NCIMB 10462 revealed that this is an alkalophilic, non-fermentative, gram-negative, oxidase-positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium has few characteristics consistent with a classification of P. fluorescens and a very low probability match with the genus Sphingomonas. However, total lipid analysismore » did not reveal that any sphingolipid bases are produced by this bacterium. NCIMB 10462 grows best aerobically, but also grows well in complex media under reducing conditions. NCIMB 10462 grows slowly under anaerobic conditions on complex media, but growth on cellulosic media occurred only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIMB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is its ability to degrade cellulose, we suggest that it be called Pseudomonas cellulosa.« less

A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria.

PubMed

Lefèvre, Christopher T; Menguy, Nicolas; Abreu, Fernanda; Lins, Ulysses; Pósfai, Mihály; Prozorov, Tanya; Pignol, David; Frankel, Richard B; Bazylinski, Dennis A

2011-12-23

Magnetotactic bacteria contain magnetosomes--intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe(3)O(4)) or greigite (Fe(3)S(4))--that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals the presence of two different magnetosome gene clusters, suggesting that one may be responsible for greigite biomineralization and the other for magnetite.

Deferrisoma paleochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

USGS Publications Warehouse

Perez-Rodriguez, Ileana M.; Rawls, Matthew; Coykendall, D. Katharine; Foustoukos, Dionysis I.

2016-01-01

A novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l− 1 (optimum 15–20 g l− 1) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( − )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T). 

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina

PubMed Central

Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M. Sofía; Ee, Robson; Tan-Guan-Sheng, Adrian; Donati, Edgardo R.

2016-01-01

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. PMID:27540078

Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction.

PubMed

N'Guessan, A Lucie; Vrionis, Helen A; Resch, Charles T; Long, Philip E; Lovley, Derek R

2008-04-15

Previous field studies on in situ bioremediation of uranium-contaminated groundwater in an aquifer in Rifle, Colorado identified two distinct phases following the addition of acetate to stimulate microbial respiration. In phase I, Geobacter species are the predominant organisms, Fe(III) is reduced, and microbial reduction of soluble U(VI) to insoluble U(IV) removes uranium from the groundwater. In phase II, Fe(III) is depleted, sulfate is reduced, and sulfate-reducing bacteria predominate. Long-term monitoring revealed an unexpected third phase during which U(VI) removal continues even after acetate additions are stopped. All three of these phases were successfully reproduced in flow-through sediment columns. When sediments from the third phase were heat sterilized, the capacity for U(VI) removal was lost. In the live sediments U(VI) removed from the groundwater was recovered as U(VI) in the sediments. This contrasts to the recovery of U(IV) in sediments resulting from the reduction of U(VI) to U(IV) during the Fe(III) reduction phase in acetate-amended sediments. Analysis of 16S rRNA gene sequences in the sediments in which U(VI) was being adsorbed indicated that members of the Firmicutes were the predominant organisms whereas no Firmicutes sequences were detected in background sediments which did not have the capacity to sorb U(VI), suggesting that the U(VI) adsorption might be due to the presence of these living organisms or at least their intact cell components. This unexpected enhanced adsorption of U(VI) onto sediments following the stimulation of microbial growth in the subsurface may potentially enhance the cost effectiveness of in situ uranium bioremediation.

Influence of dissimilatory metal reduction on fate of organic and metal contaminants in the subsurface

NASA Astrophysics Data System (ADS)

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

Hydroxyl Radical Formation in Solutions of Fe(III) and Hydrogen Peroxide - Impact of Freezing and Thawing Process

NASA Astrophysics Data System (ADS)

Arakaki, T.; Kinjo, M.; Shiroma, K.; Shibata, M.; Miyake, T.; Hirakawa, T.; Sakugawa, H.

2003-12-01

Hydroxyl radical formation was studied by detecting concentration of formate in solutions of hydrated formaldehyde, HOOH, and Fe(III) or Cu(II). Oxidation of hydrated formaldehyde by OH radical is known to form formate. Formate formation increased by about 4 times when the solution underwent freezing and thawing. Although the reaction mechanisms are not clearly understood, we believe that the concentration effect of freezing enhanced the catalytic reactions between HOOH and Fe(III) or Cu(II) and the reduction of transition metals, i.e., Fe(III) to Fe(II) and Cu(II) to Cu(I). The concentration effect also enhanced reactions between Fe(II) and HOOH or Cu(I) and HOOH, which generated OH radical (freeze-Fenton reaction). Study of the effects of pH showed that formate formation was the highest at pH = 4.0, indicating that the speciation of Fe(III) affected the formation of formate. Concentration-dependent experiments demonstrated that Fe is probably the limiting agent under typical atmospheric conditions. Our results suggested that the freezing process could be an important source of hydroxyl radical in high cloud, winter fog, rime ice and freezing acidic rain, and more importantly, a potentially additional oxidation mechanism in the atmosphere.

Naphthalene and benzene degradation under Fe(III)-reducing conditions in petroleum-contaminated aquifers

USGS Publications Warehouse

Anderson, Robert T.; Lovely, Derek R.

1999-01-01

Naphthalene was oxidized anaerobically to CO2 in sediments collected from a petroleum-contaminated aquifer in Bemidji, Minnesota in which Fe(III) reduction was the terminal electron-accepting process. Naphthalene was not oxidized in sediments from the methanogenic zone at Bemidji or in sediments from the Fe(III)-reducing zone of other petroleum-contaminated aquifers studied. In a profile across the Fe(III)-reducing zone of the Bemidji aquifer, rates of naphthalene oxidation were fastest in sediments with the highest proportion of Fe(III), which was also the zone of the most rapid degradation of benzene, toluene, and acetate. The comparative studies attempted to elucidate factors that might account for the fact that unsubstituted aromatic hydrocarbons such as benzene and naphthalene were degraded under Fe(III)-reducing conditions at Bemidji, but not at the other aquifers examined. These studies indicated that the ability of Fe(III)-reducing microorganisms to degrade benzene and naphthalene at the Bemidji site cannot be attributed to groundwater components that make Fe(III) more available for reduction or other potential factors that were evaluated. However, unlike the other aquifers evaluated, uncontaminated sediments at the Bemidji site could be adapted for anaerobic benzene degradation merely with the addition of benzene. These findings indicate that Bemidji sediments naturally contain Fe(III) reducers capable of degradation of unsubstituted aromatic hydrocarbons.

Limitations for current production in Geobacter sulfurreducens biofilms.

PubMed

Bonanni, P Sebastian; Bradley, Dan F; Schrott, Germán D; Busalmen, Juan Pablo

2013-04-01

Devices that exploit electricity produced by electroactive bacteria such as Geobacter sulfurreducens have not yet been demonstrated beyond the laboratory scale. The current densities are far from the maximum that the bacteria can produce because fundamental properties such as the mechanism of extracellular electron transport and factors limiting cell respiration remain unclear. In this work, a strategy for the investigation of electroactive biofilms is presented. Numerical modeling of the response of G. sulfurreducens biofilms cultured on a rotating disk electrode has allowed for the discrimination of different limiting steps in the process of current production within a biofilm. The model outputs reveal that extracellular electron transport limits the respiration rate of the cells furthest from the electrode to the extent that cell division is not possible. The mathematical model also demonstrates that recent findings such as the existence of a redox gradient in actively respiring biofilms can be explained by an electron hopping mechanism but not when considering metallic-like conductivities. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of Fe(III)-OM complexes and Fe(III) polymerization on SOM pools reactivity under different land uses

NASA Astrophysics Data System (ADS)

Giannetta, B.; Plaza, C.; Zaccone, C.; Siebecker, M. G.; Rovira, P.; Vischetti, C.; Sparks, D. L.

2017-12-01

Soil organic matter (SOM) protection and long-term accumulation are controlled by adsorption to mineral surfaces in different ways, depending on its molecular structure and pedo-climatic conditions. Iron (Fe) oxides are known to be key regulators of the soil carbon (C) cycle, and Fe speciation in soils is highly dependent on environmental conditions and chemical interactions with SOM. However, the molecular structure and hydrolysis of Fe species formed in association with SOM is still poorly described. We hypothesize the existence of two pools of Fe which interact with SOM: mononuclear Fe(III)-SOM complexes and precipitated Fe(III) hydroxides. To verify our hypothesis, we investigated the interactions between Fe(III) and physically isolated soil fractions by means of batch experiments at pH 7. Specifically, we examined the fine silt plus clay (FSi+C) fraction, obtained by ultrasonic dispersion and wet sieving. The soil samples spanned several land uses, including coniferous forest (CFS), grassland (GS), technosols (TS) and agricultural (AS) soils. Solid phase products and supernatants were analyzed for C and Fe content. X-ray diffraction (XRD) and Brunauer-Emmett-Teller (BET) analysis were also performed. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to assess the main C functional groups involved in C complexation and desorption experiments. Preliminary linear combination fitting (LCF) of Fe K-edge extended X-ray absorption fine structure (EXAFS) spectra suggested the formation of ferrihydrite-like polymeric Fe(III) oxides in reacted CFS and GS samples, with higher C and Fe concentration. Conversely, mononuclear Fe(III) OM complexes dominated the speciation for TS and AS samples, characterized by lower C and Fe concentration, inhibiting the hydrolysis and polymerization of Fe (III). This approach will help revealing the mechanisms by which SOM pools can control Fe(III) speciation, and will elucidate how both Fe

Physiological stratification in electricity-producing biofilms of Geobacter sulfurreducens.

PubMed

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. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina.

PubMed

Willis Poratti, Graciana; Yaakop, Amira Suriaty; Chan, Chia Sing; Urbieta, M Sofía; Chan, Kok-Gan; Ee, Robson; Tan-Guan-Sheng, Adrian; Goh, Kian Mau; Donati, Edgardo R

2016-08-18

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment. Copyright © 2016 Willis Poratti et al.

K 3 Fe(CN) 6 under External Pressure: Dimerization of CN – Coupled with Electron Transfer to Fe(III)

DOE PAGES

Li, Kuo; Zheng, Haiyan; Wang, Lijuan; ...

2015-09-14

The addition polymerization of charged monomers like C≡C 2– and C≡N– is scarcely seen at ambient conditions but can progress under external pressure with their conductivity significantly enhanced, which expands the research field of polymer science to inorganic salts. Moreover, the reaction pressures of transition metal cyanides like Prussian blue and K 3Fe(CN) 6 are much lower than that of alkali cyanides. To figure out the effect of the transition metal on the reaction, the crystal structure and electronic structure of K 3Fe(CN) 6 under external pressure are investigated by in situ neutron diffraction, in situ X-ray absorption fine structuremore » (XAFS), and neutron pair distribution functions (PDF) up to ~15 GPa. The cyanide anions react following a sequence of approaching–bonding–stabilizing. The Fe(III) brings the cyanides closer which makes the bonding progress at a low pressure (2–4 GPa). At ~8 GPa, an electron transfers from the CN to Fe(III), reduces the charge density on cyanide ions, and stabilizes the reaction product of cyanide. Finally, from this study we can conclude that bringing the monomers closer and reducing their charge density are two effective routes to decrease the reaction pressure, which is important for designing novel pressure induced conductor and excellent electrode materials.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dantas, Joana M.; Campelo, Luísa M.; Duke, Norma E. C.

2015-04-10

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 ofmore » -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.« less

The Impact of Gamma Radiation on Sediment Microbial Processes

PubMed Central

Brown, Ashley R.; Boothman, Christopher; Pimblott, Simon M.

2015-01-01

Microbial communities have the potential to control the biogeochemical fate of some radionuclides in contaminated land scenarios or in the vicinity of a geological repository for radioactive waste. However, there have been few studies of ionizing radiation effects on microbial communities in sediment systems. Here, acetate and lactate amended sediment microcosms irradiated with gamma radiation at 0.5 or 30 Gy h−1 for 8 weeks all displayed NO3− and Fe(III) reduction, although the rate of Fe(III) reduction was decreased in 30-Gy h−1 treatments. These systems were dominated by fermentation processes. Pyrosequencing indicated that the 30-Gy h−1 treatment resulted in a community dominated by two Clostridial species. In systems containing no added electron donor, irradiation at either dose rate did not restrict NO3−, Fe(III), or SO42− reduction. Rather, Fe(III) reduction was stimulated in the 0.5-Gy h−1-treated systems. In irradiated systems, there was a relative increase in the proportion of bacteria capable of Fe(III) reduction, with Geothrix fermentans and Geobacter sp. identified in the 0.5-Gy h−1 and 30-Gy h−1 treatments, respectively. These results indicate that biogeochemical processes will likely not be restricted by dose rates in such environments, and electron accepting processes may even be stimulated by radiation. PMID:25841009

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.

PubMed

Rajeev, Lara; Luning, Eric G; Dehal, Paramvir S; Price, Morgan N; Arkin, Adam P; Mukhopadhyay, Aindrila

2011-10-12

Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dees, C.; Ringleberg, D.; Scott, T.C.

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescensmore » with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.« less

Ammonium Oxidation Under Iron Reducing Conditions: Environmental Factors Characterization and Process Optimization

NASA Astrophysics Data System (ADS)

Huang, Shan; Ruiz, Melany; Jaffe, Peter

2015-04-01

Ammonium (NH4+) oxidation coupled to iron (Fe) reduction in the absence of oxygen and nitrate/nitrite (NO3-/NO2-) has been reported by several investigators and is referred to as Feammox. Feammox is a biological reaction, where Fe(III) is the electron acceptor, which is reduced to Fe(II), and NH4+ is the electron donor, which is oxidized to NO2-. An Acidimicrobiaceae bacterium named A6, a previously unreported species in the Acidimicrobiaceae family, has been identified as being responsible for the Feammox process(1, 2) Feammox process was noted in riparian wetland soils in New Jersey(1,3), in tropical rainforest soils in Puerto Rico (4) and in paddy soils in China (5). In addition to these published locations, Feammox process was also found in samples collected from a series of local wetland-, upland-, as well as storm-water detention pond-sediments in New Jersey, river sediments from South Carolina, and forested soils near an acid mine drainage (Dabaoshan, Guangdong province) in China. Using primers acm342f - 439r (2), Acidimicrobiaceae bacterium A6 was detected in samples where Feammox was observed, after strictly anaerobic incubations. According to a canonical correspondence analysis with environmental characteristics and soil microbial communities, the species-environment relationship indicated that pH and Fe oxides content were the primary factors controlling Feammox process. Anaerobic incubations of Feammox enrichment cultures adjusted to different pH, revealed that the optimal pH for Feammox is 4 ~ 5, and the reaction does not proceed when pH > 7. No correlation was found between the distributions of Feammox bacteria and other NH4+ oxidation bacteria. Pure Acidimicrobiaceae bacterium A6 strain was isolated in an autotrophic medium, from an active Feammox membrane reactor (A6 was enriched to 65.8% of the total bacteria). A 13C labeled CO2 amendment was conducted, and the 13C in cells of A6 increased from 1.80% to 10.3% after 14 days incubation. In a separate

Effects of Aerobic Growth on the Fatty Acid and Hydrocarbon Compositions of Geobacter bemidjiensis BemT.

PubMed

Ueno, Akio; Shimizu, Satoru; Hashimoto, Mikako; Adachi, Takumi; Matsushita, Takako; Okuyama, Hidetoshi; Yoshida, Kiyohito

2017-01-01

Geobacter spp., regarded as strict anaerobes, have been reported to grow under aerobic conditions. To elucidate the role of fatty acids in aerobiosis of Geobacter spp., we studied the effect of aerobiosis on fatty acid composition and turnover in G. bemidjiensis Bem T . G. bemidjiensis Bem T was grown under the following different culture conditions: anaerobic culture for 4 days (type 1) and type 1 culture followed by 2-day anaerobic (type 2) or aerobic culture (anaerobic-to-aerobic shift; type 3). The mean cell weight of the type 3 culture was approximately 2.5-fold greater than that of type 1 and 2 cultures. The fatty acid methyl ester and hydrocarbon fraction contained hexadecanoic (16:0), 9-cis-hexadecenoic [16:1(9c)], tetradecanoic (14:0), tetradecenoic [14:1(7c)] acids, hentriacontanonaene, and hopanoids, but not long-chain polyunsaturated fatty acids. The type 3 culture contained higher levels of 14:0 and 14:1(7c) and lower levels of 16:0 and 16:1(9c) compared with type 1 and 2 cultures. The weight ratio of extracted lipid per dry cell was lower in the type 3 culture than in the type 1 and 2 cultures. We concluded that anaerobically-grown G. bemidjiensis Bem T followed by aerobiosis were enhanced in growth, fatty acid turnover, and de novo fatty acid synthesis.

Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria

PubMed Central

O'Reilly, S Erin; Watkins, Janet; Furukawa, Yoko

2005-01-01

Experimental batch and miscible-flow cultures were studied in order to determine the mechanistic pathways of microbial Fe(III) respiration in ferruginous smectite clay, NAu-1. The primary purpose was to resolve if alteration of smectite and release of Fe precedes microbial respiration. Alteration of NAu-1, represented by the morphological and mineralogical changes, occurred regardless of the extent of microbial Fe(III) reduction in all of our experimental systems, including those that contained heat-killed bacteria and those in which O2, rather than Fe(III), was the primary terminal electron acceptor. The solid alteration products observed under transmission electron microscopy included poorly crystalline smectite with diffuse electron diffraction signals, discrete grains of Fe-free amorphous aluminosilicate with increased Al/Si ratio, Fe-rich grains, and amorphous Si globules in the immediate vicinity of bacterial cells and extracellular polymeric substances. In reducing systems, Fe was also found as siderite. The small amount of Fe partitioned to the aqueous phase was primarily in the form of dissolved Fe(III) species even in the systems in which Fe(III) was the primary terminal electron acceptor for microbial respiration. From these observations, we conclude that microbial respiration of Fe(III) in our laboratory systems proceeded through the following: (1) alteration of NAu-1 and concurrent release of Fe(III) from the octahedral sheets of NAu-1; and (2) subsequent microbial respiration of Fe(III).

Identification of the lipopolysaccharide modifications controlled by the Salmonella PmrA/PmrB system mediating resistance to Fe(III) and Al(III)

PubMed Central

Nishino, Kunihiko; Hsu, Fong-Fu; Turk, John; Cromie, Michael J; Wösten, Marc M S M; Groisman, Eduardo A

2006-01-01

Iron is an essential metal but can be toxic in excess. While several homeostatic mechanisms prevent oxygen-dependent killing promoted by Fe(II), little is known about how cells cope with Fe(III), which kills by oxygen-independent means. Several Gram-negative bacterial species harbour a regulatory system – termed PmrA/PmrB – that is activated by and required for resistance to Fe(III). We now report the identification of the PmrA-regulated determinants mediating resistance to Fe(III) and Al(III) in Salmonella enterica serovar Typhimurium. We establish that these determinants remodel two regions of the lipopolysaccharide, decreasing the negative charge of this major constituent of the outer membrane. Remodelling entails the covalent modification of the two phosphates in the lipid A region with phosphoethanolamine and 4-aminoarabinose, which has been previously implicated in resistance to polymyxin B, as well as dephosphorylation of the Hep(II) phosphate in the core region by the PmrG protein. A mutant lacking the PmrA-regulated Fe(III) resistance genes bound more Fe(III) than the wild-type strain and was defective for survival in soil, suggesting that these PmrA-regulated lipopolysaccharide modifications aid Salmonella's survival and spread in non-host environments. PMID:16803591

Isolation and identification of ferric reducing bacteria and evaluation of their roles in iron availability in two calcareous soils

NASA Astrophysics Data System (ADS)

Ghorbanzadeh, N.; Lakzian, A.; Haghnia, G. H.; Karimi, A. R.

2014-12-01

Iron is an essential element for all organisms which plays a crucial role in important biochemical processes such as respiration and photosynthesis. Iron deficiency seems to be an important problem in many calcareous soils. Biological dissimilatory Fe(III) reduction increases iron availability through reduction of Fe(III) to Fe(II). The aim of this study was to isolate, identify and evaluate some bacterial isolates for their abilities to reduce Fe(III) in two calcareous soils. Three bacterial isolates were selected and identified from paddy soils by using 16S rRNA amplification and then inoculated to sterilized and non-sterilized calcareous soils in the presence and absence of glucose. The results showed that all isolates belonged to Bacillus genus and were capable of reducing Fe(III) to Fe(II) in vitro condition. The amount of Fe(III) reduction in sterilized calcareous soils was significantly higher when inoculated with PS23 isolate and Shewanella putrefaciens ( S. putrefaciens) (as positive control) compared to PS16 and PS11 isolates. No significant difference was observed between PS11 and PS16 isolates in the presence of indigenous microbial community. The results also revealed that glucose had a significant effect on Fe(III) reduction in the examined calcareous soil samples. The amount of Fe(III) reduction increased two-fold when soil samples were treated with glucose and inoculated by S. putrefaciens and PS23 in non-sterilized soils.

Microbial Reduction of Fe(III) and U(VI) in Aquifers: Simulations Exploring Coupled Effects of Heterogeneity and Fe(II) Sorption

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Fang, Y.; Roden, E. E.; Brooks, S. C.; Chien, Y.; Murray, C. J.

2004-05-01

Uranium is a significant groundwater contaminant at many former mining and processing sites. In its oxidized state, U(VI) is soluble and mobile, although strongly retarded by sorption to natural iron oxide surfaces. It has been demonstrated that commonly occurring subsurface microorganisms can reduce uranium and other metals when provided sufficient carbon as an electron donor. Reduced U(IV) precipitates as a solid phase; therefore biostimulation provides a potential strategy for in situ removal from contaminated groundwater. However, these biogeochemical reactions occur in the context of a complex heterogeneous environment in which flow and transport dynamics and abiotic reactions can have significant impacts. We have constructed a high-resolution numerical model of groundwater flow and multicomponent reactive transport that incorporates heterogeneity in hydraulic conductivity and initial Fe(III) distribution, microbial growth and transport dynamics, and effects of sorption or precipitation of biogenic Fe(II) on availability of Fe(III) as an electron acceptor. The biogeochemical reaction models and their parameters are based on laboratory experiments; the heterogeneous field-scale property distributions are based on interpretations of geophysical and other observations at a highly characterized field site. The model is being run in Monte Carlo mode to examine the controls that these factors exert on 1) the initial distribution of sorbed uranium in an oxic environment and 2) the reduction and immobilization of uranium upon introduction of a soluble electron donor.

Arsenic Mobilization Through Microbial Bioreduction of Ferrihydrite Nanoparticles

NASA Astrophysics Data System (ADS)

Tadanier, C. J.; Roller, J.; Schreiber, M. E.

2004-12-01

Under anaerobic conditions Fe(III)-reducing microorganisms can couple the reduction of solid phase Fe(III) (hydr)oxides with the oxidation of organic carbon. Nutrients and trace metals, such as arsenic, associated with Fe(III) hydroxides may be mobilized through microbially-mediated surface reduction. Although arsenic mobilization has been attributed to mineral surface reduction in a variety of pristine and contaminated environments, minimal information exists on the mechanisms causing this arsenic mobilization. Understanding of the fundamental biochemical and physicochemical processes involved in these mobilization mechanisms is still limited, and has been complicated by the often contradictory and interchangeable terminology used in the literature to describe them. We studied arsenic mobilization mechanisms using a series of controlled microcosm experiments containing aggregated arsenic-bearing ferrihydrite nanoparticles and an Fe(III)-reducing microorganism, Geobacter metallireducens. The phase distribution of iron and arsenic was determined through filtration and ultracentrifugation techniques. Experimental results showed that in the biotic trials, approximately 10 percent of the Fe(III) was reduced to Fe(II) by microbial activity, which remained associated with ferrihydrite surfaces. Biotic activity resulted in changes in nanoparticle surface potential and caused deflocculation of nanoparticle aggregates. Deflocculated nanoparticles were able to pass through a 0.2 micron filter and could only be removed from solution by ultracentrifugation. Arsenic mobilized over time in the biotic trials was found to be exclusively associated with the nanoparticles; 98 percent of arsenic that passed through a 0.2 micron filter was removed from solution by ultracentrifugation. None of these changes were observed in abiotic controls. Because arsenic contamination of natural waters due to mobilization from mineral surfaces is a significant route of human arsenic exposure

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Uranium(VI) reduction by nanoscale zero-valent iron in anoxic batch systems: the role of Fe(II) and Fe(III).

PubMed

Yan, Sen; Chen, Yongheng; Xiang, Wu; Bao, Zhengyu; Liu, Chongxuan; Deng, Baolin

2014-12-01

The role of Fe(II) and Fe(III) in U(VI) reduction by nanoscale zerovalent iron (nanoFe0) was investigated using two iron chelators 1,10-phenanthroline and triethanolamine (TEA) under a CO2-free anoxic condition. The results showed that U(VI) reduction was strongly inhibited by 1,10-phenanthroline and TEA in a pH range from 6.9 to 9.0. For instance, at pH 6.9 the observed U(VI) reduction rates decreased by 81% and 82% in the presence of 1,10-phenanthroline and TEA, respectively. The inhibition was attributed to the formation of stable complexes between 1,10-phenanthroline and Fe(II) or TEA and Fe(III). In the absence of iron chelators, U(VI) reduction can be enhanced by surface-bound Fe(II) on nanoFe0. Our results suggested that Fe(III) and Fe(II) possibly acted as an electron shuttle to ferry the electrons from nanoFe0 to U(VI), therefore a combined system with Fe(II), Fe(III) and nanoFe0 could facilitate U(VI) reductive immobilization in the contaminated groundwater.

Uranium(VI) reduction by nanoscale zero-valent iron in anoxic batch systems: The role of Fe(II) and Fe(III)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Sen; Chen, Yongheng; Xiang, Wu

2014-12-01

The role of Fe(II) and Fe(III) on U(VI) reduction by nanoscale zerovalent iron (nanoFe0) was investigated using two iron chelators 1,10-phenanthroline and triethanolamine (TEA) under a CO2-free anoxic condition. The results showed U(VI) reduction was strongly inhibited by 1,10-phenanthroline and TEA in a pH range from 6.92 to 9.03. For instance, at pH 6.92 the observed U(VI) reduction rates decreased by 80.7% and 82.3% in the presence of 1,10-phenanthroline and TEA, respectively. The inhibition was attributed to the formation of stable complexes between 1,10-phenanthroline and Fe(II) or TEA and Fe(III). In the absence of iron chelators, U(VI) reduction can bemore » enhanced by surface-bound Fe(II) on nanoFe0. Our results suggested that Fe(III) and Fe(II) probably acted as an electron shuttle to mediate the transfer of electrons from nanoFe0 to U(VI), therefore a combined system with Fe(II), Fe(III) and nanoFe0 can facilitate the U(VI) reductive immobilization in the contaminated groundwater.« less

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

PubMed Central

2011-01-01

Background Two component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems. Results We report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study. Conclusions The gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms. PMID:21992415

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

NASA Astrophysics Data System (ADS)

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

Impact of Fe(III) as an effective electron-shuttle mediator for enhanced Cr(VI) reduction in microbial fuel cells: Reduction of diffusional resistances and cathode overpotentials.

PubMed

Wang, Qiang; Huang, Liping; Pan, Yuzhen; Quan, Xie; Li Puma, Gianluca

2017-01-05

The role of Fe(III) was investigated as an electron-shuttle mediator to enhance the reduction rate of the toxic heavy metal hexavalent chromium (Cr(VI)) in wastewaters, using microbial fuel cells (MFCs). The direct reduction of chromate (CrO 4 - ) and dichromate (Cr 2 O 7 2- ) anions in MFCs was hampered by the electrical repulsion between the negatively charged cathode and Cr(VI) functional groups. In contrast, in the presence of Fe(III), the conversion of Cr(VI) and the cathodic coulombic efficiency in the MFCs were 65.6% and 81.7%, respectively, 1.6 times and 1.4 folds as those recorded in the absence of Fe(III). Multiple analytical approaches, including linear sweep voltammetry, Tafel plot, cyclic voltammetry, electrochemical impedance spectroscopy and kinetic calculations demonstrated that the complete reduction of Cr(VI) occurred through an indirect mechanism mediated by Fe(III). The direct reduction of Cr(VI) with cathode electrons in the presence of Fe(III) was insignificant. Fe(III) played a critical role in decreasing both the diffusional resistance of Cr(VI) species and the overpotential for Cr(VI) reduction. This study demonstrated that the reduction of Cr(VI) in MFCs was effective in the presence of Fe(III), providing an alternative and environmentally benign approach for efficient remediation of Cr(VI) contaminated sites with simultaneous production of renewable energy. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization and Properties of Activated Carbon Prepared from Tamarind Seeds by KOH Activation for Fe(III) Adsorption from Aqueous Solution

PubMed Central

Mopoung, Sumrit; Moonsri, Phansiri; Palas, Wanwimon; Khumpai, Sataporn

2015-01-01

This research studies the characterization of activated carbon from tamarind seed with KOH activation. The effects of 0.5 : 1–1.5 : 1 KOH : tamarind seed charcoal ratios and 500–700°C activation temperatures were studied. FTIR, SEM-EDS, XRD, and BET were used to characterize tamarind seed and the activated carbon prepared from them. Proximate analysis, percent yield, iodine number, methylene blue number, and preliminary test of Fe(III) adsorption were also studied. Fe(III) adsorption was carried out by 30 mL column with 5–20 ppm Fe(III) initial concentrations. The percent yield of activated carbon prepared from tamarind seed with KOH activation decreased with increasing activation temperature and impregnation ratios, which were in the range from 54.09 to 82.03 wt%. The surface functional groups of activated carbon are O–H, C=O, C–O, –CO3, C–H, and Si–H. The XRD result showed high crystallinity coming from a potassium compound in the activated carbon. The main elements found in the activated carbon by EDS are C, O, Si, and K. The results of iodine and methylene blue adsorption indicate that the pore size of the activated carbon is mostly in the range of mesopore and macropore. The average BET pore size and BET surface area of activated carbon are 67.9764 Å and 2.7167 m2/g, respectively. Finally, the tamarind seed based activated carbon produced with 500°C activation temperature and 1.0 : 1 KOH : tamarind seed charcoal ratio was used for Fe(III) adsorption test. It was shown that Fe(III) was adsorbed in alkaline conditions and adsorption increased with increasing Fe(III) initial concentration from 5 to 20 ppm with capacity adsorption of 0.0069–0.019 mg/g. PMID:26689357

Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium.

PubMed

Finster, K; Liesack, W; Tindall, B J

1997-10-01

The isolation of a new motile, gram-negative, heterotrophic, sulfur-reducing, microaerophilic, vibrioid bacterium, strain F1F6, from oxidized marine surface sediment (Arcachon Bay, French Atlantic coast) is described. Hydrogen (with acetate as the carbon source), formate (with acetate as the carbon source), pyruvate, lactate, alpha-ketoglutarate, glutarate, glutamate, and yeast extract supported growth with elemental sulfur under anaerobic conditions. Apart from H2 and formate, the oxidation of the substrates was incomplete. Microaerophilic growth was supported with hydrogen (acetate as the carbon source), formate (acetate as the carbon source), acetate, propionate, pyruvate, lactate, alpha-ketoglutarate, glutamate, yeast extract, fumarate, succinate, malate, citrate, and alanine. The isolate grew fermentatively with fumarate, succinate being the only organic product. Elemental sulfur and oxygen were the only electron acceptors used. Vitamins or amino acids were not required. The isolate was oxidase, catalase, and urease positive. Comparative 16S rDNA sequence analysis revealed a tight cluster consisting of the validly described species Sulfurospirillum deleyianum and the strains SES-3 and CCUG 13942 as the closest relatives of strain F1F6 (level of sequence similarity, 91.7 to 92.4%). Together with strain F1F6, these organisms form a novel lineage within the epsilon subclass of proteobacteria clearly separated from the described species of the genera Arcobacter, Campylobacter, Wolinella, and Helicobacter. Due to the phenotypic characteristics shared by strain F1F6 and S. deleyianum and considering their phylogenetic relationship, we propose the inclusion of strain F1F6 in the genus Sulfurospirillum, namely, as S. arcachonense sp. nov. Based on the results of this study, an emended description of the genus Sulfurospirillum is given.

Environmentally-relevant concentrations of Al(III) and Fe(III) cations induce aggregation of free DNA by complexation with phosphate group.

PubMed

Qin, Chao; Kang, Fuxing; Zhang, Wei; Shou, Weijun; Hu, Xiaojie; Gao, Yanzheng

2017-10-15

Environmental persistence of free DNA is influenced by its complexation with other chemical species and its aggregation mechanisms. However, it is not well-known how naturally-abundant metal ions, e.g., Al(III) and Fe(III), influence DNA aggregation. This study investigated aggregation behaviors of model DNA from salmon testes as influenced by metal cations, and elucidated the predominant mechanism responsible for DNA aggregation. Compared to monovalent (K + and Na + ) and divalent (Ca 2+ and Mg 2+ ) cations, Al(III) and Fe(III) species in aqueous solution caused rapid DNA aggregations. The maximal DNA aggregation occurred at 0.05 mmol/L Al(III) or 0.075 mmol/L Fe(III), respectively. A combination of atomic force microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy revealed that Al(III) and Fe(III) complexed with negatively charged phosphate groups to neutralize DNA charges, resulting in decreased electrostatic repulsion and subsequent DNA aggregation. Zeta potential measurements and molecular computation further support this mechanism. Furthermore, DNA aggregation was enhanced at higher temperature and near neutral pH. Therefore, DNA aggregation is collectively determined by many environmental factors such as ion species, temperature, and solution pH. Copyright © 2017 Elsevier Ltd. All rights reserved.

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilkins, Michael J.; Wrighton, Kelly C.; Nicora, Carrie D.

2013-03-05

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 throughmore » 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.« less

Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuous-flow column

NASA Astrophysics Data System (ADS)

Azizian, Mohammad F.; Marshall, Ian P. G.; Behrens, Sebastian; Spormann, Alfred M.; Semprini, Lewis

2010-04-01

A continuous-flow column study was conducted to analyze the reductive dehalogenation of trichloroethene (TCE) with aquifer material with high content of iron oxides. The column was bioaugmented with the Point Mugu (PM) culture, which is a mixed microbial enrichment culture capable of completely transforming TCE to ethene (ETH). We determined whether lactate, formate, or propionate fermentation resulted in more effective dehalogenation. Reductive dehalogenation, fermentation, and sulfate, Fe(III), and Mn(IV) reduction were all exhibited within the column. Different steady-states of dehalogenation were achieved based on the concentration of substrates added, with effective transformation to ETH obtained when ample electron donor equivalents were provided. Most of the metabolic reducing equivalents were channeled to sulfate, Fe(III), and Mn(IV) reduction. When similar electron reducing equivalents were added, the most effective dehalogenation was achieved with formate, with 14% of the electron equivalents going towards dehalogenation reactions, compared to 6.5% for lactate and 9.6% for propionate. Effective dehalogenation was maintained over 1000 days of column operation. Over 90% of electron equivalents added could be accounted for by the different electron accepting processes in the column, with 50% associated with soluble and precipitated Fe(II) and Mn(II). Bulk Fe(III) and Mn(IV) reduction was rather associated with lactate and propionate addition than formate addition. Sulfate reduction was a competing electron acceptor reaction with all three electron donors. DNA was extracted from solid coupon samples obtained during the course of the experiment and analyzed using 16S rRNA gene clone libraries and quantitative PCR. Lactate and propionate addition resulted in a significant increase in Geobacter, Spirochaetes, and Desulfitobacterium phylotypes relative to " Dehalococcoides" when compared to formate addition. Results from the molecular biological analyses support

Separation and Determination of Fe(III) and Fe(II) in Natural and Waste Waters Using Silica Gel Sequentially Modified with Polyhexamethylene Guanidine and Tiron

PubMed Central

Maksimov, Nikolay; Trofimchuk, Anatoly; Zaporogets, Olga

2017-01-01

Silica gel, sequentially modified with polyhexamethylene guanidine and pyrocatechin-3,5-disulfonic acid (Tiron), was suggested for sorption separation and determination of Fe(III) and Fe(II). It was found that quantitative extraction of Fe(III) and its separation from Fe(II) were attained at pH 2.5–4.0, while quantitative extraction of Fe(II) was observed at pH 6.0–7.5. An intensive signal with g = 4.27, which is characteristic for Fe(III), appeared in EPR spectra of the sorbents after Fe(II) and Fe(III) sorption. During interaction between Fe(II) and Tiron, fixed on the sorbent surface, its oxidation up to Fe(III) occurred. Red-lilac complexes of the composition FeL3 were formed on the sorbent surface during sorption regardless of initial oxidation level of iron. Diffuse reflectance spectrum of surface complexes exhibited wide band with slightly expressed maxima at 480 and 510 nm. Procedures for separation and photometric determination of Fe(III) and Fe(II) at the joint presence and total Fe content determination as Fe(II) in waste and natural waters was developed. The limit of detection for iron was 0.05 μg per 0.100 g of the sorbent. The calibration graph was linear up to 20.0 μg of Fe per 0.100 g of the sorbent. The RSD in the determination of more than 0.2 μg of Fe was less than 0.06. PMID:29214095

Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1

NASA Astrophysics Data System (ADS)

Beller, H. R.; Han, R.; Karaoz, U.; Lim, H.; Brodie, E. L.

2012-12-01

Pelosinus species are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in Pelosinus sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with Hanford 100H aquifer sediment (constituting 80% of the total bacterial population in the columns). Strain HCF1 ferments lactate to propionate and acetate (a complete fermentation pathway was identified in the genome) and its genome encodes both [NiFe]- and [FeFe]-hydrogenases for H2 cycling. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides. In this strain, either H2 or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of nitrate reductases and hydrogenases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.

Alkaline Anaerobic Respiration: Isolation and Characterization of a Novel Alkaliphilic and Metal-Reducing Bacterium

PubMed Central

Ye, Qi; Roh, Yul; Carroll, Susan L.; Blair, Benjamin; Zhou, Jizhong; Zhang, Chuanlun L.; Fields, Matthew W.

2004-01-01

Iron-reducing enrichments were obtained from leachate ponds at the U.S. Borax Company in Boron, Calif. Based on partial small-subunit (SSU) rRNA gene sequences (approximately 500 nucleotides), six isolates shared 98.9% nucleotide identity. As a representative, the isolate QYMF was selected for further analysis. QYMF could be grown with Fe(III)-citrate, Fe(III)-EDTA, Co(III)-EDTA, or Cr(VI) as electron acceptors, and yeast extract and lactate could serve as electron donors. Growth during iron reduction occurred over the pH range of 7.5 to 11.0 (optimum, pH 9.5), a sodium chloride range of 0 to 80 g/liter (optimum, 20 g/liter), and a temperature range of 4 to 45°C (optimum, approximately 35°C), and iron precipitates were formed. QYMF was a strict anaerobe that could be grown in the presence of borax, and the cells were straight rods that produced endospores. Sodium chloride and yeast extract stimulated growth. Phylogenetic analysis of the SSU rRNA gene indicated that the bacterium was a low-G+C gram-positive microorganism and had 96 and 92% nucleotide identity with Alkaliphilus transvaalensis and Alkaliphilus crotonatoxidans, respectively. The major phospholipid fatty acids were 14:1, 16:1ω7c, and 16:0, which were different from those of other alkaliphiles but similar to those of reported iron-reducing bacteria. The results demonstrated that the isolate might represent a novel metal-reducing alkaliphilic species. The name Alkaliphilus metalliredigens sp. nov. is proposed. The isolation and activity of metal-reducing bacteria from borax-contaminated leachate ponds suggest that bioremediation of metal-contaminated alkaline environments may be feasible and have implications for alkaline anaerobic respiration. PMID:15345448

Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments.

PubMed

Küsel, K; Dorsch, T; Acker, G; Stackebrandt, E; Drake, H L

2000-03-01

A strictly anaerobic, H2-utilizing bacterium, strain SL1, was isolated from the sediment of an acidic coal mine pond. Cells of strain SL1 were sporulating, motile, long rods with a multilayer cell wall. Growth was observed at 5-35 degrees C and pH 3.9-7.0. Acetate was the sole end product of H2 utilization and was produced in stoichiometries indicative of an acetyl-CoA-pathway-dependent metabolism. Growth and substrate utilization also occurred with CO/CO2, vanillate, syringate, ferulate, ethanol, propanol, 1-butanol, glycerine, cellobiose, glucose, fructose, mannose, xylose, formate, lactate, pyruvate and gluconate. With most substrates, acetate was the main or sole product formed. Growth in the presence of H2/CO2 or CO/CO2 was difficult to maintain in laboratory cultures. Methoxyl, carboxyl and acrylate groups of various aromatic compounds were O-demethylated, decarboxylated and reduced, respectively. Small amounts of butyrate were produced during the fermentation of sugars. The acrylate group of ferulate was reduced. Nitrate, sulfate, thiosulfate, dimethylsulfoxide and Fe(III) were not utilized as electron acceptors. Analysis of the 16S rRNA gene sequence of strain SL1 demonstrated that it is closely related to Clostridium scatologenes (99.6% sequence similarity), an organism characterized as a fermentative anaerobe but not previously shown to be capable of acetogenic growth. Comparative experiments with C. scatologenes DSM 757T demonstrated that it utilized H2/CO2 (negligible growth), CO/CO2 (negligible growth), formate, ethanol and aromatic compounds according to stoichiometries indicative of the acetyl-CoA pathway. CO dehydrogenase, formate dehydrogenase and hydrogenase activities were present in both strain SL1 and C. scatologenes DSM 757T. These results indicate that (i) sediments of acidic coal mine ponds harbour acetogens and (ii) C. scatologenes is an acetogen that tends to lose its capacity to grow acetogenically under H2/CO2 or CO/CO2 after prolonged

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

USGS Publications Warehouse

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.

Anaerobic mineralization of vinyl chloride in Fe(III)-reducing, aquifer sediments

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.

1996-01-01

Within anaerobic aquifer systems, reductive dehalogenation of polychlorinated ethenes commonly results in the accumulation of vinyl chloride, which is highly toxic and carcinogenic to humans. Anaerobic reduction of vinyl chloride is considered to be slow and incomplete. Here, we provide the first evidence for anaerobic oxidation of vinyl chloride under Fe(III)reducing conditions. Addition of chelated Fe(III) (as Fe-EDTA) to anaerobic aquifer microcosms resulted in mineralization of up to 34% of [1,2- 14C]vinyl chloride within 84 h. The results indicate that vinyl chloride can be mineralized under anaerobic, Fe(III)-reducing conditions and that the bioavailability of Fe(III) is an important factor affecting the rates of mineralization.

Oxygen-Dependent Growth of the Sulfate-Reducing Bacterium Desulfovibrio oxyclinae in Coculture with Marinobacter sp. Strain MB in an Aerated Sulfate-Depleted Chemostat

PubMed Central

Sigalevich, Pavel; Cohen, Yehuda

2000-01-01

A chemostat coculture of the sulfate-reducing bacterium Desulfovibrio oxyclinae and the facultatively aerobic heterotroph Marinobacter sp. strain MB was grown for 1 week under anaerobic conditions at a dilution rate of 0.05 h−1. It was then exposed to an oxygen flux of 223 μmol min−1 by gassing the growth vessel with 5% O2. Sulfate reduction persisted under these conditions, though the amount of sulfate reduced decreased by 45% compared to the amount reduced during the initial anaerobic mode. After 1 week of growth under these conditions, sulfate was excluded from the incoming medium. The sulfate concentration in the growth vessel decreased exponentially from 4.1 mM to 2.5 μM. The coculture consumed oxygen effectively, and no residual oxygen was detected during either growth mode in which oxygen was supplied. The proportion of D. oxyclinae cells in the coculture as determined by in situ hybridization decreased from 86% under anaerobic conditions to 70% in the microaerobic sulfate-reducing mode and 34% in the microaerobic sulfate-depleted mode. As determined by the most-probable-number (MPN) method, the numbers of viable D. oxyclinae cells during the two microaerobic growth modes decreased compared to the numbers during the anaerobic growth mode. However, there was no significant difference between the MPN values for the two modes when oxygen was supplied. The patterns of consumption of electron donors and acceptors suggested that when oxygen was supplied in the absence of sulfate and thiosulfate, D. oxyclinae performed incomplete aerobic oxidation of lactate to acetate. This is the first observation of oxygen-dependent growth of a sulfate-reducing bacterium in the absence of either sulfate or thiosulfate. Cells harvested during the microaerobic sulfate-depleted stage and exposed to sulfate and thiosulfate in a respiration chamber were capable of anaerobic sulfate and thiosulfate reduction. PMID:11055958

Measuring “Free” Iron Levels in Caenorhabditis Elegans Using Low-Temperature Fe(III) Electron Paramagnetic Resonance Spectroscopy

PubMed Central

Pate, Kira T.; Rangel, Natalie A.; Fraser, Brian; Clement, Matthew H. S.; Srinivasan, Chandra

2007-01-01

Oxidative stress, caused by free radicals within the body, has been associated with the process of aging and many human diseases. As free radicals, in particular superoxide, are difficult to measure, an alternative indirect method for measuring oxidative stress levels has been successfully used in E. coli and yeast. This method is based on a proposed connection between elevated superoxide levels and release of iron from solvent exposed [4Fe-4S] enzyme clusters, which eventually leads to an increase in hydroxyl radical production. In past studies using bacteria and yeast, a positive correlation was found between superoxide production or oxidative stress due to superoxide within the organism and EPR (electron paramagnetic resonance) detectable “free” iron levels. In the present study, we have developed a reliable and an efficient method for measuring “free” iron levels in C. elegans using low temperature Fe(III) EPR at g = 4.3. This method utilizes synchronized worm cultures grown on plates, which are homogenized and treated with desferrioxamine, an Fe(III) chelator, prior to packing the EPR tube. Homogenization was found not to alter “free” iron levels, while desferrioxamine treatment significantly raised these levels, indicating presence of both Fe(II) and Fe(III) in the “free” iron pool. The correlation between free radical levels and the observed “free” iron levels was examined by using heat stress and paraquat treatment. The intensity of the Fe(III) EPR signal and thus, the concentration of the “free” iron pool, varied with the treatments that altered radical levels without changing the total iron levels. This study provides the groundwork needed to uncover the correlation between oxidative stress, “free” iron levels, and longevity in C. elegans. PMID:17010298

Dissociation kinetics of Fe(III)- and Al(III)-natural organic matter complexes at pH 6.0 and 8.0 and 25 °C

NASA Astrophysics Data System (ADS)

Jones, Adele M.; Pham, A. Ninh; Collins, Richard N.; Waite, T. David

2009-05-01

The rate at which iron- and aluminium-natural organic matter (NOM) complexes dissociate plays a critical role in the transport of these elements given the readiness with which they hydrolyse and precipitate. Despite this, there have only been a few reliable studies on the dissociation kinetics of these complexes suggesting half-times of some hours for the dissociation of Fe(III) and Al(III) from a strongly binding component of NOM. First-order dissociation rate constants are re-evaluated here at pH 6.0 and 8.0 and 25 °C using both cation exchange resin and competing ligand methods for Fe(III) and a cation exchange resin method only for Al(III) complexes. Both methods provide similar results at a particular pH with a two-ligand model accounting satisfactorily for the dissociation kinetics results obtained. For Fe(III), half-times on the order of 6-7 h were obtained for dissociation of the strong component and 4-5 min for dissociation of the weak component. For aluminium, the half-times were on the order of 1.5 h and 1-2 min for the strong and weak components, respectively. Overall, Fe(III) complexes with NOM are more stable than analogous complexes with Al(III), implying Fe(III) may be transported further from its source upon dilution and dispersion.

Polarized Neutron Diffraction to Probe Local Magnetic Anisotropy of a Low-Spin Fe(III) Complex.

PubMed

Ridier, Karl; Mondal, Abhishake; Boilleau, Corentin; Cador, Olivier; Gillon, Béatrice; Chaboussant, Grégory; Le Guennic, Boris; Costuas, Karine; Lescouëzec, Rodrigue

2016-03-14

We have determined by polarized neutron diffraction (PND) the low-temperature molecular magnetic susceptibility tensor of the anisotropic low-spin complex PPh4 [Fe(III) (Tp)(CN)3]⋅H2O. We found the existence of a pronounced molecular easy magnetization axis, almost parallel to the C3 pseudo-axis of the molecule, which also corresponds to a trigonal elongation direction of the octahedral coordination sphere of the Fe(III) ion. The PND results are coherent with electron paramagnetic resonance (EPR) spectroscopy, magnetometry, and ab initio investigations. Through this particular example, we demonstrate the capabilities of PND to provide a unique, direct, and straightforward picture of the magnetic anisotropy and susceptibility tensors, offering a clear-cut way to establish magneto-structural correlations in paramagnetic molecular complexes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed Central

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

Electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clays. Role in U and Hg(II) transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scherer, Michelle

2016-08-31

During this project, we investigated Fe electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clay minerals. We used selective chemical extractions, enriched Fe isotope tracer experiments, computational molecular modeling, and Mössbauer spectroscopy. Our findings indicate that structural Fe(III) in clay minerals is reduced by aqueous Fe(II) and that electron transfer occurs when Fe(II) is sorbed to either basal planes and edge OH-groups of clay mineral. Findings from highly enriched isotope experiments suggest that up to 30 % of the Fe atoms in the structure of some clay minerals exhanges with aqueous Fe(II). First principles calculations usingmore » a small polaron hopping approach suggest surprisingly fast electron mobility at room temperature in a nontronite clay mineral and are consistent with temperature dependent Mössbauer data Fast electron mobility suggests that electrons may be able to conduct through the mineral fast enough to enable exchange of Fe between the aqueous phase and clay mineral structure. over the time periods we observed. Our findings suggest that Fe in clay minerals is not as stable as previously thought.« less

Fe(II) sorption on pyrophyllite: Effect of structural Fe(III) (impurity) in pyrophyllite on nature of layered double hydroxide (LDH) secondary mineral formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starcher, Autumn N.; Li, Wei; Kukkadapu, Ravi K.

Fe(II)-Al(III)-LDH (layered double hydroxide) phases have been shown to form from reactions of aqueous Fe(II) with Fe-free Al-bearing minerals (phyllosilicate/clays and Al-oxides). To our knowledge, the effect of small amounts of structural Fe(III) impurities in “neutral” clays on such reactions, however, were not studied. In this study to understand the role of structural Fe(III) impurity in clays, laboratory batch studies with pyrophyllite (10 g/L), an Al-bearing phyllosilicate, containing small amounts of structural Fe(III) impurities and 0.8 mM and 3 mM Fe(II) (both natural and enriched in 57Fe) were carried out at pH 7.5 under anaerobic conditions (4% H2 – 96%more » N2 atmosphere). Samples were taken up to 4 weeks for analysis by Fe-X-ray absorption spectroscopy and 57Fe Mössbauer spectroscopy. In addition to the precipitation of Fe(II)-Al(III)-LDH phases as observed in earlier studies with pure minerals (no Fe(III) impurities in the minerals), the analyses indicated formation of small amounts of Fe(III) containing solid(s), most probably hybrid a Fe(II)-Al(III)/Fe(III)-LDH phase. The mechanism of Fe(II) oxidation was not apparent but most likely was due to interfacial electron transfer from the sorbed Fe(II) to the structural Fe(III) and/or surface-sorption-induced electron-transfer from the sorbed Fe(II) to the clay lattice. Increase in the Fe(II)/Al ratio of the LDH with reaction time further indicated the complex nature of the samples. This research provides evidence for the formation of both Fe(II)-Al(III)-LDH and Fe(II)-Fe(III)/Al(III)-LDH-like phases during reactions of Fe(II) in systems that mimic the natural environments. Better understanding Fe phase formation in complex laboratory studies will improve models of natural redox systems.« less

Deletion of the rbo Gene Increases the Oxygen Sensitivity of the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

PubMed Central

Voordouw, Johanna K.; Voordouw, Gerrit

1998-01-01

The rbo gene of Desulfovibrio vulgaris Hildenborough encodes rubredoxin oxidoreductase (Rbo), a 14-kDa iron sulfur protein; forms an operon with the gene for rubredoxin; and is preceded by the gene for the oxygen-sensing protein DcrA. We have deleted the rbo gene from D. vulgaris with the sacB mutagenesis procedure developed previously (R. Fu and G. Voordouw, Microbiology 143:1815–1826, 1997). The absence of the rbo-gene in the resulting mutant, D. vulgaris L2, was confirmed by PCR and protein blotting with Rbo-specific polyclonal antibodies. D. vulgaris L2 grows like the wild type under anaerobic conditions. Exposure to air for 24 h caused a 100-fold drop in CFU of L2 relative to the wild type. The lag times of liquid cultures of inocula exposed to air were on average also greater for L2 than for the wild type. These results demonstrate that Rbo, which is not homologous with superoxide dismutase or catalase, acts as an oxygen defense protein in the anaerobic, sulfate-reducing bacterium D. vulgaris Hildenborough and likely also in other sulfate-reducing bacteria and anaerobic archaea in which it has been found. PMID:9687445

Growth of Iron(III)-Reducing Bacteria on Clay Minerals as the Sole Electron Acceptor and Comparison of Growth Yields on a Variety of Oxidized Iron Forms†

PubMed Central

Kostka, Joel E.; Dalton, Dava D.; Skelton, Hayley; Dollhopf, Sherry; Stucki, Joseph W.

2002-01-01

Smectite clay minerals are abundant in soils and sediments worldwide and are typically rich in Fe. While recent investigations have shown that the structural Fe(III) bound in clay minerals is reduced by microorganisms, previous studies have not tested growth with clay minerals as the sole electron acceptor. Here we have demonstrated that a pure culture of Shewanella oneidensis strain MR-1 as well as enrichment cultures of Fe(III)-reducing bacteria from rice paddy soil and subsurface sediments are capable of conserving energy for growth with the structural Fe(III) bound in smectite clay as the sole electron acceptor. Pure cultures of S. oneidensis were used for more detailed growth rate and yield experiments on various solid- and soluble-phase electron acceptors [smectite, Fe(III) oxyhydroxide FeOOH, Fe(III) citrate, and oxygen] in the same minimal medium. Growth was assessed as direct cell counts or as an increase in cell carbon (measured as particulate organic carbon). Cell counts showed that similar growth of S. oneidensis (108 cells ml−1) occurred with smectitic Fe(III) and on other Fe forms [amorphous Fe(III) oxyhydroxide, and Fe citrate] or oxygen as the electron acceptor. In contrast, cell yields of S. oneidensis measured as the increase in cell carbon were similar on all Fe forms tested while yields on oxygen were five times higher, in agreement with thermodynamic predictions. Over a range of particle loadings (0.5 to 4 g liter−1), the increase in cell number was highly correlated to the amount of structural Fe in smectite reduced. From phylogenetic analysis of the complete 16S rRNA gene sequences, a predominance of clones retrieved from the clay mineral-reducing enrichment cultures were most closely related to the low-G+C gram-positive members of the Bacteria (Clostridium and Desulfitobacterium) and the δ-Proteobacteria (members of the Geobacteraceae). Results indicate that growth with smectitic Fe(III) is similar in magnitude to that with Fe(III

Microbial Communities and Electrochemical Performance of Titanium-Based Anodic Electrodes in a Microbial Fuel Cell▿

PubMed Central

Michaelidou, Urania; ter Heijne, Annemiek; Euverink, Gerrit Jan W.; Hamelers, Hubertus V. M.; Stams, Alfons J. M.; Geelhoed, Jeanine S.

2011-01-01

Four types of titanium (Ti)-based electrodes were tested in the same microbial fuel cell (MFC) anodic compartment. Their electrochemical performances and the dominant microbial communities of the electrode biofilms were compared. The electrodes were identical in shape, macroscopic surface area, and core material but differed in either surface coating (Pt- or Ta-coated metal composites) or surface texture (smooth or rough). The MFC was inoculated with electrochemically active, neutrophilic microorganisms that had been enriched in the anodic compartments of acetate-fed MFCs over a period of 4 years. The original inoculum consisted of bioreactor sludge samples amended with Geobacter sulfurreducens strain PCA. Overall, the Pt- and Ta-coated Ti bioanodes (electrode-biofilm association) showed higher current production than the uncoated Ti bioanodes. Analyses of extracted DNA of the anodic liquid and the Pt- and Ta-coated Ti electrode biofilms indicated differences in the dominant bacterial communities. Biofilm formation on the uncoated electrodes was poor and insufficient for further analyses. Bioanode samples from the Pt- and Ta-coated Ti electrodes incubated with Fe(III) and acetate showed several Fe(III)-reducing bacteria, of which selected species were dominant, on the surface of the electrodes. In contrast, nitrate-enriched samples showed less diversity, and the enriched strains were not dominant on the electrode surface. Isolated Fe(III)-reducing strains were phylogenetically related, but not all identical, to Geobacter sulfurreducens strain PCA. Other bacterial species were also detected in the system, such as a Propionicimonas-related species that was dominant in the anodic liquid and Pseudomonas-, Clostridium-, Desulfovibrio-, Azospira-, and Aeromonas-related species. PMID:21131513

Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.

PubMed

Zavarzina, Daria G; Zhilina, Tatyana N; Kuznetsov, Boris B; Kolganova, Tatyana V; Osipov, Georgy A; Kotelev, Mikhail S; Zavarzin, Georgy A

2013-12-01

An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45-50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) ( = DSM 24923(T) = VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.

Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater

DOE PAGES

Dong, Yiran; Sanford, Robert A.; Boyanov, Maxim I.; ...

2016-10-01

Here, a Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9 T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9 T were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9 T grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI)more » when H 2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S 0). The G+C content of the DNA from strain Z9 T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9 T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus, T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9 T represents a novel species within the genus Tepidibacillus, for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9 T (=ATCC BAA-2644 T=DSM 103037 T).« less

Tepidibacillus decaturensis sp. nov., a microaerophilic, moderately thermophilic iron-reducing bacterium isolated from 1.7 km depth groundwater

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Yiran; Sanford, Robert A.; Boyanov, Maxim I.

Here, a Gram-stain-negative, microaerophilic rod-shaped organism designated as strain Z9 T was isolated from groundwater of 1.7 km depth from the Mt. Simon Sandstone of the Illinois Basin, Illinois, USA. Cells of strain Z9 T were rod shaped with dimensions of 0.3×(1–10) µm and stained Gram-negative. Strain Z9 T grew within the temperature range 20–60 °C (optimum at 30–40 °C), between pH 5 and 8 (optimum 5.2–5.8) and under salt concentrations of 1–5 % (w/v) NaCl (optimum 2.5 % NaCl). In addition to growth by fermentation and nitrate reduction, this strain was able to reduce Fe(III), Mn(IV), Co(III) and Cr(VI)more » when H 2 or organic carbon was available as the electron donor, but did not actively reduce oxidized sulfur compounds (e.g. sulfate, thiosulfate or S 0). The G+C content of the DNA from strain Z9 T was 36.1 mol%. Phylogenetic analysis of the 16S rRNA gene from strain Z9 T showed that it belongs to the class Bacilli and shares 97 % sequence similarity with the only currently characterized member of the genus Tepidibacillus, T. fermentans. Based on the physiological distinctness and phylogenetic information, strain Z9 T represents a novel species within the genus Tepidibacillus, for which the name Tepidibacillus decaturensis sp. nov. is proposed. The type strain is Z9 T (=ATCC BAA-2644 T=DSM 103037 T).« less

Direct determination of oxidation state of gold deposits in metal-reducing bacterium Shewanella algae using X-ray absorption near-edge structure spectroscopy (XANES).

PubMed

Konishi, Yasuhiro; Tsukiyama, Takeshi; Saitoh, Norizoh; Nomura, Toshiyuki; Nagamine, Shinsuke; Takahashi, Yoshio; Uruga, Tomoya

2007-06-01

X-ray absorption near-edge structure spectroscopy (XANES) was successfully employed to determine the gold valence in the metal-reducing bacterium Shewanella algae after exposure to a 1 mM aqueous HAuCl4 solution for 10-120 min. XANES spectra revealed the oxidation state of gold in the bacterial cells to be Au(0) without any contribution from Au(III), demonstrating that S. algae cells can reduce AuCl4- ions to elemental gold. Transmission electron microscopy (TEM) and energy dispersive X-ray (EDX) analysis confirmed that gold nanoparticles 5-15 nm in size were deposited in the periplasmic space of the bacterial cells; a preferable, cell surface location for the easy recovery of biogenic nanoparticles.

A voltammetric method for Fe(iii) in blood serum using a screen-printed electrode modified with a Schiff base ionophore.

PubMed

Mittal, Susheel K; Rana, Sonia; Kaur, Navneet; Banks, Craig E

2018-05-23

Herein, a potent electrochemical ionophore (SMS-2) based on a Schiff base has been used for the modification of a screen-printed electrode (SPE). The modified disposable electrode can selectively detect ferric ions in an aqueous medium. Redox behavior of the proposed strip was characterized using cyclic voltammetry (CV) and differential pulse voltammetry (DPV). Incorporation of the ligand in the ink of the SPE enhanced the analytical performance of the electrode, and its surface modification was confirmed by SEM and EDX analysis. Shifting/quenching of the cathodic peak potential of the ionophore after binding with Fe(iii) ions was used to detect and measure the ferric ion concentration. This sensor can identify Fe(iii) in the detection range from 0.625 μM to 7.5 μM. The modified SPE can selectively detect ferric ions in the presence of many other interfering ions and has been successfully used to determine the Fe(iii) content in blood serum samples. The metal-ionophore complex structure was optimized using DFT calculations to study the energetics of the metal-ionophore interactions.

Impact of Microcystis aeruginosa Exudate on the Formation and Reactivity of Iron Oxide Particles Following Fe(II) and Fe(III) Addition.

PubMed

Garg, Shikha; Wang, Kai; Waite, T David

2017-05-16

Impact of the organic exudate secreted by a toxic strain of Microcystis aeruginosa on the formation, aggregation, and reactivity of iron oxides that are formed on addition of Fe(II) and Fe(III) salts to a solution of the exudate is investigated in this study. The exudate has a stabilizing effect on the particles formed with decreased aggregation rate and increased critical coagulant concentration required for diffusion-limited aggregation to occur. These results suggest that the presence of algal exudates from Microcystis aeruginosa may significantly influence particle aggregation both in natural water bodies where Fe(II) oxidation results in oxide formation and in water treatment where Fe(III) salts are commonly added to aid particle growth and contaminant capture. The exudate also affects the reactivity of iron oxide particles formed with exudate coated particles undergoing faster dissolution than bare iron oxide particles. This has implications to iron availability, especially where algae procure iron via dissolution of iron oxide particles as a result of either reaction with reducing moieties, light-mediated ligand to metal charge transfer and/or reaction with siderophores. The increased reactivity of exudate coated particles is attributed, for the most part, to the smaller size of these particles, higher surface area and increased accessibility of surface sites.

Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1

PubMed Central

Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T.; McShan, W. Michael; Gillaspy, Allison F.

2014-01-01

Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. PMID:25081260

Biofilm Formation by a Metabolically Versatile Bacterium

DTIC Science & Technology

2009-03-19

ABSTRACT Rhodopseudomonas palustris is a photosynthetic bacterium that has good potential as a biocatalyst for the production ofhydrogen gas, a biofuel...Biofilm formation by a metabolically versatile bacterium: final report Report Title ABSTRACT Rhodopseudomonas palustris is a photosynthetic bacterium...agricultural waste. We characterized five new Rhodopseudomonas genome sequences and isolated and described R. palustris mutant strains that produce

Effect of Fe(III) on 1,1,2,2-tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen proving ground

USGS Publications Warehouse

Jones, E.J.P.; Voytek, M.A.; Lorah, M.M.

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek, MD, where dechlorination occurred. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways led to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The effect of adding Fe(III) to TeCA-amended microcosms of wetland sediment was studied. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than no AFO microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and decreasing the microbial capability to produce VC from 1,2-dichloroethylene. VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Otwell, Annie E.; Sherwood, Roberts; Zhang, Sheng

Metal reduction capability has been found in numerous species of environmentally abundant Gram-positive bacteria. However, understanding of microbial metal reduction is based almost solely on studies of Gram-negative organisms. In this study, we focus on Desulfotomaculum reducens MI-1, a Gram-positive metal reducer whose genome lacks genes with similarity to any characterized metal reductase. D. reducens has been shown to reduce not only Fe(III), but also the environmentally important contaminants U(VI) and Cr(VI). By extracting, separating, and analyzing the functional proteome of D. reducens, using a ferrozine-based assay in order to screen for chelated Fe(III)-NTA reduction with NADH as electron donor,more » we have identified proteins not previously characterized as iron reductases. Their function was confirmed by heterologous expression in E. coli. These are the protein NADH:flavin oxidoreductase (Dred_2421) and a protein complex composed of oxidoreductase FAD/NAD(P)-binding subunit (Dred_1685) and dihydroorotate dehydrogenase 1B (Dred_1686). Dred_2421 was identified in the soluble proteome and is predicted to be a cytoplasmic protein. Dred_1685 and Dred_1686 were identified in both the soluble as well as the insoluble (presumably membrane) protein fraction, suggesting a type of membrane-association, although PSORTb predicts both proteins are cytoplasmic. Furthermore, we show that these proteins have the capability to reduce soluble Cr(VI) and U(VI) with NADH as electron donor. This study is the first functional proteomic analysis of D. reducens, and one of the first analyses of metal and radionuclide reduction in an environmentally relevant Gram-positive bacterium.« less

Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1.

PubMed

Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T; McShan, W Michael; Gillaspy, Allison F; Bazylinski, Dennis A

2014-07-31

Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. Copyright © 2014 Trubitsyn et al.

Assessing bioavailability levels of metals in effluent-affected rivers: effect of Fe(III) and chelating agents on the distribution of metal speciation.

PubMed

Han, Shuping; Naito, Wataru; Masunaga, Shigeki

To assess the effects of Fe(III) and anthropogenic ligands on the bioavailability of Ni, Cu, Zn, and Pb, concentrations of bioavailable metals were measured by the DGT (diffusive gradients in thin films) method in some urban rivers, and were compared with concentrations calculated by a chemical equilibrium model (WHAM 7.0). Assuming that dissolved Fe(III) (<0.45 μm membrane filtered) was in equilibrium with colloidal iron oxide, the WHAM 7.0 model estimated that bioavailable concentrations of Ni, Cu, and Zn were slightly higher than the corresponding values estimated assuming that dissolved Fe(III) was absent. In contrast, lower levels of free Pb were predicted by the WHAM 7.0 model when dissolved Fe(III) was included. Estimates showed that most of the dissolved Pb was present as colloidal iron-Pb complex. Ethylene-diamine-tetra-acetic acid (EDTA) concentrations at sampling sites were predicted from the relationship between EDTA and the calculated bioavailable concentration of Zn. When both colloidal iron and predicted EDTA concentrations were included in the WHAM 7.0 calculations, dissolved metals showed a strong tendency to form EDTA complexes, in the order Ni > Cu > Zn > Pb. With the inclusion of EDTA, bioavailable concentrations of Ni, Cu, and Zn predicted by WHAM 7.0 were different from those predicted considering only humic substances and colloidal iron.

Characterization of microbially Fe(III)-reduced nontronite: Environmental cell-transmission electron microscopy study

USGS Publications Warehouse

Kim, Jin-wook; Furukawa, Yoko; Daulton, Tyrone L.; Lavoie, Dawn L.; Newell, Steven W.

2003-01-01

Microstructural changes induced by the microbial reduction of Fe(III) in nontronite by Shewanella oneidensis were studied using environmental cell (EC)-transmission electron microscopy (TEM), conventional TEM, and X-ray powder diffraction (XRD). Direct observations of clays by EC-TEM in their hydrated state allowed for the first time an accurate and unambiguous TEM measurement of basal layer spacings and the contraction of layer spacing caused by microbial effects, most likely those of Fe(III) reduction. Non-reduced and Fe(III)-reduced nontronite, observed by EC-TEM, exhibited fringes with mean d001 spacings of 1.50 nm (standard deviation, σ = 0.08 nm) and 1.26 nm (σ = 0.10 nm), respectively. In comparison, the same samples embedded with Nanoplast resin, sectioned by microtome, and observed using conventional TEM, displayed layer spacings of 1.0–1.1 nm (non-reduced) and 1.0 nm (reduced). The results from Nanoplast-embedded samples are typical of conventional TEM studies, which have measured nearly identical layer spacings regardless of Fe oxidation state. Following Fe(III) reduction, both EC- and conventional TEM showed an increase in the order of nontronite selected area electron diffraction patterns while the images exhibited fewer wavy fringes and fewer layer terminations. An increase in stacking order in reduced nontronite was also suggested by XRD measurements. In particular, the ratio of the valley to peak intensity (v/p) of the 1.7 nm basal 001 peak of ethylene glycolated nontronite was measured at 0.65 (non-reduced) and 0.85 (microbially reduced).

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

PubMed Central

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; Dohnalkova, Alice C.; Fredrickson, James K.; Madigan, Michael T.; Beyenal, Haluk

2017-01-01

Microbial phototrophs, key primary producers on Earth, use H2O, H2, H2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis'. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii does not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. This process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities. PMID:28067226

Reductive Dissolution of Goethite and Hematite by Reduced Flavins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Zhi; Zachara, John M.; Wang, Zheming

2013-10-02

The abiotic reductive dissolution of goethite and hematite by the reduced forms of flavin mononucleotide (FMNH2) and riboflavin (RBFH2), electron transfer mediators (ETM) secreted by the dissimilatory iron-reducing bacterium Shewanella, was investigated under stringent anaerobic conditions. In contrast to the rapid redox reaction rate observed for ferrihydrite and lepidocrocite (Shi et al., 2012), the reductive dissolution of crystalline goethite and hematite was slower, with the extent of reaction limited by the thermodynamic driving force at circumneutral pH. Both the initial reaction rate and reaction extent increased with decreasing pH. On a unit surface area basis, goethite was less reactive thanmore » hematite between pH 4.0 and 7.0. AH2DS, the reduced form of the well-studied synthetic ETM anthraquinone-2,6-disulfonate (AQDS), yielded higher rates than FMNH2 under most reaction conditions, despite the fact that FMNH2 was a more effective reductant than AH2DS for ferryhydrite and lepidocrocite. Two additional model compounds, methyl viologen and benzyl viologen, were investigated under similar reaction conditions to explore the relationship between reaction rate and thermodynamic properties. Relevant kinetic data from the literature were also included in the analysis to span a broad range of half-cell potentials. Other conditions being equal, the surface area normalized initial reaction rate (ra) increased as the redox potential of the reductant became more negative. A non-linear, parabolic relationship was observed between log ra and the redox potential for eight reducants at pH 7.0, as predicted by Marcus theory for electron transfer. When pH and reductant concentration were fixed, log ra was positively correlated to the redox potential of four Fe(III) oxides over a wide pH range, following a non-linear parabolic relationship as well.« less

The Effect of Temperature and Hydrogen Limited Growth on the Fractionation of Sulfur Isotopes by Thermodesulfatator indicus, a Deep-sea Hydrothermal Vent Sulfate-Reducing Bacterium

NASA Astrophysics Data System (ADS)

Hoek, J.; Reysenbach, A.; Habicht, K.; Canfield, D. E.

2004-12-01

Sulfate-reducing bacteria fractionate sulfur isotopes during dissimilatory sulfate reduction, producing sulfide depleted in 34S. Although isotope fractionation during sulfate reduction of pure cultures has been extensively studied, most of the research to date has focused on mesophilic sulfate reducers, particularly for the species Desulfovibrio desulfuricans. Results from these studies show that: 1) fractionations range from 3-46‰ with an average around 18‰ , 2) when organic electron donors are utilized, the extent of fractionation is dependent on the rate of sulfate reduction, with decreasing fractionations observed with higher specific rates, 3) fractionations are suppressed with low sulfate concentrations, and when hydrogen is used as the electron donor. High specific sulfate-reduction rates are encountered when sulfate-reducing bacteria metabolize at their optimal temperature and under non-limiting substrate conditions. Changes in both temperature and substrate availability could shift fractionations from those expressed under optimal growth conditions. Sulfate reducers may frequently experience substrate limitation and sub-optimal growth temperatures in the environment. Therefore it is important to understand how sulfate-reducing bacteria fractionate sulfur isotopes under conditions that more closely resemble the restrictions imposed by the environment. In this study the fractionation of sulfur isotopes by Thermodesulfatator indicus was explored during sulfate reduction under a wide range of temperatures and with both hydrogen-saturating and hydrogen-limited conditions. T. indicus is a thermophilic (temperature optimum = 70° C) chemolithotrophic sulfate-reducing bacterium, which was recently isolated from a deep-sea hydrothermal vent on the Central Indian Ridge. This bacterium represents the type species of a new genus and to date is the most deeply branching sulfate-reducing bacterium known. T. indicus was grown in carbonate-buffered salt-water medium

Organic carbon and reducing conditions lead to cadmium immobilization by secondary Fe mineral formation in a pH-neutral soil.

PubMed

Muehe, E Marie; Adaktylou, Irini J; Obst, Martin; Zeitvogel, Fabian; Behrens, Sebastian; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

2013-01-01

Cadmium (Cd) is of environmental relevance as it enters soils via Cd-containing phosphate fertilizers and endangers human health when taken up by crops. Cd is known to associate with Fe(III) (oxyhydr)oxides in pH-neutral to slightly acidic soils, though it is not well understood how the interrelation of Fe and Cd changes under Fe(III)-reducing conditions. Therefore, we investigated how the mobility of Cd changes when a Cd-bearing soil is faced with organic carbon input and reducing conditions. Using fatty acid profiles and quantitative PCR, we found that both fermenting and Fe(III)-reducing bacteria were stimulated by organic carbon-rich conditions, leading to significant Fe(III) reduction. The reduction of Fe(III) minerals was accompanied by increasing soil pH, increasing dissolved inorganic carbon, and decreasing Cd mobility. SEM-EDX mapping of soil particles showed that a minor fraction of Cd was transferred to Ca- and S-bearing minerals, probably carbonates and sulfides. Most of the Cd, however, correlated with a secondary iron mineral phase that was formed during microbial Fe(III) mineral reduction and contained mostly Fe, suggesting an iron oxide mineral such as magnetite (Fe3O4). Our data thus provide evidence that secondary Fe(II) and Fe(II)/Fe(III) mixed minerals could be a sink for Cd in soils under reducing conditions, thus decreasing the mobility of Cd in the soil.

Harvesting visible light with MoO3 nanorods modified by Fe(iii) nanoclusters for effective photocatalytic degradation of organic pollutants.

PubMed

Alam, U; Kumar, S; Bahnemann, D; Koch, J; Tegenkamp, C; Muneer, M

2018-02-07

The photocatalytic performance of MoO 3 is limited due to its weak visible light absorption ability and quick recombination of charge carriers. In the present work, we report the facile synthesis of Fe(iii)-grafted MoO 3 nanorods using a hydrothermal method followed by an impregnation technique with the aim of enhancing the light harvesting ability and photocatalytic efficiency of MoO 3 . The prepared samples were characterized through the standard analytical techniques of XRD, SEM-EDS, TEM, XPS, UV-Vis-DRS, FT-IR, TG-DTA and PL spectrophotometry. XPS and TEM analyses reveal that Fe(iii) ions are successfully grafted onto the surface of the MoO 3 nanorod with intimate interfacial contact. The photocatalytic performances of the prepared samples were investigated by studying the degradation of methylene blue (MB), rhodamine B (RhB) and 4-nitrophenol (4-NP) under visible light irradiation. The surface-modified MoO 3 with Fe(iii) ions showed excellent photocatalytic activity towards the degradation of the above-mentioned pollutants, where Fe(iii) ions act as effective cocatalytic sites to produce hydroxyl radicals through multi-electron reduction of oxygen molecules. The improved photocatalytic activity could be ascribed to the effective separation of charge carriers and efficient production of hydroxyl radicals via the rapid capture of electrons by Fe(iii) through a well-known photoinduced interfacial charge transfer mechanism. Based on scavenger analysis study, a mechanism for the enhanced photocatalytic activity has been discussed and proposed. The concept of surface grafting onto large bandgap semiconductors with ubiquitous elements opens up a new avenue for the development of visible-light-responsive photocatalysts with excellent photocatalytic activity.

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

PubMed

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

IR, UV-Vis, magnetic and thermal characterization of chelates of some catecholamines and 4-aminoantipyrine with Fe(III) and Cu(II)

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Zayed, M. A.; El-Dien, F. A. Nour; El-Nahas, Reham G.

2004-07-01

The dopamine derivatives participate in the regulation of wide variety of physiological functions in the human body and in medication life. Increase and/or decrease in the concentration of dopamine in human body reflect an indication for diseases such as Schizophrenia and/or Parkinson diseases. α-Methyldopa (α-MD) in tablets is used in medication of hypertension. The Fe(III) and Cu(II) chelates with coupled products of adrenaline hydrogen tartarate (AHT), levodopa (LD), α-MD and carbidopa (CD) with 4-aminoantipyrine (4-AAP) are prepared and characterized. Different physico-chemical methods like IR, magnetic and UV-Vis spectra are used to investigate the structure of these chelates. Fe(III) form 1:2 (M:catecholamines) chelates while Cu(II) form 1:1 chelates. Catecholamines behave as a bidentate mono- or dibasic ligands in binding to the metal ions. IR spectra show that the catecholamines are coordinated to the metal ions in a bidentate manner with O,O donor sites of the phenolic - OH. Magnetic moment measurements reveal the presence of Fe(III) chelates in octahedral geometry while the Cu(II) chelates are square planar. The thermal decomposition of Fe(III) and Cu(II) complexes is studied using thermogravimetric (TGA) and differential thermal analysis (DTA) techniques. The water molecules are removed in the first step followed immediately by decomposition of the ligand molecules. The activation thermodynamic parameters, such as, energy of activation, enthalpy, entropy and free energy change of the complexes are evaluated and the relative thermal stability of the complexes are discussed.

Molecular structure and biological studies on Cr(III), Mn(II) and Fe(III) complexes of heterocyclic carbohydrazone ligand.

PubMed

Abu El-Reash, G M; El-Gammal, O A; Radwan, A H

2014-01-01

The chelating behavior of the ligand (H2APC) based on carbohydrazone core modified with pyridine end towards Cr(III), Mn(II) and Fe(III) ions have been examined. The (1)H NMR and IR data for H2APC revealed the presence of two stereoisomers syn and anti in both solid state and in solution in addition to the tautomeric versatility based on the flexible nature of the hydrazone linkage leading to varied coordination modes. The spectroscopic data confirmed that the ligand behaves as a monobasic tridentate in Cr(III) and Fe(III) complexes and as neutral tetradentate in Mn(II) complex. The electronic spectra as well as the magnetic measurements confirmed the octahedral geometry for all complexes. The bond length and angles were evaluated by DFT method using material studio program for all complexes. The thermal behavior and the kinetic parameters of degradation were determined using Coats-Redfern and Horowitz-Metzger methods. The antioxidant (DDPH and ABTS methods), anti-hemolytic and cytotoxic activities of the compounds have been screened. Cr(III) complex and H2APC showed the highest antioxidant activity using ABTS and DPPH methods. With respect to in vitro Ehrlich ascites assay, H2APC exhibited the potent activity followed by Fe(III) and Cr(III)complexes. Copyright © 2013 Elsevier B.V. All rights reserved.

A Simple Small Size and Low Cost Sensor Based on Surface Plasmon Resonance for Selective Detection of Fe(III)

PubMed Central

Cennamo, Nunzio; Alberti, Giancarla; Pesavento, Maria; D'Agostino, Girolamo; Quattrini, Federico; Biesuz, Raffaela; Zeni, Luigi

2014-01-01

A simple, small size, and low cost sensor based on a Deferoxamine Self Assembled Monolayer (DFO-SAM) and Surface Plasmon Resonance (SPR) transduction, in connection with a Plastic Optical Fiber (POF), has been developed for the selective detection of Fe(III). DFO-SAM sensors based on appropriate electrochemical techniques can be frequently found in the scientific literature. In this work, we present the first example of a DFO-SAM sensor based on SPR in an optical fiber. The SPR sensing platform was realized by removing the cladding of a plastic optical fiber along half the circumference, spin coating a buffer of Microposit S1813 photoresist on the exposed core, and finally sputtering a thin gold film. The hydroxamate siderophore deferoxamine (DFO), having high binding affinity for Fe(III), is then used in its immobilized form, as self-assembled monolayer on the gold layer surface of the POF sensor. The results showed that the DFO-SAM-POF-sensor was able to sense the formation of the Fe(III)/DFO complex in the range of concentrations between 1 μm and 50 μm with a linearity range from 0 to 30 μm of Fe(III). The selectivity of the sensor was also proved by interference tests. PMID:24608007

A simple small size and low cost sensor based on surface plasmon resonance for selective detection of Fe(III).

PubMed

Cennamo, Nunzio; Alberti, Giancarla; Pesavento, Maria; D'Agostino, Girolamo; Quattrini, Federico; Biesuz, Raffaela; Zeni, Luigi

2014-03-07

A simple, small size, and low cost sensor based on a Deferoxamine Self Assembled Monolayer (DFO-SAM) and Surface Plasmon Resonance (SPR) transduction, in connection with a Plastic Optical Fiber (POF), has been developed for the selective detection of Fe(III). DFO-SAM sensors based on appropriate electrochemical techniques can be frequently found in the scientific literature. In this work, we present the first example of a DFO-SAM sensor based on SPR in an optical fiber. The SPR sensing platform was realized by removing the cladding of a plastic optical fiber along half the circumference, spin coating a buffer of Microposit S1813 photoresist on the exposed core, and finally sputtering a thin gold film. The hydroxamate siderophore deferoxamine (DFO), having high binding affinity for Fe(III), is then used in its immobilized form, as self-assembled monolayer on the gold layer surface of the POF sensor. The results showed that the DFO-SAM-POF-sensor was able to sense the formation of the Fe(III)/DFO complex in the range of concentrations between 1 μm and 50 μm with a linearity range from 0 to 30 μm of Fe(III). The selectivity of the sensor was also proved by interference tests.

Comparison of lactate, formate, and propionate as hydrogen donors for the reductive dehalogenation of trichloroethene in a continuous-flow column.

PubMed

Azizian, Mohammad F; Marshall, Ian P G; Behrens, Sebastian; Spormann, Alfred M; Semprini, Lewis

2010-04-01

A continuous-flow column study was conducted to analyze the reductive dehalogenation of trichloroethene (TCE) with aquifer material with high content of iron oxides. The column was bioaugmented with the Point Mugu (PM) culture, which is a mixed microbial enrichment culture capable of completely transforming TCE to ethene (ETH). We determined whether lactate, formate, or propionate fermentation resulted in more effective dehalogenation. Reductive dehalogenation, fermentation, and sulfate, Fe(III), and Mn(IV) reduction were all exhibited within the column. Different steady-states of dehalogenation were achieved based on the concentration of substrates added, with effective transformation to ETH obtained when ample electron donor equivalents were provided. Most of the metabolic reducing equivalents were channeled to sulfate, Fe(III), and Mn(IV) reduction. When similar electron reducing equivalents were added, the most effective dehalogenation was achieved with formate, with 14% of the electron equivalents going towards dehalogenation reactions, compared to 6.5% for lactate and 9.6% for propionate. Effective dehalogenation was maintained over 1000 days of column operation. Over 90% of electron equivalents added could be accounted for by the different electron accepting processes in the column, with 50% associated with soluble and precipitated Fe(II) and Mn(II). Bulk Fe(III) and Mn(IV) reduction was rather associated with lactate and propionate addition than formate addition. Sulfate reduction was a competing electron acceptor reaction with all three electron donors. DNA was extracted from solid coupon samples obtained during the course of the experiment and analyzed using 16S rRNA gene clone libraries and quantitative PCR. Lactate and propionate addition resulted in a significant increase in Geobacter, Spirochaetes, and Desulfitobacterium phylotypes relative to "Dehalococcoides" when compared to formate addition. Results from the molecular biological analyses support

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation

PubMed Central

Park, Sunhwa; Kim, Dong-Hun; Lee, Ji-Hoon; Hur, Hor-Gil

2014-01-01

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575T under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575T grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575T are dominant under anoxic conditions. Furthermore, strain DSM 6575T forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575T, and could contribute to biogeochemical cycles of Fe and N in the environment. PMID:24965827

Elucidation of an Alternate Isoleucine Biosynthesis Pathway in Geobacter sulfurreducens▿

PubMed Central

Risso, Carla; Van Dien, Stephen J.; Orloff, Amber; Lovley, Derek R.; Coppi, Maddalena V.

2008-01-01

The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were identified and knocked out. Mutants lacking both of these enzymes were auxotrophs for isoleucine, whereas single mutants were capable of growth in the absence of isoleucine. Biochemical characterization of the single mutants revealed deficiencies in citramalate synthase and threonine ammonia-lyase activity. Thus, in G. sulfurreducens, 2-oxobutanoate can be synthesized either from citramalate or threonine, with the former being the main pathway for isoleucine biosynthesis. The citramalate synthase of G. sulfurreducens constitutes the first characterized member of a phylogenetically distinct clade of citramalate synthases, which contains representatives from a wide variety of microorganisms. PMID:18245290

NREL Researchers Discover How a Bacterium, Clostridium thermocellum,

Science.gov Websites

containing the bacterium actually promotes the growth of C. thermocellum, yet its mechanistic details remained a puzzle. This enhanced growth implied the bacterium had the ability to use CO2 and prompted NREL researchers to investigate the phenomena enhancing the bacterium's growth. "It took us by surprise that

Isolation of Phyllosilicate–Iron Redox Cycling Microorganisms from an Illite–Smectite Rich Hydromorphic Soil

PubMed Central

Shelobolina, Evgenya; Konishi, Hiromi; Xu, Huifang; Benzine, Jason; Xiong, Mai Yia; Wu, Tao; Blöthe, Marco; Roden, Eric

2012-01-01

The biogeochemistry of phyllosilicate–Fe redox cycling was studied in a Phalaris arundinacea (reed canary grass) dominated redoximorphic soil from Shovelers Sink, a small glacial depression near Madison, WI. The clay size fraction of Shovelers Sink soil accounts for 16% of the dry weight of the soil, yet contributes 74% of total Fe. The dominant mineral in the clay size fraction is mixed layer illite–smectite, and in contrast to many other soils and sediments, Fe(III) oxides are present in low abundance. We examined the Fe biogeochemistry of Shovelers Sink soils, estimated the abundance of Fe redox cycling microorganisms, and isolated in pure culture representative phyllosilicate–Fe oxidizing and reducing organisms. The abundance of phyllosilicate–Fe reducing and oxidizing organisms was low compared to culturable aerobic heterotrophs. Both direct isolation and dilution-to-extinction approaches using structural Fe(II) in Bancroft biotite as a Fe(II) source, and O2 as the electron acceptor, resulted in recovery of common rhizosphere organisms including Bradyrhizobium spp. and strains of Cupriavidus necator and Ralstonia solanacearum. In addition to oxidizing biotite and soluble Fe(II) with O2, each of these isolates was able to oxidize Fe(II) in reduced NAu-2 smectite with NO3- as the electron acceptor. Oxidized NAu-2 smectite or amorphous Fe(III) oxide served as electron acceptors for enrichment and isolation of Fe(III)-reducing microorganisms, resulting in recovery of a strain related to Geobacter toluenoxydans. The ability of the recovered microorganisms to cycle phyllosilicate–Fe was verified in an experiment with native Shovelers Sink clay. This study confirms that Fe in the native Shovelers Sink clay is readily available for microbial redox transformation and can be cycled by the Fe(III)-reducing and Fe(II)-oxidizing microorganisms recovered from the soil. PMID:22493596

Isolation of phyllosilicate-iron redox cycling microorganisms from an illite-smectite rich hydromorphic soil.

PubMed

Shelobolina, Evgenya; Konishi, Hiromi; Xu, Huifang; Benzine, Jason; Xiong, Mai Yia; Wu, Tao; Blöthe, Marco; Roden, Eric

2012-01-01

The biogeochemistry of phyllosilicate-Fe redox cycling was studied in a Phalaris arundinacea (reed canary grass) dominated redoximorphic soil from Shovelers Sink, a small glacial depression near Madison, WI. The clay size fraction of Shovelers Sink soil accounts for 16% of the dry weight of the soil, yet contributes 74% of total Fe. The dominant mineral in the clay size fraction is mixed layer illite-smectite, and in contrast to many other soils and sediments, Fe(III) oxides are present in low abundance. We examined the Fe biogeochemistry of Shovelers Sink soils, estimated the abundance of Fe redox cycling microorganisms, and isolated in pure culture representative phyllosilicate-Fe oxidizing and reducing organisms. The abundance of phyllosilicate-Fe reducing and oxidizing organisms was low compared to culturable aerobic heterotrophs. Both direct isolation and dilution-to-extinction approaches using structural Fe(II) in Bancroft biotite as a Fe(II) source, and O(2) as the electron acceptor, resulted in recovery of common rhizosphere organisms including Bradyrhizobium spp. and strains of Cupriavidus necator and Ralstonia solanacearum. In addition to oxidizing biotite and soluble Fe(II) with O(2), each of these isolates was able to oxidize Fe(II) in reduced NAu-2 smectite with [Formula: see text] as the electron acceptor. Oxidized NAu-2 smectite or amorphous Fe(III) oxide served as electron acceptors for enrichment and isolation of Fe(III)-reducing microorganisms, resulting in recovery of a strain related to Geobacter toluenoxydans. The ability of the recovered microorganisms to cycle phyllosilicate-Fe was verified in an experiment with native Shovelers Sink clay. This study confirms that Fe in the native Shovelers Sink clay is readily available for microbial redox transformation and can be cycled by the Fe(III)-reducing and Fe(II)-oxidizing microorganisms recovered from the soil.

Effect of Fe(III) on 1,1,2,2-Tetrachloroethane degradation and vinyl chloride accumulation in wetland sediments of the Aberdeen Proving Ground

USGS Publications Warehouse

Jones, Elizabeth; Voytek, Mary; Lorah, Michelle

2004-01-01

1,1,2,2-Tetrachloroethane (TeCA) contaminated groundwater at the Aberdeen Proving Ground discharges through an anaerobic wetland in West Branch Canal Creek (MD), where dechlorination occurs. Two microbially mediated pathways, dichloroelimination and hydrogenolysis, account for most of the TeCA degradation at this site. The dichloroelimination pathways lead to the formation of vinyl chloride (VC), a recalcitrant carcinogen of great concern. The goal of this investigation was to determine whether microbially-available Fe(III) in the wetland surface sediment influenced the fate of TeCA and its daughter products. Differences were identified in the TeCA degradation pathway between microcosms treated with amorphous ferric oxyhydroxide (AFO-treated) and untreated (no AFO) microcosms. TeCA degradation was accompanied by a lower accumulation of VC in AFO-treated microcosms than untreated microcosms. The microcosm incubations and subsequent experiments with the microcosm materials showed that AFO treatment resulted in lower production of VC by (1) shifting TeCA degradation from dichloroelimination pathways to production of a greater proportion of chlorinated ethane products, and (2) decreasing the microbial capability to produce VC from 1,2-dichloroethene (DCE). VC degradation was not stimulated in the presence of Fe(III). Rather, VC degradation occurred readily under methanogenic conditions and was inhibited under Fe(III)-reducing conditions.

Cysteine Inhibits Mercury Methylation by Geobacter sulfurreducens PCA Mutant Δ omcBESTZ

DOE PAGES

Lin, Hui; Lu, Xia; Liang, Liyuan; ...

2015-04-21

For cysteine enhances Hg uptake and methylation by Geobacter sulfurreducens PCA wild type (WT) strain in short-term assays. The prevalence of this enhancement in other strains remains poorly understood. We examined the influence of cysteine concentration on time-dependent Hg(II) reduction, sorption and methylation by PCA-WT and its c-type cytochrome-deficient mutant ( omcBESTZ) in phosphate buffered saline. Without cysteine, the mutant methylated twice as much Hg(II) as the PCA-WT, whereas addition of cysteine inhibited Hg methylation, regardless of the reaction time. PCA-WT, but, exhibited both time-dependent and cysteine concentration-dependent methylation. In 144 hour assay, nearly complete sorption of the Hg(II) bymore » PCA-WT occurred in the presence of 1 mM cysteine, resulting in our highest observed methylmercury production. Moreover, the chemical speciation modeling and experimental data suggest that uncharged Hg(II) species are more readily taken up, and that this uptake is kinetic limiting, thereby affecting Hg methylation by both mutant and WT.« less

Can direct extracellular electron transfer occur in the absence of outer membrane cytochromes in Desulfovibrio vulgaris?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elias, Dwayne A; Zane, Mr. Grant M.; Auer, Dr. Manfred

2010-01-01

Extracellular electron transfer has been investigated over several decades via forms of soluble electron transfer proteins that are exported for extracellular reoxidation. More recently, several organisms have been shown to reduce extracellular metals via the direct transfer of electron through appendages; also known as nanowires. They have been reported most predominantly in Shewanella and Geobacter. While the relevancy and composition of these structures in each genus has been debated, both possess outer membrane cytochrome complexes that could theoretically come into direct contact with solid phase oxidized metals. Members of the genus Desulfovibrio apparently have no such cytochromes although similar appendagesmore » are present, are electrically conductive, and are different from flagella. Upon U(VI)-reduction, the structures in Desulfovibrio become coated with U(IV). Deletion of flagellar genes did not alter soluble or amorphous Fe(III) or U(VI) reduction, or appendage appearance. Removal of the chromosomal pilA gene hampered amorphous Fe(III)-reduction by ca. 25%, but cells lacking the native plasmid, pDV1, reduced soluble Fe(III) and U(VI) at ca. 50% of the wild type rate while amorphous Fe(III)-reduction slowed to ca. 20% of the wild type rate. Appendages were present in all deletions as well as pDV1, except pilA. Gene complementation restored all activities and morphologies to wild type levels. This suggests that pilA encodes the structural component, whereas genes within pDV1 may provide the reactive members. How such appendages function without outer membrane cytochromes is under investigation.« less

Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments.

PubMed

Hakil, Florence; Amin-Ali, Oulfat; Hirschler-Réa, Agnès; Mollex, Damien; Grossi, Vincent; Duran, Robert; Matheron, Robert; Cravo-Laureau, Cristiana

2014-02-01

A novel sulfate-reducing bacterium designated strain BE2801(T) was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801(T) occurred at 30-32 °C, 0.5-1.5% NaCl (w/v) and pH 7.2-7.4. Strain BE2801(T) grew with C4 to C20 fatty acids or C12 to C20 n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C(16 : 1)ω7c and C(18 : 1)ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801(T) was a member of the family Desulfobacteraceae within the class Deltaproteobacteria. DNA-DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801(T) ( = DSM 25524(T) = JCM 18157(T)) is proposed to be a representative of a novel species of the genus Desulfatiferula, for which the name Desulfatiferula berrensis sp. nov. is suggested.

Desulfobulbus mediterraneus sp. nov., a sulfate-reducing bacterium growing on mono- and disaccharides.

PubMed

Sass, Andrea; Rütters, Heike; Cypionka, Heribert; Sass, Henrik

2002-06-01

A new sulfate-reducing bacterium, strain 86FS1, was isolated from a deep-sea sediment in the western Mediterranean Sea with sodium lactate as electron and carbon source. Cells were ovoid, gram-negative and motile. Strain 86FS1 contained b- and c-type cytochromes. The organism was able to utilize propionate, pyruvate, lactate, succinate, fumarate, malate, alanine, primary alcohols (C(2)-C(5)), and mono- and disaccharides (glucose, fructose, galactose, ribose, sucrose, cellobiose, lactose) as electron donors for the reduction of sulfate, sulfite or thiosulfate. The major products of carbon metabolism were acetate and CO(2), with exception of n-butanol and n-pentanol, which were oxidized only to the corresponding fatty acids. The growth yield with sulfate and glucose or lactate was 8.3 and 15 g dry mass, respectively, per mol sulfate. The temperature limits for growth were 10 degrees C and 30 degrees C with an optimum at 25 degrees C. Growth was observed at salinities ranging from 10 to 70 g NaCl l(-1). Sulfide concentrations above 4 mmol l(-1) inhibited growth. The fatty acid pattern of strain 86FS1 resembled that of Desulfobulbus propionicus with n-14:0, n-16:1omega7, n-16:1 omega5, n-17:1 omega6 and n-18:1 omega7 as dominant fatty acids. On the basis of its phylogenetic position and its phenotypic properties, strain 86FS1 affiliates with the genus Desulfobulbus and is described as a new species, Desulfobulbus mediterraneus sp. nov.

Influence of Reactive Transport on the Reduction of U(VI) in the Presence of Fe(III) and Nitrate: Implications for U(VI) Immobilization by Bioremediation / Biobarriers- Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

B.D. Wood

2007-01-01

Subsurface contamination by metals and radionuclides represent some of the most challenging remediation problems confronting the Department of Energy (DOE) complex. In situ remediation of these contaminants by dissimilatory metal reducing bacteria (DMRB) has been proposed as a potential cost effective remediation strategy. The primary focus of this research is to determine the mechanisms by which the fluxes of electron acceptors, electron donors, and other species can be controlled to maximize the transfer of reductive equivalents to the aqueous and solid phases. The proposed research is unique in the NABIR portfolio in that it focuses on (i) the role ofmore » flow and transport in the initiation of biostimulation and the successful sequestration of metals and radionuclides [specifically U(VI)], (ii) the subsequent reductive capacity and stability of the reduced sediments produced by the biostimulation process, and (iii) the potential for altering the growth of biomass in the subsurface by the addition of specific metabolic uncoupling compounds. A scientifically-based understanding of these phenomena are critical to the ability to design successful bioremediation schemes. The laboratory research will employ Shewanella putrefaciens (CN32), a facultative DMRB that can use Fe(III) oxides as a terminal electron acceptor. Sediment-packed columns will be inoculated with this organism, and the reduction of U(VI) by the DMRB will be stimulated by the addition of a carbon and energy source in the presence of Fe(III). Separate column experiments will be conducted to independently examine: (1) the importance of the abiotic reduction of U(VI) by biogenic Fe(II); (2) the influence of the transport process on Fe(III) reduction and U(VI) immobilization, with emphasis on methods for controlling the fluxes of aqueous species to maximize uranium reduction; (3) the reductive capacity of biologically-reduced sediments (with respect to re-oxidation by convective fluxes of O2 and NO3

Aerobic Reduction of Arsenate by a Bacterium Isolated From Activated Sludge

NASA Astrophysics Data System (ADS)

Kozai, N.; Ohnuki, T.; Hanada, S.; Nakamura, K.; Francis, A. J.

2006-12-01

Microlunatus phosphovorus strain NM-1 is a polyphosphate-accumulating bacterium isolated from activated sludge. This bacterium takes up a large amount of polyphosphate under aerobic conditions and release phosphate ions by hydrolysis of polyphosphate to orthophosphate under anaerobic conditions to derive energy for taking up substrates. To understand the nature of this strain, especially, influence of potential contaminants in sewage and wastewater on growth, we have been investigating behavior of this bacterium in media containing arsenic. The present paper mainly reports reduction of arsenate by this bacterium under aerobic conditions. The strain NM-1 (JCM 9379) was aerobically cultured at 30 °C in a nutrient medium containing 2.5 g/l peptone, 0.5 g/l glucose, 1.5 g/l yeast extract, and arsenic [Na2HAsO4 (As(V)) or Na3AsO3 (As(III))] at concentrations between 0 and 50 mM. The cells collected from arsenic-free media were dispersed in buffer solutions containing 2mM HEPES, 10mM NaCl, prescribed concentrations of As(V), and 0-0.2 percent glucose. Then, this cell suspension was kept at 20 °C under aerobic or anaerobic conditions. The speciation of arsenic was carried out by ion chromatography and ICP-MS. The growth of the strain under aerobic conditions was enhanced by the addition of As(V) at the concentration between 1 and 10 mM. The maximum optical density of the culture in the medium containing 5mM As(V) was 1.4 times greater than that of the control culture. Below the As(V) concentration of 10mM, most of the As(V) was reduced to As(III). The growth of the strain under anaerobic conditions has not been observed so far. The cells in the buffer solutions reduced As(V) under aerobic condition. The reduction was enhanced by the addition of glucose. However, the cell did not reduce As(V) under anaerobic conditions. The strain NM-1 showed high resistance to As(V) and As(III). The maximum optical density of the culture grown in a medium containing 50 mM As(V) was only

["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

PubMed

Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

2005-01-01

From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."

Graphene oxide-dependent growth and self-aggregation into a hydrogel complex of exoelectrogenic bacteria

PubMed Central

Yoshida, Naoko; Miyata, Yasushi; Doi, Kasumi; Goto, Yuko; Nagao, Yuji; Tero, Ryugo; Hiraishi, Akira

2016-01-01

Graphene oxide (GO) is reduced by certain exoelectrogenic bacteria, but its effects on bacterial growth and metabolism are a controversial issue. This study aimed to determine whether GO functions as the terminal electron acceptor to allow specific growth of and electricity production by exoelectrogenic bacteria. Cultivation of environmental samples with GO and acetate as the sole substrate could specifically enrich exoelectrogenic bacteria with Geobacter species predominating (51–68% of the total populations). Interestingly, bacteria in these cultures self-aggregated into a conductive hydrogel complex together with biologically reduced GO (rGO). A novel GO-respiring bacterium designated Geobacter sp. strain R4 was isolated from this hydrogel complex. This organism exhibited stable electricity production at >1000 μA/cm3 (at 200 mV vs Ag/AgCl) for more than 60 d via rGO while temporary electricity production using graphite felt. The better electricity production depends upon the characteristics of rGO such as a large surface area for biofilm growth, greater capacitance, and smaller internal resistance. This is the first report to demonstrate GO-dependent growth of exoelectrogenic bacteria while forming a conductive hydrogel complex with rGO. The simple put-and-wait process leading to the formation of hydrogel complexes of rGO and exoelectrogens will enable wider applications of GO to bioelectrochemical systems. PMID:26899353

Inoculation of a phenanthrene-degrading endophytic bacterium reduces the phenanthrene level and alters the bacterial community structure in wheat.

PubMed

Liu, Juan; Xiang, Yanbing; Zhang, Zhiming; Ling, Wanting; Gao, Yanzheng

2017-06-01

Colonization by polycyclic aromatic hydrocarbon (PAH)-degrading endophytic bacteria (PAHDEB) can reduce the PAH contamination risk in plant. However, little information is available on the impact of PAHDEB colonization on the endophytic bacterial community of inner plant tissues. A phenanthrene-degrading endophytic bacterium (PDEB), Massilia sp. Pn2, was inoculated onto the roots of wheat and subjected to greenhouse container experiments. The endophytic bacterial community structure in wheat was investigated using high-throughput sequencing technology. The majority of endophytic bacteria in wheat were Proteobacteria, and the dominant genus was Pseudomonas. Phenanthrene contamination clearly increased the diversity of endophytic bacteria in wheat. The cultivable endophytic bacteria counts in wheat decreased with increasing the level of phenanthrene contamination; the endophytic bacterial community structure changed correspondingly, and the bacterial richness first increased and then decreased. Inoculation of strain Pn2 reduced the phenanthrene contamination in wheat, enlarged the biomass of wheat roots, changed the bacterial community structure and enhanced the cell counts, diversity and richness of endophytic bacteria in phenanthrene-contaminated wheat in a contamination level-dependent manner. The findings of this investigation provide insight into the responses of endophytic bacterial community in plant to external PAH contamination and PAHDEB colonization.

[Anaerobic reduction of humus/Fe (III) and electron transport mechanism of Fontibacter sp. SgZ-2].

PubMed

Ma, Chen; Yang, Gui-qin; Lu, Qin; Zhou, Shun-gui

2014-09-01

Humus and Fe(III) respiration are important extracellular respiration metabolism. Electron transport pathway is the key issue of extracellular respiration. To understand the electron transport properties and the environmental behavior of a novel Fe(III)- reducing bacterium, Fontibacter sp. SgZ-2, capacities of anaerobic humus/Fe(III) reduction and electron transport mechanisms with four electron acceptors were investigated in this study. The results of anaerobic batch experiments indicated that strain SgZ-2 had the ability to reduce humus analog [ 9,10-anthraquinone-2,6-disulfonic acid (AQDS) and 9,10-anthraquinone-2-sulfonic acid (AQS)], humic acids (HA), soluble Fe(III) (Fe-EDTA and Fe-citrate) and Fe(III) oxides [hydrous ferric oxide (HFO)]. Fermentative sugars (glucose and sucrose) were the most effective electron donors in the humus/Fe(III) reduction by strain SgZ-2. Additionally, differences of electron carrier participating in the process of electron transport with different electron acceptors (i. e. , oxygen, AQS, Fe-EDTA and HFO) were investigated using respiratory inhibitors. The results suggested that similar respiratory chain components were involved in the reducing process of oxygen and Fe-EDTA, including dehydrogenase, quinones and cytochromes b-c. In comparison, only dehydrogenase was found to participate in the reduction of AQS and HFO. In conclusion, different electron transport pathways may be employed by strain SgZ-2 between insoluble and soluble electron acceptors or among soluble electron acceptors. Preliminary models of electron transport pathway with four electron acceptors were proposed for strain SgZ-2, and the study of electron transport mechanism was explored to the genus Fontibacter. All the results from this study are expected to help understand the electron transport properties and the environmental behavior of the genus Fontibacter.

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

PubMed Central

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 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. PMID:17581116

In situ expression of nifD in Geobacteraceae in subsurface sediments

USGS Publications Warehouse

Holmes, Dawn E.; Nevin, Kelly P.; Lovely, Derek R.

2004-01-01

In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.

Fervidicola ferrireducens gen. nov., sp. nov., a thermophilic anaerobic bacterium from geothermal waters of the Great Artesian Basin, Australia.

PubMed

Ogg, Christopher D; Patel, Bharat K C

2009-05-01

A strictly anaerobic, thermophilic bacterium, designated strain Y170(T), was isolated from a microbial mat colonizing thermal waters of a run-off channel created by the free-flowing waters of a Great Artesian Basin (GAB) bore well (New Lorne bore; registered number 17263). Cells of strain Y170(T) were slightly curved rods (1.2-12x0.8-1.1 mum) and stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 70 degrees C (temperature range for growth was 55-80 degrees C) and pH 7 (pH range for growth was 5-9). Strain Y170(T) grew poorly on yeast extract as a sole carbon source, but not on tryptone (0.2 %). Yeast extract could not be replaced by tryptone and was obligately required for growth on tryptone, peptone, glucose, fructose, galactose, cellobiose, mannose, sucrose, xylose, mannitol, formate, pyruvate, Casamino acids and threonine. No growth was observed on arabinose, lactose, maltose, raffinose, chitin, xylan, pectin, starch, acetate, benzoate, lactate, propionate, succinate, myo-inositol, ethanol, glycerol, amyl media, aspartate, leucine, glutamate, alanine, arginine, serine and glycine. End products detected from glucose fermentation were acetate, ethanol and presumably CO(2) and H(2). Iron(III), manganese(IV), thiosulfate and elemental sulfur, but not sulfate, sulfite, nitrate or nitrite, were used as electron acceptors in the presence of 0.2 % yeast extract. Iron(III) in the form of amorphous Fe(III) oxhydroxide and Fe(III) citrate was also reduced in the presence of tryptone, peptone and Casamino acids, but not with chitin, xylan, pectin, formate, starch, pyruvate, acetate, benzoate, threonine, lactate, propionate, succinate, inositol, ethanol, glycerol, mannitol, aspartate, leucine, glutamate, alanine, arginine, serine or glycine. Strain Y170(T) was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). Chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin and

Coexistence of spin crossover and magnetic ordering in a dendrimeric Fe(III) complex

NASA Astrophysics Data System (ADS)

Vorobeva, V. E.; Domracheva, N. E.; Pyataev, A. V.; Gruzdev, M. S.; Chervonova, U. V.

2015-01-01

The magnetic properties of a new dendrimeric spin crossover Fe(III) complex, [Fe(L)2]+PF6-, where L = 3,5-di[3,4,5-tris(tetradecyloxy) benzoyloxy]benzoyl-4-salicylidene-N-ethyl-N-ethylene-diamine, are reported for the first time. EPR studies show that this compound undergoes a gradual spin transition in the temperature range 70-300 K and has antiferromagnetic ordering below 10 K. Mössbauer spectroscopy at 5 K confirms the presence of magnetic ordering in the dendrimeric iron complex.

A Simple and Low-Cost Procedure for Growing Geobacter sulfurreducens Cell Cultures and Biofilms in Bioelectrochemical Systems

PubMed Central

O’Brien, J. Patrick; Malvankar, Nikhil S.

2017-01-01

Anaerobic microorganisms play a central role in several environmental processes and regulate global biogeochemical cycling of nutrients and minerals. Many anaerobic microorganisms are important for the production of bioenergy and biofuels. However, the major hurdle in studying anaerobic microorganisms in the laboratory is the requirement for sophisticated and expensive gassing stations and glove boxes to create and maintain the anaerobic environment. This appendix presents a simple design for a gassing station that can be used readily by an inexperienced investigator for cultivation of anaerobic microorganisms. In addition, this appendix also details the low-cost assembly of bioelectrochemical systems and outlines a simplified procedure for cultivating and analyzing bacterial cell cultures and biofilms that produce electric current, using Geobacter sulfurreducens as a model organism. PMID:27858972

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

NASA Astrophysics Data System (ADS)

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.

Syntrophic anaerobic photosynthesis via direct interspecies electron transfer

DOE PAGES

Ha, Phuc T.; Lindemann, Stephen R.; Shi, Liang; ...

2017-01-09

Microbial phototrophs, key primary producers on Earth, use H 2O, H 2, H 2S and other reduced inorganic compounds as electron donors. Here we describe a form of metabolism linking anoxygenic photosynthesis to anaerobic respiration that we call ‘syntrophic anaerobic photosynthesis’. We show that photoautotrophy in the green sulfur bacterium Prosthecochloris aestaurii can be driven by either electrons from a solid electrode or acetate oxidation via direct interspecies electron transfer from a heterotrophic partner bacterium, Geobacter sulfurreducens. Photosynthetic growth of P. aestuarii using reductant provided by either an electrode or syntrophy is robust and light-dependent. In contrast, P. aestuarii doesmore » not grow in co-culture with a G. sulfurreducens mutant lacking a trans-outer membrane porin-cytochrome protein complex required for direct intercellular electron transfer. Syntrophic anaerobic photosynthesis is therefore a carbon cycling process that could take place in anoxic environments. Lastly, this process could be exploited for biotechnological applications, such as waste treatment and bioenergy production, using engineered phototrophic microbial communities.« less

Sphaerotilus natans encrusted with nanoball-shaped Fe(III) oxide minerals formed by nitrate-reducing mixotrophic Fe(II) oxidation.

PubMed

Park, Sunhwa; Kim, Dong-Hun; Lee, Ji-Hoon; Hur, Hor-Gil

2014-10-01

Ferrous iron has been known to function as an electron source for iron-oxidizing microorganisms in both anoxic and oxic environments. A diversity of bacteria has been known to oxidize both soluble and solid-phase Fe(II) forms coupled to the reduction of nitrate. Here, we show for the first time Fe(II) oxidation by Sphaerotilus natans strain DSM 6575(T) under mixotrophic condition. Sphaerotilus natans has been known to form a sheath structure enclosing long chains of rod-shaped cells, resulting in a thick biofilm formation under oxic conditions. Here, we also demonstrate that strain DSM 6575(T) grows mixotrophically with pyruvate, Fe(II) as electron donors and nitrate as an electron acceptor and single cells of strain DSM 6575(T) are dominant under anoxic conditions. Furthermore, strain DSM 6575(T) forms nanoball-shaped amorphous Fe(III) oxide minerals encrusting on the cell surfaces through the mixotrophic iron oxidation reaction under anoxic conditions. We propose that cell encrustation results from the indirect Fe(II) oxidation by biogenic nitrite during nitrate reduction and that causes the bacterial morphological change to individual rod-shaped single cells from filamentous sheath structures. This study extends the group of existing microorganisms capable of mixotrophic Fe(II) oxidation by a new strain, S. natans strain DSM 6575(T) , and could contribute to biogeochemical cycles of Fe and N in the environment. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

An Analytical Chemistry Experiment in Simultaneous Spectrophotometric Determination of Fe(III) and Cu(II) with Hexacyanoruthenate(II) Reagent.

ERIC Educational Resources Information Center

Mehra, M. C.; Rioux, J.

1982-01-01

Experimental procedures, typical observations, and results for the simultaneous analysis of Fe(III) and Cu(II) in a solution are discussed. The method is based on selective interaction between the two ions and potassium hexacyanoruthenate(II) in acid solution involving no preliminary sample preparations. (Author/JN)

Acetate availability and its influence on sustainable bioremediation of Uranium-contaminated groundwater

USGS Publications Warehouse

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

genome during the period of optimal U(VI) removal. Gene transcript levels during "Big Rusty" were quantified for Geobacter-specific citrate synthase (gltA), with ongoing transcription during sulfate reduction indicating that members of the Geobacteraceae were still active and likely contributing to U(VI) removal. The persistence of reducible Fe(III) in sediments recovered from an area of prolonged (110-day) sulfate reduction is consistent with this conclusion. These results indicate that acetate availability and its ability to sustain the activity of iron- and uranyl-respiring Geobacter strains during sulfate reduction exerts a primary control on optimized U(VI) removal from groundwater at the Rifle IFRC site over extended time scales (>50 days). ?? Taylor & Francis Group, LLC.

Single Bacterium Detection Using Sers

NASA Astrophysics Data System (ADS)

Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

2016-02-01

This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

Identification of an anaerobic bacterium which reduces perchlorate and chlorate as Wolinella succinogenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, W.; Attaway, H.

1995-12-31

Perchlorate and chlorate salts are widely used by the chemical, aerospace and defense industries as oxidizers in propellant, explosives and pyrotechnics. The authors have isolated a anaerobic bacterium which is capable of the dissimilatory reduction of both perchlorate and chlorate for energy and growth. Strain HAP-1 is a gram negative, thin rod, non-sporeforming, highly motile strict anaerobe. Antibiotic resistance profiles, utilization of carbon substrates and electron acceptors demonstrated similar physiological characteristics to Wolinella succinogenes. Pairwise comparisons of 16S RNA sequences showed only a 0.75% divergence between strain HAP-1 and W. succinogenes. Physiological, morphological and 16S RRNA sequence data indicate strainmore » HAP-1 is a subspecies of W. succinogenes that can utilize perchlorate and chlorate as terminal electron acceptors.« less

Interactions of the periplasmic binding protein CeuE with Fe(III) n-LICAM4- siderophore analogues of varied linker length

NASA Astrophysics Data System (ADS)

Wilde, Ellis J.; Hughes, Adam; Blagova, Elena V.; Moroz, Olga V.; Thomas, Ross P.; Turkenburg, Johan P.; Raines, Daniel J.; Duhme-Klair, Anne-Kathrin; Wilson, Keith S.

2017-04-01

Bacteria use siderophores to mediate the transport of essential Fe(III) into the cell. In Campylobacter jejuni the periplasmic binding protein CeuE, an integral part of the Fe(III) transport system, has adapted to bind tetradentate siderophores using a His and a Tyr side chain to complete the Fe(III) coordination. A series of tetradentate siderophore mimics was synthesized in which the length of the linker between the two iron-binding catecholamide units was increased from four carbon atoms (4-LICAM4-) to five, six and eight (5-, 6-, 8-LICAM4-, respectively). Co-crystal structures with CeuE showed that the inter-planar angles between the iron-binding catecholamide units in the 5-, 6- and 8-LICAM4- structures are very similar (111°, 110° and 110°) and allow for an optimum fit into the binding pocket of CeuE, the inter-planar angle in the structure of 4-LICAM4- is significantly smaller (97°) due to restrictions imposed by the shorter linker. Accordingly, the protein-binding affinity was found to be slightly higher for 5- compared to 4-LICAM4- but decreases for 6- and 8-LICAM4-. The optimum linker length of five matches that present in natural siderophores such as enterobactin and azotochelin. Site-directed mutagenesis was used to investigate the relative importance of the Fe(III)-coordinating residues H227 and Y288.

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

PubMed

Zhou, Aifen; Lau, Rebecca; Baran, Richard; Ma, Jincai; von Netzer, Frederick; Shi, Weiling; Gorman-Lewis, Drew; Kempher, Megan L; He, Zhili; Qin, Yujia; Shi, Zhou; Zane, Grant M; Wu, Liyou; Bowen, Benjamin P; Northen, Trent R; Hillesland, Kristina L; Stahl, David A; Wall, Judy D; Arkin, Adam P; Zhou, Jizhong

2017-11-14

Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

PubMed Central

Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

2016-01-01

We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

High-Spin Ferric Ions in Saccharomyces cerevisiae Vacuoles Are Reduced to the Ferrous State during Adenine-Precursor Detoxification

PubMed Central

2015-01-01

The majority of Fe in Fe-replete yeast cells is located in vacuoles. These acidic organelles store Fe for use under Fe-deficient conditions and they sequester it from other parts of the cell to avoid Fe-associated toxicity. Vacuolar Fe is predominantly in the form of one or more magnetically isolated nonheme high-spin (NHHS) FeIII complexes with polyphosphate-related ligands. Some FeIII oxyhydroxide nanoparticles may also be present in these organelles, perhaps in equilibrium with the NHHS FeIII. Little is known regarding the chemical properties of vacuolar Fe. When grown on adenine-deficient medium (A↓), ADE2Δ strains of yeast such as W303 produce a toxic intermediate in the adenine biosynthetic pathway. This intermediate is conjugated with glutathione and shuttled into the vacuole for detoxification. The iron content of A↓ W303 cells was determined by Mössbauer and EPR spectroscopies. As they transitioned from exponential growth to stationary state, A↓ cells (supplemented with 40 μM FeIII citrate) accumulated two major NHHS FeII species as the vacuolar NHHS FeIII species declined. This is evidence that vacuoles in A↓ cells are more reducing than those in adenine-sufficient cells. A↓ cells suffered less oxidative stress despite the abundance of NHHS FeII complexes; such species typically promote Fenton chemistry. Most Fe in cells grown for 5 days with extra yeast-nitrogen-base, amino acids and bases in minimal medium was HS FeIII with insignificant amounts of nanoparticles. The vacuoles of these cells might be more acidic than normal and can accommodate high concentrations of HS FeIII species. Glucose levels and rapamycin (affecting the TOR system) affected cellular Fe content. This study illustrates the sensitivity of cellular Fe to changes in metabolism, redox state and pH. Such effects broaden our understanding of how Fe and overall cellular metabolism are integrated. PMID:24919141

Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

PubMed Central

Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

2016-01-01

A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4–86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4–84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy. PMID:27677458

Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

NASA Astrophysics Data System (ADS)

Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

2016-09-01

A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4-86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4-84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy.

Pathogenicity of Moraxella osloensis, a bacterium associated with the nematode Phasmarhabditis hermaphrodita, to the slug Deroceras reticulatum.

PubMed

Tan, L; Grewal, P S

2001-11-01

Moraxella osloensis, a gram-negative bacterium, is associated with Phasmarhabditis hermaphrodita, a nematode parasite of slugs. This bacterium-feeding nematode has potential for the biological control of slugs, especially the grey garden slug, Deroceras reticulatum. Infective juveniles of P. hermaphrodita invade the shell cavity of the slug, develop into self-fertilizing hermaphrodites, and produce progeny, resulting in host death. However, the role of the associated bacterium in the pathogenicity of the nematode to the slug is unknown. We discovered that M. osloensis alone is pathogenic to D. reticulatum after injection into the shell cavity or hemocoel of the slug. The bacteria from 60-h cultures were more pathogenic than the bacteria from 40-h cultures, as indicated by the higher and more rapid mortality of the slugs injected with the former. Coinjection of penicillin and streptomycin with the 60-h bacterial culture reduced its pathogenicity to the slug. Further work suggested that the reduction and loss of pathogenicity of the aged infective juveniles of P. hermaphrodita to D. reticulatum result from the loss of M. osloensis from the aged nematodes. Also, axenic J1/J2 nematodes were nonpathogenic after injection into the shell cavity. Therefore, we conclude that the bacterium is the sole killing agent of D. reticulatum in the nematode-bacterium complex and that P. hermaphrodita acts only as a vector to transport the bacterium into the shell cavity of the slug. The identification of the toxic metabolites produced by M. osloensis is being pursued.

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

DOEpatents

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.

Amphorous hydrated Fe(III) sulfate: metastable product and bio-geochemical marker of iron oxidizing thiobacilli

NASA Astrophysics Data System (ADS)

Lazaroff, Norman; Jollie, John; Dugan, Patrick R.

1998-07-01

Chemolithotrophic iron oxidation by Thiobacillus ferrooxidans and other iron oxidizing thiobacilli produce an Fe(III) sulfato complex that polymerizes as x-ray amorphous filaments approximately 40 nm in diameter. The precursor complex in solutionis seen by ATR-FTIR spectroscopy to have a sulfate spectrum resembling the v(subscript 3) and v(subscript 1) vibrational modes of the precipitated polymer. Chemically similar precipitates prepared by oxidation of acid ferrous sulfate with hydrogen peroxide have a different micromorphology, higher iron/sulfur ratio and acid solubility than the bacterial product. They possess coalescing globular microstructures composed of compacted micro-fibrils. Scanning electron microscopy and diffuse reflectance FTIR show the formation of iron polymer on the surface of immobilized cells of T. ferrooxidans, oxidizing iron during the corrosion of steel. Although spatially separated form the steel coupons by a membrane filter, the cell walls become covered with tufts of amorphous hydrated Fe(III) sulfate. The metastable polymer is converted to crystalline goethite, lepidocrocite, and magnetite in that order, as the pH rises due to proton reduction at cathodic sites on the steel. The instability of the iron polymer to changes in pH is also evidenced by the loss of sulfate when washed with lithium hydroxide solution at pH 8. Under those conditions there is little change in micromorphology, but restoration of sulfate with sulfuric acid at pH 2.5, fails to re-establish the original chemical structure. Adding sulfate salts of appropriate cations to solutions of the Fe(III) sulfato complex or suspensions of its precipitated polymer in dilute sulfuric acid, result in dissociation of the metastable complex followed by crystallization of ferric ions and sulfate in jarosites. Jarosites and other derivatives of iron precipitation by iron oxidizing thiobacilli, form conspicuous deposits in areas of natural pyrite leaching. The role of iron oxidizing

Continuous production of succinic acid by a fumarate-reducing bacterium immobilized in a hollow-fiber bioreactor.

PubMed

Wee, Young-Jung; Yun, Jong-Sun; Kang, Kui-Hyun; Ryu, Hwa-Won

2002-01-01

Enterococcus faecalis RKY1, a fumarate-reducing bacterium, was immobilized in an asymmetric hollow-fiber bioreactor (HFBR) for the continuous production of succinic acid. The cells were inoculated into the shell side of the HFBR, which was operated in transverse mode. Since the pH values in the HFBR declined during continuous operation to about 5.7, it was necessary to change the feed pH from 7.0 to 8.0 after 24 h of operation in order to enhance production of succinic acid. During continuous operation with a medium containing fumarate and glycerol, the productivity of succinate was 3.0-10.9 g/(L x h) with an initial concentration of 30 g/L of fumarate, 4.9-14.9 g/(L x h) with 50 g/L of fumarate, and 7.2-17.1 g/(L x h) with 80 g/L of fumarate for dilution rates between 0.1 and 0.4 h(-1). The maximum productivity of succinate obtained by the HFBR (17.1 g of succinate/[L x h]) was 1.7 times higher than that of the batch bioconversions (9.9 g of succinate/ [L x h]) with 80 g/L of fumarate. Furthermore, the long-term stability of the HFBR was demonstrated with a continuously efficient production of succinate for more than 15 d (360 h).

Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton-Brehm, Scott D.; Gibson, Robert A.; Green, Stefan J.

2013-01-24

A novel sulfate-reducing bacterium designated OPF15T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70 90 C and an optimum of 83 C. Optimal pH was around 6.5 7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve asmore » electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15T was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15T representing the type strain.« less

Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park.

PubMed

Hamilton-Brehm, Scott D; Gibson, Robert A; Green, Stefan J; Hopmans, Ellen C; Schouten, Stefan; van der Meer, Marcel T J; Shields, John P; Damsté, Jaap S S; Elkins, James G

2013-03-01

A novel sulfate-reducing bacterium designated OPF15(T) was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism displayed hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H2 or formate as an electron donor and CO2 as a carbon source. Electron acceptors supporting growth included sulfate, thiosulfate, and elemental sulfur. Lactate, acetate, pyruvate, benzoate, oleic acid, and ethanol did not serve as electron donors. Membrane lipid analysis revealed diacyl glycerols and acyl/ether glycerols which ranged from C14:0 to C20:0. Alkyl chains present in acyl/ether and diether glycerol lipids ranged from C16:0 to C18:0. Straight, iso- and anteiso-configurations were found for all lipid types. The presence of OPF15(T) was also shown to increase cellulose consumption during co-cultivation with Caldicellulosiruptor obsidiansis, a fermentative, cellulolytic extreme thermophile isolated from the same environment. On the basis of phylogenetic, phenotypic, and structural analyses, Thermodesulfobacterium geofontis sp. nov. is proposed as a new species with OPF15(T) representing the type strain.

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

DOE PAGES

Rajeev, Lara; Chen, Amy; Kazakov, Alexey E.; ...

2015-08-17

Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness atmore » low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. Here we discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. The NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Finally, our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB.« less

A C-Type Cytochrome and a Transcriptional Regulator Responsible for Enhanced Extracellular Electron Transfer in Geobacter Sulfurreducens Revealed by Adaptive Evolution

DTIC Science & Technology

2010-01-01

dance of pgcA transcripts, consistent with increased expression of pgcA in the adapted strains. One of the mutations doubled the rate of Fe(III) oxide...sequenced bacterial genomes. BMC Genomics 8: 274. Herring, C.D., Raghunathan, A., Honisch, C., Patel, T., Apple- bee , M.K., Joyce, A.R., et al. (2006

Detection of Salmonella bacterium in drinking water using microring resonator.

PubMed

Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

2016-01-01

A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

Purification and characterization of homo- and hetero-dimeric acetate kinases from the sulfate-reducing bacterium Desulfovibrio vulgaris.

PubMed

Yu, L; Ishida, T; Ozawa, K; Akutsu, H; Horiike, K

2001-03-01

Two distinct forms of acetate kinase were purified to homogeneity from a sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki F. The enzymes were separated from the soluble fraction of the cells on anion exchange columns. One acetate kinase (AK-I) was a homodimer (alpha(S)(2)) and the other (AK-II) was a heterodimer (alpha(S)alpha(L)). On SDS-PAGE, alpha(L) and alpha(S) subunits migrated as bands of 49.3 and 47.8 kDa, respectively, but they had an identical N-terminal amino acid sequence. A rapid HPLC method was developed to directly measure ADP and ATP in assay mixtures. Initial velocity data for AK-I and AK-II were collected by this method and analyzed based on a random sequential mechanism, assuming rapid equilibrium for the substrate binding steps. All kinetic parameters for both the forward acetyl phosphate formation and the reverse ATP formation catalyzed by AK-I and AK-II were successfully determined. The two enzymes showed similar kinetic properties in Mg(2+) requirement, pH-dependence and magnitude of kinetic parameters. These results suggest that two forms of acetate kinase are produced to finely regulate the enzyme function by post-translational modifications of a primary gene product in Desulfovibrio vulgaris.

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

NASA Technical Reports Server (NTRS)

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.

Halotolerant and Resistant to High pH Hydrogenase from Haloalkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans

NASA Technical Reports Server (NTRS)

Detkova, Ekaterina N.; Pikuta, Elena V.; Hoover, Richard B.

2004-01-01

Hydrogenase is the key enzyme of energetic metabolism in cells, it catalyzing the converse reaction of hydrogen oxidation and responsible for consumption and excretion of hydrogen in bacteria. Hydrogenases are proteins containing either Nickel and Iron, or the only Iron in theirs active center. Hydrogenases have been found in many microorganisms, such as Methanogenic, acetogenic, nitrogen-fixing, photosynthetic and sulfate-reducing bacteria that could utilize the hydrogen as energy source or use it as electron sink. Hydrogenases are subject for wide physiological, biochemical, physicochemical and genetic studies due to theirs abilities produce the molecular hydrogen as alternative source of pure energy. Notwithstanding on enough large quantity of works that deal with intracellular and extrasellular enzymes of halophilic bacteria, the data about hydrogenases and theirs functions of salts practically are absent. The study of hydrogenase in cell-free extracts of extremely halophilic eubacterium Acetohalobium mabaticum showed dramatic increasing activity of the enzyme at high concentrations of NaCl and KCI (close to saturated solution). Here we present the data of free-cells extracted hydrogenase from new haloalkaliphilic sulfate-reducing bacterium Desulfonatronum thiodismutans, which grow on highly miniralized carbonate-bicarbonate medium in salinity range 1 to 7 % and at pH 7.8 - 10.5. Studied enzyme was active in Concentration range from 0 to 4.3 M NaCl with optimum at 1.0 M NaCl. At 1.0 M NaCl the enzyme activity was increased on 20 %, but with changing concentration from 2.1 M to 3.4 M the activity decreased and was kept on constant level. NaHCO3 inhibited hydrogenase activity on more then 30 %. The maximum of enzyme activity was observed at pH 9.5 with limits 7.5 and 11.5 that practically equal to pH optimum of bacterial growth. Therefore the hydrogenase of Desulfanatronum thiodismutans is tolerant to high concentrations of sodium salts and it also resistant to

Recovery of Humic-Reducing Bacteria from a Diversity of Environments

PubMed Central

Coates, John D.; Ellis, Debra J.; Blunt-Harris, Elizabeth L.; Gaw, Catherine V.; Roden, Eric E.; Lovley, Derek R.

1998-01-01

To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments. PMID:9546186

A novel strategy for acetonitrile wastewater treatment by using a recombinant bacterium with biofilm-forming and nitrile-degrading capability.

PubMed

Li, Chunyan; Yue, Zhenlei; Feng, Fengzhao; Xi, Chuanwu; Zang, Hailian; An, Xuejiao; Liu, Keran

2016-10-01

There is a great need for efficient acetonitrile removal technology in wastewater treatment to reduce the discharge of this pollutant in untreated wastewater. In this study, a nitrilase gene (nit) isolated from a nitrile-degrading bacterium (Rhodococcus rhodochrous BX2) was cloned and transformed into a biofilm-forming bacterium (Bacillus subtilis N4) that expressed the recombinant protein upon isopropylthio-β-galactoside (IPTG) induction. The recombinant bacterium (B. subtilis N4-pHT01-nit) formed strong biofilms and had nitrile-degrading capability. Further testing demonstrated that biofilms formed by B. subtilis N4-pHT01-nit were highly resistant to loading shock from acetonitrile and almost completely degraded the initial concentration of acetonitrile (800 mg L(-1)) within 24 h in a moving bed biofilm reactor (MBBR) after operation for 35 d. The bacterial composition of the biofilm, identified by high-throughput sequencing, in a reactor in which the B. subtilis N4-pHT01-nit bacterium was introduced indicated that the engineered bacterium was successfully immobilized in the reactor and became dominant genus. This work demonstrates that an engineered bacterium with nitrile-degrading and biofilm-forming capacity can improve the degradation of contaminants in wastewater. This approach offers a novel strategy for enhancing the biological oxidation of toxic pollutants in wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pathogenicity of Moraxella osloensis, a Bacterium Associated with the Nematode Phasmarhabditis hermaphrodita, to the Slug Deroceras reticulatum

PubMed Central

Tan, Li; Grewal, Parwinder S.

2001-01-01

Moraxella osloensis, a gram-negative bacterium, is associated with Phasmarhabditis hermaphrodita, a nematode parasite of slugs. This bacterium-feeding nematode has potential for the biological control of slugs, especially the grey garden slug, Deroceras reticulatum. Infective juveniles of P. hermaphrodita invade the shell cavity of the slug, develop into self-fertilizing hermaphrodites, and produce progeny, resulting in host death. However, the role of the associated bacterium in the pathogenicity of the nematode to the slug is unknown. We discovered that M. osloensis alone is pathogenic to D. reticulatum after injection into the shell cavity or hemocoel of the slug. The bacteria from 60-h cultures were more pathogenic than the bacteria from 40-h cultures, as indicated by the higher and more rapid mortality of the slugs injected with the former. Coinjection of penicillin and streptomycin with the 60-h bacterial culture reduced its pathogenicity to the slug. Further work suggested that the reduction and loss of pathogenicity of the aged infective juveniles of P. hermaphrodita to D. reticulatum result from the loss of M. osloensis from the aged nematodes. Also, axenic J1/J2 nematodes were nonpathogenic after injection into the shell cavity. Therefore, we conclude that the bacterium is the sole killing agent of D. reticulatum in the nematode-bacterium complex and that P. hermaphrodita acts only as a vector to transport the bacterium into the shell cavity of the slug. The identification of the toxic metabolites produced by M. osloensis is being pursued. PMID:11679319

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Aifen; Lau, Rebecca; Baran, Richard

ABSTRACT. Rapid genetic and phenotypic adaptation of the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, inmore » addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance inD. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE. High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

DOE PAGES

Zhou, Aifen; Lau, Rebecca; Baran, Richard; ...

2017-11-14

ABSTRACT. Rapid genetic and phenotypic adaptation of the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, inmore » addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance inD. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE. High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is

Biodegradation of polyethylene by the thermophilic bacterium Brevibacillus borstelensis.

PubMed

Hadad, D; Geresh, S; Sivan, A

2005-01-01

To select a polyethylene-degrading micro-organism and to study the factors affecting its biodegrading activity. A thermophilic bacterium Brevibaccillus borstelensis strain 707 (isolated from soil) utilized branched low-density polyethylene as the sole carbon source and degraded it. Incubation of polyethylene with B. borstelensis (30 days, 50 degrees C) reduced its gravimetric and molecular weights by 11 and 30% respectively. Brevibaccillus borstelensis also degraded polyethylene in the presence of mannitol. Biodegradation of u.v. photo-oxidized polyethylene increased with increasing irradiation time. Fourier Transform Infra-Red (FTIR) analysis of photo-oxidized polyethylene revealed a reduction in carbonyl groups after incubation with the bacteria. This study demonstrates that polyethylene--considered to be inert--can be biodegraded if the right microbial strain is isolated. Enrichment culture methods were effective for isolating a thermophilic bacterium capable of utilizing polyethylene as the sole carbon and energy source. Maximal biodegradation was obtained in combination with photo-oxidation, which showed that carbonyl residues formed by photo-oxidation play a role in biodegradation. Brevibaccillus borstelensis also degraded the CH2 backbone of nonirradiated polyethylene. Biodegradation of polyethylene by a single bacterial strain contributes to our understanding of the process and the factors affecting polyethylene biodegradation.

Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth.

PubMed

Pikuta, Elena V; Hoover, Richard B; Bej, Asim K; Marsic, Damien; Whitman, William B; Cleland, David; Krader, Paul

2003-09-01

A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7x1.2-2.7 micro m in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 degrees C (optimum, 37 degrees C), >1-7 % NaCl, w/v (optimum, 3 %) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(T), exhibited 51 % homology. Also, the genome size (1.6x10(9) Da) and T(m) value of the genomic DNA (71+/-2 degrees C) for strain MLF1(T) were significantly different from the genome size (2.1x10(9) Da) and T(m) value (63+/-2 degrees C) for Desulfonatronum lacustre Z-7951(T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(T)=ATCC BAA-395(T)=DSM 14708(T)).

Desulfonatronum Thiodismutans sp. nov., a Novel Alkaliphilic, Sulfate-reducing Bacterium Capable of Lithoautotrophic Growth

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.; Bej, Asim K.; Marsic, Damien; Whitman, William B.; Cleland, David; Krader, Paul

2003-01-01

A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(sup T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7 x 1.2-2.7 microns in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 C (optimum, 37 C), > 1-7 % NaCI, w/v (optimum, 3%) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(sup T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(sup T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(sup T), exhibited 51 % homology. Also, the genome size (1.6 x 10(exp 9) Da) and T(sub m) value of the genomic DNA (71 +/- 2 C) for strain MLF1(sup T) were significantly different from the genome size (2.1 x 10(exp 9) Da) and T(sub m) value (63 +/- 2 C) for Desulfonatronum lacustre Z-7951(sup T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(sup T) = ATCC BAA-395(sup T) = DSM 14708(sup T)).

Structural, spectroscopic and thermal characterization of 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester and its Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes.

PubMed

Mohamed, Gehad G; El-Gamel, Nadia E A

2005-04-01

Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes with the ligand 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester (HL(2)) have been prepared and characterized by elemental analyses, molar conductance, magnetic moment, thermal analysis and spectral data. 1:1 M:HL(2) complexes, with the general formula [M(HL(2))X(2)].nH(2)O (where M = Co(II) (X = Cl, n = 0), Ni(II) (X = Cl, n = 3), Cu(II) (grey colour, X = AcO, n = 1), Cu(II) (yellow colour, X = Cl, n = 0) and Zn(II) (X = Br, n = 0). In addition, the Fe(III) and UO(2)(II) complexes of the type 1:2 M:HL(2) and with the formulae [Fe(L(2))(2)]Cl and [UO(2)(HL(2))(2)](NO(3))(2) are prepared. From the IR data, it is seen that HL(2) ligand behaves as a terdentate ligand coordinated to the metal ions via the pyridyl N, carboxylate O and protonated NH group; except the Fe(III) complex, it coordinates via the deprotonated NH group. This is supported by the molar conductance data, which show that all the complexes are non-electrolytes, while the Fe(III) and UO(2)(II) complexes are 1:1 electrolytes. IR and H1-NMR spectral studies suggest a similar behaviour of the Zn(II) complex in solid and solution states. From the solid reflectance spectral data and magnetic moment measurements, the complexes have a trigonal bipyramidal (Co(II), Ni(II), Cu(II) and Zn(II) complexes) and octahedral (Fe(III), UO(2)(II) complexes) geometrical structures. The thermal behaviour of the complexes is studied and the different dynamic parameters are calculated applying Coats-Redfern equation.

Desulfomusa hansenii gen. nov., sp. nov., a novel marine propionate-degrading, sulfate-reducing bacterium isolated from Zostera marina roots.

PubMed

Finster, K; Thomsen, T R; Ramsing, N B

2001-11-01

The physiology and phylogeny of a novel sulfate-reducing bacterium, isolated from surface-sterilized roots of the marine macrophyte Zostera marina, are presented. The strain, designated P1T, was enriched and isolated in defined oxygen-free, bicarbonate-buffered, iron-reduced seawater medium with propionate as sole carbon source and electron donor and sulfate as electron acceptor. Strain P1T had a rod-shaped, slightly curved cell morphology and was motile by means of a single polar flagellum. Cells generally aggregated in clumps throughout the growth phase. High CaCl2 (10 mM) and MgCl2 (50 mM) concentrations were required for optimum growth. In addition to propionate, strain P1T utilized fumarate, succinate, pyruvate, ethanol, butanol and alanine. Oxidation of propionate was incomplete and acetate was formed in stoichiometric amounts. Strain P1T thus resembles members of the sulfate-reducing genera Desulfobulbus and Desulforhopalus, which both oxidize propionate incompletely and form acetate in addition to CO2. However, sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P1T was unrelated to the incomplete oxidizers Desulfobulbus and Desulforhopalus and that it constitutes a novel lineage affiliated with the genera Desulfococcus, Desulfosarcina, Desulfonema and 'Desulfobotulus'. Members of this branch, with the exception of 'Desulfobotulus sapovorans', oxidize a variety of substrates completely to CO2. Strain P1T (= DSM 12642T = ATCC 700811T) is therefore proposed as Desulfomusa hansenii gen. nov., sp. nov. Strain p1T thus illustrates the difficulty of extrapolating rRNA similarities to physiology and/or ecological function.

Hexavalent chromium removal by chitosan modified-bioreduced nontronite

NASA Astrophysics Data System (ADS)

Singh, Rajesh; Dong, Hailiang; Zeng, Qiang; Zhang, Li; Rengasamy, Karthikeyan

2017-08-01

Recent efforts have focused on structural Fe(II) in chemically or biologically reduced clay minerals to immobilize Cr(VI) from aqueous solution, but the coulombic repulsion between the negatively charged clay surface and the polyanionic form of Cr(VI), e.g., dichromate, can hinder the effectiveness of this process. The purpose of this study was to investigate the efficiency and mechanism of Cr(VI) removal by a charge-reversed nontronite (NAu-2), an Fe-rich smectite. Chitosan, a linear polysaccharide derived from chitin found in soil and groundwater, was used to reverse the charge of NAu-2. Intercalation of chitosan into NAu-2 interlayer increased the basal d-spacing of NAu-2 from 1.23 nm to 1.83 nm and zeta potential from -27.17 to +34.13 mV, with the amount of increase depending on chitosan/NAu-2 ratio. Structural Fe(III) in chitosan-exchanged NAu-2 was then biologically reduced by an iron-reducing bacterium Shewanella putrefaciens CN32 in bicarbonate buffer with lactate as the sole electron donor, with and without electron shuttle, AQDS. Without AQDS, the extent of Fe(III) reduction increased from the lowest (∼9%) for the chitosan-free NAu-2 to the highest (∼12%) for the highest chitosan loaded NAu-2 (3:1 ratio). This enhancement of Fe(III) reduction was likely due to the attachment of negatively charged bacterial cells to charge-reversed (e.g., positively charged) NAu-2 surfaces, facilitating the electron transfer between cells and structural Fe(III). With AQDS, Fe(III) reduction extent doubled relative to those without AQDS, but the enhancement effect was similar across all chitosan loadings, suggesting that AQDS was more important than chitosan in enhancing Fe(III) bioreduction. Chitosan-exchanged, biologically reduced NAu-2 was then utilized for removing Cr(VI) in batch experiments with three consecutive spikes of 50 μM Cr. With the first Cr spike, the rate of Cr(VI) removal by charged-reversed NAu-2 that was bioreduced without and with AQDS was ∼1

Desulfonatronum paiuteum sp. nov.: A New Alkaliphilic, Sulfate-Reducing Bacterium, Isolated from Soda Mono Lake, California

NASA Technical Reports Server (NTRS)

Pikuta, Elena; Hoover, Richard B.; Marsic, Damien; Whitman, William; Cleland, David; Krader, Paul; Six, N. Frank (Technical Monitor)

2002-01-01

A novel alkaliphilic, sulfate reducing bacterium strain MLF1(sup T) was isolated from sediments of soda Mono Lake, California. Gram-negative vibrion cells, motile by singular polar flagellum, with sizes 0.5 - 0.6x 1.2 - 2.0 micron occurred singly, in pairs or short spirilla. Growth was observed over the temperature range of +15 C to +48 C (optimum +37 C), NaCl concentration range is greater than 1 - 7 %, wt/vol (optimum 3 %, wt/vol) and pH range 7.8 - 10.5 (optimum pH 9.0 - 9.4). The novel isolate is strictly alkaliphilic, requires high carbonate concentration in medium, obligately anaerobic and catalase negative. As electron donors strain MLF1(sup T) uses hydrogen, formate, ethanol. Sulfate, sulfite, and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The sole end product of growth on formate was H2S. Strain MLF1(sup T) is resistant to kanamycin and gentamycin, but sensitive to chloramphenicol and tetracycline. Na2MoO4 inhibits growth of strain MLF1(sup T). The sum of G+C in DNA is 63.1 mol% (by HPLC method). On the basis of physiological and molecular properties, the isolate was considered as novel species of genus Desulfonatronum; and the name Desulfonatronum paiuteum sp. nov., is proposed (type strain MLF1(sup T) = ATCC BAA-395(sup T) = DSMZ 14708(sup T).

Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal potomac river.

PubMed

Lovley, D R; Phillips, E J

1986-10-01

The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in the 0- to 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe(3)O(4) and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments. The availability of microbially reducible Fe(III) in surficial sediments demonstrates that microbial Fe(III) reduction can be important to organic matter decomposition and iron geochemistry. However, the overall extent of microbial Fe(III) reduction is governed by the inability of microorganisms to reduce most of the Fe(III) in the sediment.

Biological activity of Fe(III) aquo-complexes towards ferric chelate reductase (FCR).

PubMed

Escudero, Rosa; Gómez-Gallego, Mar; Romano, Santiago; Fernández, Israel; Gutiérrez-Alonso, Ángel; Sierra, Miguel A; López-Rayo, Sandra; Nadal, Paloma; Lucena, Juan J

2012-03-21

In this study we have obtained experimental evidence that confirms the high activity of aquo complexes III and IV towards the enzyme FCR, responsible for the reduction of Fe(III) to Fe(II) in the process of iron acquisition by plants. The in vivo FCR assays in roots of stressed cucumber plants have shown a higher efficiency of the family of complexes III and a striking structure-activity relationship with the nature of the substituent placed in a phenyl group far away from the metal center. The results obtained in this work demonstrate that all the aquo compounds tested interact efficiently with the enzyme FCR and hence constitute a new concept of iron chelates that could be of great use in agronomy.

Enhanced degradation of trichloroethene by calcium peroxide activated with Fe(III) in the presence of citric acid

PubMed Central

ZHANG, Xiang; GU, Xiaogang; LU, Shuguang; MIAO, Zhouwei; XU, Minhui; FU, Xiaori; DANISH, Muhammad; Brusseau, Mark L.; QIU, Zhaofu; SUI, Qian

2017-01-01

Trichloroethene (TCE) degradation by Fe(III)-activated calcium peroxide (CP) in the presence of citric acid (CA) in aqueous solution was investigated. The results demonstrated that the presence of CA enhanced TCE degradation significantly by increasing the concentration of soluble Fe(III) and promoting H2O2 generation. The generation of HO• and O2−• in both the CP/Fe(III) and CP/Fe(III)/CA systems was confirmed with chemical probes. The results of radical scavenging tests showed that TCE degradation was due predominantly o direct oxidation by HO•, while O2−• strengthened the generation of HO• by promoting Fe(III) transformation in the CP/Fe(III)/CA system. Acidic pH conditions were favorable for TCE degradation, and the TCE degradation rate decreased with increasing pH. The presence of Cl−, HCO3−, and humic acid (HA) inhibited TCE degradation to different extents for the CP/Fe(III)/CA system. Analysis of Cl− production suggested that TCE degradation in the CP/Fe(III)/CA system occurred through a dechlorination process. In summary, this study provided detailed information for the application of CA-enhanced Fe(III)-activated calcium peroxide for treating TCE contaminated groundwater. PMID:28959499

Electron Spin Relaxation Rates for High-Spin Fe(III) in Iron Transferrin Carbonate and Iron Transferrin Oxalate

PubMed Central

Gaffney, Betty Jean; Eaton, Gareth R.; Eaton*, Sandra S.

2005-01-01

To optimize simulations of CW EPR spectra for high-spin Fe(III) with zero-field splitting comparable to the EPR quantum, information is needed on the factors that contribute to the line shapes and line widths. Continuous wave electron paramagnetic resonance (EPR) spectra obtained for iron transferrin carbonate from 4 to 150 K and for iron transferrin oxalate from 4 to 100 K did not exhibit significant temperature dependence of the line shape, which suggested that the line shapes were not relaxation determined. To obtain direct information concerning the electron spin relaxation rates, electron spin echo and inversion recovery EPR were used to measure T1 and Tm for the high-spin Fe(III) in iron transferrin carbonate and iron transferrin oxalate between 5 and 20–30 K. For comparison with the data for the transferrin complexes, relaxation times were obtained for tris(oxalato)ferrate(III). The relaxation rates are similar for the three complexes and do not exhibit a strong dependence on position in the spectrum. Extrapolation of the observed temperature dependence of the relaxation rates to higher temperatures gives values consistent with the conclusion that the CW line shapes are not relaxation determined up to 150 K. PMID:16429607

Dissolution of Fe(III) (hydr) oxides by metal-EDTA complexes

NASA Astrophysics Data System (ADS)

Ngwack, Bernd; Sigg, Laura

1997-03-01

The dissolution of Fe(III)(hydr)oxides (goethite and hydrous ferric oxide) by metal-EDTA complexes occurs by ligand-promoted dissolution. The process is initiated by the adsorption of metal-EDTA complexes to the surface and is followed by the dissociation of the complex at the surface and the release of Fe(III)EDTA into solution. The dissolution rate is decreased to a great extent if EDTA is complexed by metals in comparison to the uncomplexed EDTA. The rate decreases in the order EDTA CaEDTA ≫ PbEDTA > ZnEDTA > CuEDTA > Co(II)EDTA > NiEDTA. Two different rate-limiting steps determine the dissolution process: (1) detachment of Fe(III) from the oxide-structure and (2) dissociation of the metal-EDTA complexes. In the case of goethite, step 1 is slower than step 2 and the dissolution rates by various metals are similar. In the case of hydrous ferric oxide, step 2 is rate-limiting and the effect of the complexed metal is very pronounced.

Modification of Natural Zeolite with Fe(III) and Its Application as Adsorbent Chloride and Carbonate ions

NASA Astrophysics Data System (ADS)

Suhartana; Sukmasari, Emmanuella; Azmiyawati, Choiril

2018-04-01

The aim of the research is to natural zeolite with Fe(III) using anion exchange process to improve the anion exchange capacity. Natural zeolite was activated using HNO3 1 N and then mixed with FeCl3 solution and refluxed followed by oven and calcination at a temperature of 550°C. The influence of Fe(III) to zeolite was characterized by FTIR while presence of Fe in zeolite characterized by AAS. Zeolite and Zeolite-Fe adsorption capacity of chloride and carbonate anions were determined through adsorption test by variation of pH and contact time. In advanced, and then to determining the Fe adsorbed concentration at Zeolite using UV-Vis spectrophotometer. FTIR analysis result showed that the addition of Fe does not affect the zeolite’s structure but change the intensity of the zeolite spectra. The Fe concentration in Zeolite-Fe of 714 mg L-1, indicate that Fe was present in the zeolite. Both Zeolite and Zeolite-Fe adsorbtion results showed that optimum pH of Chloride anion is 2, with adsorption capacity 2,33 x 10-3 gg-1 and optimum contact time is 8 minutes. While Zeolite and Zeolite-Fe adsorbtion results showed that optimum pH of Carbonate anion is 5, with adsorption capacity 5,31 x 10-3 gg-1 and optimum contact time is 8 minutes.

Preliminary study on the photoproduction of hydroxyl radicals in aqueous solution with Aldrich humic acid, algae and Fe(III) under high-pressure mercury lamp irradiation.

PubMed

Liu, Xianli; Xu, Dong; Wu, Feng; Liao, Zhenhuan; Liu, Jiantong; Deng, Nansheng

2004-03-01

Under a high-pressure mercury lamp (HPML) and using an exposure time of 4 h, the photoproduction of hydroxyl radicals (*OH) could be induced in an aqueous solution containing humic acid (HA). Hydroxyl radicals were determined by high-performance liquid chromatography using benzene as a probe. The results showed that *OH photoproduction increased from 1.80 to 2.74 microM by increasing the HA concentration from 10 to 40 mg L(-1) at an exposure time of 4 h (pH 6.5). Hydroxyl radical photoproduction in aqueous solutions of HA containing algae was greater than that in the aqueous solutions of HA without algae. The photoproduction of *OH in the HA solution with Fe(III) was greater than that of the solution without Fe(III) at pH ranging from 4.0 to 8.0. The photoproduction of *OH in HA solution with algae with or without Fe(III) under a 250 W HPML was greater than that under a 125 W HPML. The photoproduction of *OH in irradiated samples was influenced by the pH. The results showed that HPML exposure for 4 h in the 4-8 pH range led to the highest *OH photoproduction at pH 4.0.

Molecular evolution of the nif gene cluster carrying nifI1 and nifI2 genes in the Gram-positive phototrophic bacterium Heliobacterium chlorum.

PubMed

Enkh-Amgalan, Jigjiddorj; Kawasaki, Hiroko; Seki, Tatsuji

2006-01-01

A major nif cluster was detected in the strictly anaerobic, Gram-positive phototrophic bacterium Heliobacterium chlorum. The cluster consisted of 11 genes arranged within a 10 kb region in the order nifI1, nifI2, nifH, nifD, nifK, nifE, nifN, nifX, fdx, nifB and nifV. The phylogenetic position of Hbt. chlorum was the same in the NifH, NifD, NifK, NifE and NifN trees; Hbt. chlorum formed a cluster with Desulfitobacterium hafniense, the closest neighbour of heliobacteria based on the 16S rRNA phylogeny, and two species of the genus Geobacter belonging to the Deltaproteobacteria. Two nifI genes, known to occur in the nif clusters of methanogenic archaea between nifH and nifD, were found upstream of the nifH gene of Hbt. chlorum. The organization of the nif operon and the phylogeny of individual and concatenated gene products showed that the Hbt. chlorum nif operon carrying nifI genes upstream of the nifH gene was an intermediate between the nif operon with nifI downstream of nifH (group II and III of the nitrogenase classification) and the nif operon lacking nifI (group I). Thus, the phylogenetic position of Hbt. chlorum nitrogenase may reflect an evolutionary stage of a divergence of the two nitrogenase groups, with group I consisting of the aerobic diazotrophs and group II consisting of strictly anaerobic prokaryotes.

Hypothesis testing for the validation of the kinetic spectrophotometric methods for the determination of lansoprazole in bulk and drug formulations via Fe(III) and Zn(II) chelates.

PubMed

Rahman, Nafisur; Kashif, Mohammad

2010-03-01

Point and interval hypothesis tests performed to validate two simple and economical, kinetic spectrophotometric methods for the assay of lansoprazole are described. The methods are based on the formation of chelate complex of the drug with Fe(III) and Zn(II). The reaction is followed spectrophotometrically by measuring the rate of change of absorbance of coloured chelates of the drug with Fe(III) and Zn(II) at 445 and 510 nm, respectively. The stoichiometric ratio of lansoprazole to Fe(III) and Zn(II) complexes were found to be 1:1 and 2:1, respectively. The initial-rate and fixed-time methods are adopted for determination of drug concentrations. The calibration graphs are linear in the range 50-200 µg ml⁻¹ (initial-rate method), 20-180 µg ml⁻¹ (fixed-time method) for lansoprazole-Fe(III) complex and 120-300 (initial-rate method), and 90-210 µg ml⁻¹ (fixed-time method) for lansoprazole-Zn(II) complex. The inter-day and intra-day precision data showed good accuracy and precision of the proposed procedure for analysis of lansoprazole. The point and interval hypothesis tests indicate that the proposed procedures are not biased. Copyright © 2010 John Wiley & Sons, Ltd.

Magnetic and low temperature phonon studies of CoCr2O4 powders doped with Fe(III) and Ni(II) ions

NASA Astrophysics Data System (ADS)

Ptak, M.; Mączka, M.; Pikul, A.; Tomaszewski, P. E.; Hanuza, J.

2014-04-01

Extensive temperature-dependent phonon studies and low-temperature magnetic measurements of CoCr2-xFexO4 (for x=0.5, 1 and 2) and Co0.9Ni0.1Cr2O4 polycrystalline powders are presented. The main aim of these studies was to obtain information on phonon and structural properties of these compounds as well as strength of spin-phonon coupling in the magnetically ordered phases. IR and Raman spectra show that doping of CoCr2O4 with Fe(III) ions leads to broadening of bands and appearance of new bands due to the formation of inverted spinel structure. In contrast to this behavior, doping with 10 mol% of Ni(II) ions leads to weak increase of band width only. Magnetization measured as a function of temperature and external magnetic field showed that magnetic properties of Co0.9Ni0.1Cr2O4 sample are similar to those reported for pure CoCr2O4, i.e., partial substitution of Ni(II) for Co(II) leads to slight shift of the ferrimagnetic phase transition at TC and spiral spin order transition at TS towards lower values. The change of crystallization preference induced by incorporation of increasing concentration of Fe(III) ions in the spinel lattice causes significant increase of TC and decrease of TS. The latter transition disappears completely for higher concentrations of Fe(III). The performed temperature-dependent IR studies revealed interesting anomalous behavior of phonons below TC for CoCr1.5Fe0.5O4 and Co0.9Ni0.1Cr2O4, which was attributed to spin-phonon coupling.

Isolation, cloning and characterization of an azoreductase from the halophilic bacterium Halomonas elongata.

PubMed

Eslami, Maryam; Amoozegar, Mohammad Ali; Asad, Sedigheh

2016-04-01

Azo dyes are a major class of colorants used in various industries including textile, paper and food. These dyes are regarded as pollutant since they are not readily reduced under aerobic conditions. Halomonas elongata, a halophilic bacterium, has the ability to decolorize different mono and di-azo dyes in anoxic conditions. In this study the putative azoreductase gene of H. elongata, formerly annotated as acp, was isolated, heterologously expressed in Escherichia coli, purified and characterized. The gene product, AzoH, was found to have a molecular mass of 22 kDa. The enzyme requires NADH, as an electron donor for its activity. The apparent Km was 63 μM for NADH and 12 μM for methyl red as a mono-azo dye substrate. The specific activity for methyl red was 0.27 μmol min(-1)mg(-1). The optimum enzyme activity was achieved in 50mM sodium phosphate buffer at pH 6. Although increased salinity resulted in reduced activity, AzoH could decolorize azo dye at NaCl concentrations up to 15% (w/v). The enzyme was also shown to be able to decolorize remazol black B as a representative of di-azo dyes. This is the first report describing the sequence and activity of an azo-reducing enzyme from a halophilic bacterium. Copyright © 2015 Elsevier B.V. All rights reserved.

The Microbial Ferrous Wheel in a Neutral pH Groundwater Seep

PubMed Central

Roden, Eric E.; McBeth, Joyce M.; Blöthe, Marco; Percak-Dennett, Elizabeth M.; Fleming, Emily J.; Holyoke, Rebecca R.; Luther, George W.; Emerson, David; Schieber, Juergen

2012-01-01

Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II) at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II) just at its surface (∼5 cm depth), suggesting an internal Fe(II) source coupled to active Fe(III) reduction. Most probable number enumerations detected microaerophilic Fe(II)-oxidizing bacteria (FeOB) and dissimilatory Fe(III)-reducing bacteria (FeRB) at densities of 102 to 105 cells mL−1 in samples from both sites. In vitro Fe(III) reduction experiments revealed the potential for immediate reduction (no lag period) of native Fe(III) oxides. Conventional full-length 16S rRNA gene clone libraries were compared with high throughput barcode sequencing of the V1, V4, or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g., Gallionella, Sideroxydans, Aquabacterium). Sequences related to recognized FeRB (e.g., Rhodoferax, Aeromonas, Geobacter, Desulfovibrio) were also well-represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode

Enhancement of survival and electricity production in an engineered bacterium by light-driven proton pumping.

PubMed

Johnson, Ethan T; Baron, Daniel B; Naranjo, Belén; Bond, Daniel R; Schmidt-Dannert, Claudia; Gralnick, Jeffrey A

2010-07-01

Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments.

Oxidation of Ethylene Glycol by a Salt-Requiring Bacterium

PubMed Central

Caskey, William H.; Taber, Willard A.

1981-01-01

Bacterium T-52, cultured on ethylene glycol, readily oxidized glycolate and glyoxylate and exhibited elevated activities of ethylene glycol dehydrogenase and glycolate oxidase. Labeled glyoxylate was identified in reaction mixtures containing [14C]-ethylene glycol, but no glycolate was detected. The most likely pathway of ethylene glycol catabolism by bacterium T-52 is sequential oxidation to glycolate and glyoxylate. PMID:16345810

Evidence for Microbial Fe(III) Reduction in Anoxic, Mining-Impacted Lake Sediments (Lake Coeur d'Alene, Idaho)

PubMed Central

Cummings, David E.; March, Anthony W.; Bostick, Benjamin; Spring, Stefan; Caccavo, Frank; Fendorf, Scott; Rosenzweig, R. Frank

2000-01-01

Mining-impacted sediments of Lake Coeur d'Alene, Idaho, contain more than 10% metals on a dry weight basis, approximately 80% of which is iron. Since iron (hydr)oxides adsorb toxic, ore-associated elements, such as arsenic, iron (hydr)oxide reduction may in part control the mobility and bioavailability of these elements. Geochemical and microbiological data were collected to examine the ecological role of dissimilatory Fe(III)-reducing bacteria in this habitat. The concentration of mild-acid-extractable Fe(II) increased with sediment depth up to 50 g kg−1, suggesting that iron reduction has occurred recently. The maximum concentrations of dissolved Fe(II) in interstitial water (41 mg liter−1) occurred 10 to 15 cm beneath the sediment-water interface, suggesting that sulfidogenesis may not be the predominant terminal electron-accepting process in this environment and that dissolved Fe(II) arises from biological reductive dissolution of iron (hydr)oxides. The concentration of sedimentary magnetite (Fe3O4), a common product of bacterial Fe(III) hydroxide reduction, was as much as 15.5 g kg−1. Most-probable-number enrichment cultures revealed that the mean density of Fe(III)-reducing bacteria was 8.3 × 105 cells g (dry weight) of sediment−1. Two new strains of dissimilatory Fe(III)-reducing bacteria were isolated from surface sediments. Collectively, the results of this study support the hypothesis that dissimilatory reduction of iron has been and continues to be an important biogeochemical process in the environment examined. PMID:10618217

Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus.

PubMed

Yang, Guiqin; Zhou, Xuemei; Zhou, Shungui; Yang, Dehui; Wang, Yueqiang; Wang, Dingmei

2013-10-01

A novel thermotolerant bacterium, designated SgZ-8(T), was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20-65 °C (optimum 50 °C) and pH 6.0-9.0 (optimum 6.5-7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6-disulphonate (AQDS), fumarate and NO3(-) as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8(T) into the genus Bacillus, with the highest similarity to Bacillus badius JCM 12228(T) (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus Bacillus. The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8(T) ( = CCTCC AB 2012108(T) = KACC 16706(T)) was designated the type strain of a novel species of the genus Bacillus, for which the name Bacillus thermotolerans sp. nov. is proposed.

Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir.

PubMed

Greene, A C; Patel, B K; Sheehy, A J

1997-04-01

A thermophilic anaerobic bacterium, designated strain BMAT (T = type strain), was isolated from the production water of Beatrice oil field in the North Sea (United Kingdom). The cells were straight to bent rods (1 to 5 by 0.3 to 0.5 microns) which stained gram negative. Strain BMAT obtained energy from the reduction of manganese (IV), iron(III), and nitrate in the presence of yeast extract, peptone, Casamino Acids, tryptone, hydrogen, malate, acetate, citrate, pyruvate, lactate, succinate, and valerate. The isolate grew optimally at 60 degrees C (temperature range for growth, 50 to 65 degrees C) and in the presence of 2% (wt/vol) NaCl (NaCl range for growth, 0 to 5% [wt/vol]). The DNA base composition was 34 mol% G + C. Phylogenetic analyses of the 16S rRNA gene indicated that strain BMAT is a member of the domain Bacteria. The closest known bacterium is the moderate thermophile Flexistipes sinusarabici (similarity value, 88%). Strain BMAT possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus; therefore, we propose that this isolate should be described as a member of a novel species of a new genus, Deferribacter thermophilus gen. nov., sp. nov.

Synthesis, iron(III) complexation properties, molecular dynamics simulations and P. aeruginosa siderophore-like activity of two pyoverdine analogs.

PubMed

Antonietti, Viviane; Boudesocque, Stéphanie; Dupont, Laurent; Farvacques, Natacha; Cézard, Christine; Da Nascimento, Sophie; Raimbert, Jean-François; Socrier, Larissa; Robin, Thierry-Johann; Morandat, Sandrine; El Kirat, Karim; Mullié, Catherine; Sonnet, Pascal

2017-09-08

P. aeruginosa ranks among the top five organisms causing nosocomial infections. Among the many novel strategies for developing new therapeutics against infection, targeting iron uptake mechanism seems promising as P. aeruginosa needs iron for its growth and survival. To scavenge iron, the bacterium produces siderophores possessing a very high affinity towards Fe(III) ions such as pyoverdines. In this work, we decided to study two pyoverdine analogs, aPvd2 and aPvd3, structurally close to the endogen pyoverdine. The pFe constants calculated with the values of formation showed a high affinity of aPvd3 towards Fe(III). Molecular dynamics calculations demonstrated that aPvd3-Fe forms with Fe(III) stable 1:1 complexes in water, whereas aPvd2 does not. Only aPvd3 is able to increase the bacterial growth and represents thus an alternative to pyoverdine for iron acquisition by the bacterium. The aPvd2-3 interaction studies with a lipid membrane indicated that they were unable to interact and to cross the plasma membrane of bacteria by passive diffusion. Consequently, the penetration of aPvd3 is ruled by a transport membrane protein. These results showed that aPvd3 may be used to inhibit pyoverdine uptake or to promote the accumulation and release of antibiotics into the cell following a Trojan horse strategy. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

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

DOEpatents

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.

Metastable electronic populations and relaxation of Fe(I), Fe(II), and Fe(III) in MgO observed by Mössbauer emission spectroscopy

NASA Astrophysics Data System (ADS)

Tuczek, F.; Spiering, H.; Gütlich, P.

1990-06-01

Magnetic-field Mössbauer emission spectra of 57Co in MgO single crystals covering a broad velocity range and measured up to high signal-to-noise ratios are presented. In accordance with a previous study, three charge states of 57Fe are found after 57Co(EC)57Fe (EC stands for electron capture). The evaluation of the Fe(III) fraction indicates nonthermalized populations of the 6A1 ground-state Zeeman levels. The field, temperature, and angular dependences of these populations are evaluated and display qualitative differences to the findings in 57Co/LiNbO3. The implications of the cubic symmetry on the spin-selective ground-state population are considered. In addition, a completely analogous phenomenon is evidenced for the first time within an Fe(II) electronic manifold, namely, the Γ5g ground state of Fe(II) in MgO, after the nuclear decay. In contrast to the Fe(III) case, these populations are not static within the Mössbauer time window. It turns out that the attainment of thermal equilibrium can be conveniently observed by changing the field value, evidencing a direct relaxation process at 4.2 K within Γ5g. The relaxation rates are compatible with static strain data; an initial alignment is observed. Finally, there is strong evidence that the Fe(I) fraction is also populated out of thermal equilibrium. In addition to these ground-state spectra, two features are present that may be attributed to metastable excited states of Fe(II) and Fe(III). It is described in detail how these various contributions can be disentangled.

Investigation of the spectral properties of a squarylium near-infrared dye and its complexation with Fe(III) and Co(II) ions

NASA Astrophysics Data System (ADS)

Tarazi, Leila; Narayanan, Nara; Sowell, John; Patonay, Gabor; Strekowski, Lucjan

2002-01-01

The spectral features of the squarylium dye NN525 in different solutions and its complexation with several metal ions were investigated. The absorbance maximum of the dye is at 669 nm in tetrahydrofuran. This value matches the output of a commercially available laser diode (650 nm), thus making use of such a source practical for excitation. The emission maximum of the dye in tetrahydrofuran is at 676 nm. The addition of either Fe(III) ion or Co(II) ion resulted in fluorescence quenching of the dye. The detection limit is 6.24×10 -8 M for Fe(III) ion and 1.55×10 -8 M for Co(II) ion. The molar ratio of the metal to the dye was established to be 1:1 for both metal ions. The stability constant KS of the metal-dye complex was calculated to be 3.14×10 6 M -1 for the Fe-dye complex and 2.64×10 5 M -1 for the Co-dye complex.

Investigation of the spectral properties of a squarylium near-infrared dye and its complexation with Fe(III) and Co(II) ions.

PubMed

Tarazi, Leila; Narayanan, Nara; Sowell, John; Patonay, Gabor; Strekowski, Lucjan

2002-01-15

The spectral features of the squarylium dye NN525 in different solutions and its complexation with several metal ions were investigated. The absorbance maximum of the dye is at 669 nm in tetrahydrofuran. This value matches the output of a commercially available laser diode (650 nm), thus making use of such a source practical for excitation. The emission maximum of the dye in tetrahydrofuran is at 676 nm. The addition of either Fe(III) ion or Co(II) ion resulted in fluorescence quenching of the dye. The detection limit is 6.24 x 10(-8) M for Fe(III) ion and 1.55 x 10(-8) M for Co(II) ion. The molar ratio of the metal to the dye was established to be 1:1 for both metal ions. The stability constant Ks of the metal-dye complex was calculated to be 3.14 x 10(6) M(-1) for the Fe-dye complex and 2.64 x 10(5) M(-1) for the Co-dye complex.

Synthesis, spectroscopic, thermal and anticancer studies of metal-antibiotic chelations: Ca(II), Fe(III), Pd(II) and Au(III) chloramphenicol complexes

NASA Astrophysics Data System (ADS)

Al-Khodir, Fatima A. I.; Refat, Moamen S.

2016-09-01

Four Ca(II), Fe(III), Pd(II) and Au(III) complexes of chloramphenicol drug have been synthesized and well characterized using elemental analyses, (infrared, electronic, and 1H-NMR) spectra, magnetic susceptibility measurement, and thermal analyses. Infrared spectral data show that the chloramphenicol drug coordinated to Ca(II), Pd(II) and Au(III) metal ions through two hydroxyl groups with 1:1 or 1:2 M ratios, but Fe(III) ions chelated towards chloramphenicol drug via the oxygen and nitrogen atoms of amide group with 1:2 ratio based on presence of keto↔enol form. The X-ray powder diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscopy (TEM) techniques were used to identify the nano-size particles of both iron(III) and gold(III) chloramphenicol complexes. The antimicrobial assessments of the chloramphenicol complexes were scanned and collected the results against of some kind of bacteria and fungi. The cytotoxic activity of the gold(III) complex was tested against the human colon carcinoma (HCT-116) and human hepatocellular carcinoma (HepG-2) tumor cell lines.

Reduction of nitric oxide catalyzed by hydroxylamine oxidoreductase from an anammox bacterium.

PubMed

Irisa, Tatsuya; Hira, Daisuke; Furukawa, Kenji; Fujii, Takao

2014-12-01

The hydroxylamine oxidoreductase (HAO) from the anammox bacterium, Candidatus Kuenenia stuttgartiensis has been reported to catalyze the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO) by using bovine cytochrome c as an oxidant. In contrast, we investigated whether the HAO from anammox bacterium strain KSU-1 could catalyze the reduction of NO with reduced benzyl viologen (BVred) and the NO-releasing reagent, NOC 7. The reduction proceeded, resulting in the formation of NH2OH as a product. The oxidation rate of BVred was proportional to the concentration of BVred itself for a short period in each experiment, a situation that was termed quasi-steady state. The analyses of the states at various concentrations of HAO allowed us to determine the rate constant for the catalytic reaction, (2.85 ± 0.19) × 10(5) M(-1) s(-1), governing NO reduction by BVred and HAO, which was comparable to that reported for the HAO from the ammonium oxidizer, Nitrosomonas with reduced methyl viologen. These results suggest that the anammox HAO functions to adjust anammox by inter-conversion of NO and NH2OH depending on the redox potential of the physiological electron transfer protein in anammox bacteria. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury Methylation▿†

PubMed Central

Gilmour, Cynthia C.; Elias, Dwayne A.; Kucken, Amy M.; Brown, Steven D.; Palumbo, Anthony V.; Schadt, Christopher W.; Wall, Judy D.

2011-01-01

We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus. PMID:21515733

Role of microbial Fe(III) reduction and solution chemistry in aggregation and settling of suspended particles in the Mississippi River Delta plain, Louisiana, USA

USGS Publications Warehouse

Jaisi, Deb P.; Ji, Shanshan; Dong, Hailiang; Blake, Ruth E.; Eberl, Dennis D.; Kim, Jinwook

2008-01-01

River-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended particles, yet factors that control particle aggregation and resulting sedimentation in these environments are poorly understood. This study was designed to investigate the role of microbial Fe(III) reduction and solution chemistry in aggregation of suspended particles in the Mississippi Delta. Three representative sites along the salinity gradient were selected and sediments were collected from the sediment-water interface. Based on quantitative mineralogical analyses 88–89 wt.% of all minerals in the sediments are clays, mainly smectite and illite. Consumption of SO42− and the formation of H2S and pyrite during microbial Fe(III) reduction of the non-sterile sediments by Shewanella putrefaciens CN32 in artificial pore water (APW) media suggest simultaneous sulfate and Fe(III) reduction activity. The pHPZNPC of the sediments was ≤3.5 and their zeta potentials at the sediment-water interface pH (6.9–7.3) varied from −35 to −45 mV, suggesting that both edges and faces of clay particles have negative surface charge. Therefore, high concentrations of cations in pore water are expected to be a predominant factor in particle aggregation consistent with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Experiments on aggregation of different types of sediments in the same APW composition revealed that the sediment with low zeta potential had a high rate of aggregation. Similarly, addition of external Fe(II) (i.e. not derived from sediments) was normally found to enhance particle aggregation and deposition in all sediments, probably resulting from a decrease in surface potential of particles due to specific Fe(II) sorption. Scanning and transmission electron microscopy (SEM, TEM) images showed predominant face-to-face clay aggregation in

Enhancement of Survival and Electricity Production in an Engineered Bacterium by Light-Driven Proton Pumping▿ †

PubMed Central

Johnson, Ethan T.; Baron, Daniel B.; Naranjo, Belén; Bond, Daniel R.; Schmidt-Dannert, Claudia; Gralnick, Jeffrey A.

2010-01-01

Microorganisms can use complex photosystems or light-dependent proton pumps to generate membrane potential and/or reduce electron carriers to support growth. The discovery that proteorhodopsin is a light-dependent proton pump that can be expressed readily in recombinant bacteria enables development of new strategies to probe microbial physiology and to engineer microbes with new light-driven properties. Here, we describe functional expression of proteorhodopsin and light-induced changes in membrane potential in the bacterium Shewanella oneidensis strain MR-1. We report that there were significant increases in electrical current generation during illumination of electrochemical chambers containing S. oneidensis expressing proteorhodopsin. We present evidence that an engineered strain is able to consume lactate at an increased rate when it is illuminated, which is consistent with the hypothesis that proteorhodopsin activity enhances lactate uptake by increasing the proton motive force. Our results demonstrate that there is coupling of a light-driven process to electricity generation in a nonphotosynthetic engineered bacterium. Expression of proteorhodopsin also preserved the viability of the bacterium under nutrient-limited conditions, providing evidence that fulfillment of basic energy needs of organisms may explain the widespread distribution of proteorhodopsin in marine environments. PMID:20453141

Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lovley, D.R.; Phillips, E.J.P.

1986-10-01

The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in themore » 0- 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe/sub 3/O/sub 4/ and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments.« less

Capsule-Transmitted Gut Symbiotic Bacterium of the Japanese Common Plataspid Stinkbug, Megacopta punctatissima

PubMed Central

Fukatsu, Takema; Hosokawa, Takahiro

2002-01-01

The Japanese common plataspid stinkbug, Megacopta punctatissima, deposits small brown particles, or symbiont capsules, on the underside of the egg mass for the purpose of transmission of symbiotic bacteria to the offspring. We investigated the microbiological aspects of the bacteria contained in the capsule, such as microbial diversity, phylogenetic placement, localization in vivo, and fitness effects on the host insect. Restriction fragment length polymorphism analysis of 16S ribosomal DNA clones revealed that a single bacterial species dominates the microbiota in the capsule. The bacterium was not detected in the eggs but in the capsules, which unequivocally demonstrated that the bacterium is transmitted to the offspring of the insect orally rather than transovarially, through probing of the capsule content. Molecular phylogenetic analysis showed that the bacterium belongs to the γ-subdivision of the Proteobacteria. In adult insects the bacterium was localized in the posterior section of the midgut. Deprivation of the bacterium from the nymphs resulted in retarded development, arrested growth, abnormal body coloration, and other symptoms, suggesting that the bacterium is essential for normal development and growth of the host insect. PMID:11772649

Swimming efficiency of bacterium Escherichia coli

PubMed Central

Chattopadhyay, Suddhashil; Moldovan, Radu; Yeung, Chuck; Wu, X. L.

2006-01-01

We use measurements of swimming bacteria in an optical trap to determine fundamental properties of bacterial propulsion. In particular, we directly measure the force required to hold the bacterium in the optical trap and determine the propulsion matrix, which relates the translational and angular velocity of the flagellum to the torques and forces propelling the bacterium. From the propulsion matrix, dynamical properties such as torques, swimming speed, and power can be obtained by measuring the angular velocity of the motor. We find significant heterogeneities among different individuals even though all bacteria started from a single colony. The propulsive efficiency, defined as the ratio of the propulsive power output to the rotary power input provided by the motors, is found to be ≈2%, which is consistent with the efficiency predicted theoretically for a rigid helical coil. PMID:16954194

Coiled to diffuse: Brownian motion of a helical bacterium.

PubMed

Butenko, Alexander V; Mogilko, Emma; Amitai, Lee; Pokroy, Boaz; Sloutskin, Eli

2012-09-11

We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.

[Partial biological characteristics and algicidal activity of an algicidal bacterium].

PubMed

Li, San-Hua; Zhang, Qi-Ya

2013-02-01

An algicidal bacterium was isolated from freshwater (Lake Donghu in Wuhan) and coded as A01. The morphology of the algicidal bacterium was observed using optical microscope and electron microscopes, the results showed that A01 was rod-shaped, approximately 1.5 microm in length and 0.45 microm in width and with no flagella structure. A01 was Gram-negative and belongs to the family Acinetobacter sp. though identification by Gram's staining and 16S rDNA gene analysis. A01 exhibited strong algicidal activity on the bloom-forming cyanobacterium Anabaena eucompacta under laboratory conditions. The removal rate of chlorophyll a after 7-day incubation with the culture supernatant of A01 and thalli were 77% and 61%, respectively. Microscopic observation showed that almost all cyanobacterial cells were destroyed within 3 d of co-incubation with the supernatant of algicidal bacterium, but a mass of the cyanobacterial cell lysis was observed only after 5 d of co-incubation with the thalli of algicidal bacterium. These results indicated that the main algicidal component of A01 was in its culture supernatant. In other words, the strain A01 could secrete algicidal component against Anabaena eucompacta.

Transformation impacts of dissolved and solid phase Fe(II) on trichloroethylene (TCE) reduction in an iron-reducing bacteria (IRB) mixed column system: a mathematical model.

PubMed

Bae, Yeunook; Kim, Dooil; Cho, Hyun-Hee; Singhal, Naresh; Park, Jae-Woo

2012-12-01

In this research, we conducted trichloroethylene (TCE) reduction in a column filled with iron and iron-reducing bacteria (IRB) and developed a mathematical model to investigate the critical reactions between active species in iron/IRB/contaminant systems. The formation of ferrous iron (Fe(II)) in this system with IRB and zero-valent iron (ZVI, Fe(0)) coated with a ferric iron (Fe(III)) crust significantly affected TCE reduction and IRB respiration in various ways. This study presents a new framework for transformation property and reducing ability of both dissolved (Fe(II)(dissolved)) and solid form ferrous iron (Fe(II)(solid)). Results showed that TCE reduction was strongly depressed by Fe(II)(solid) rather than by other inhibitors (e.g., Fe(III) and lactate), suggesting that Fe(II)(solid) might reduce IRB activation due to attachment to IRB cells. Newly exposed Fe(0) from the released Fe(II)(dissolved) was a strong contributor to TCE reduction compared to Fe(II)(solid). In addition, our research confirmed that less Fe(II)(solid) production strongly supported long-term TCE reduction because it may create an easier TCE approach to Fe(0) or increase IRB growth. Our findings will aid the understanding of the contributions of iron media (e.g., Fe(II)(solid), Fe(II)(dissolved), Fe(III), and Fe(0)) to IRB for decontamination in natural groundwater systems. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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. Copyright © 2014 Elsevier B.V. All rights reserved.

Enzymes involved in the anaerobic degradation of ortho-phthalate by the nitrate-reducing bacterium Azoarcus sp. strain PA01.

PubMed

Junghare, Madan; Spiteller, Dieter; Schink, Bernhard

2016-09-01

The pathway of anaerobic degradation of o-phthalate was studied in the nitrate-reducing bacterium Azoarcus sp. strain PA01. Differential two-dimensional protein gel profiling allowed the identification of specifically induced proteins in o-phthalate-grown compared to benzoate-grown cells. The genes encoding o-phthalate-induced proteins were found in a 9.9 kb gene cluster in the genome of Azoarcus sp. strain PA01. The o-phthalate-induced gene cluster codes for proteins homologous to a dicarboxylic acid transporter, putative CoA-transferases and a UbiD-like decarboxylase that were assigned to be specifically involved in the initial steps of anaerobic o-phthalate degradation. We propose that o-phthalate is first activated to o-phthalyl-CoA by a putative succinyl-CoA-dependent succinyl-CoA:o-phthalate CoA-transferase, and o-phthalyl-CoA is subsequently decarboxylated to benzoyl-CoA by a putative o-phthalyl-CoA decarboxylase. Results from in vitro enzyme assays with cell-free extracts of o-phthalate-grown cells demonstrated the formation of o-phthalyl-CoA from o-phthalate and succinyl-CoA as CoA donor, and its subsequent decarboxylation to benzoyl-CoA. The putative succinyl-CoA:o-phthalate CoA-transferase showed high substrate specificity for o-phthalate and did not accept isophthalate, terephthalate or 3-fluoro-o-phthalate whereas the putative o-phthalyl-CoA decarboxylase converted fluoro-o-phthalyl-CoA to fluoro-benzoyl-CoA. No decarboxylase activity was observed with isophthalyl-CoA or terephthalyl-CoA. Both enzyme activities were oxygen-insensitive and inducible only after growth with o-phthalate. Further degradation of benzoyl-CoA proceeds analogous to the well-established anaerobic benzoyl-CoA degradation pathway of nitrate-reducing bacteria. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus

PubMed Central

Xiu, Pengyuan; Liu, Rui

2017-01-01

ABSTRACT Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium (Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes (flgA and flgP) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance. IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and

Pumilacidin-Like Lipopeptides Derived from Marine Bacterium Bacillus sp. Strain 176 Suppress the Motility of Vibrio alginolyticus.

PubMed

Xiu, Pengyuan; Liu, Rui; Zhang, Dechao; Sun, Chaomin

2017-06-15

Bacterial motility is a crucial factor during the invasion and colonization processes of pathogens, which makes it an attractive therapeutic drug target. Here, we isolated a marine bacterium ( Vibrio alginolyticus strain 178) from a seamount in the tropical West Pacific that exhibits vigorous motility on agar plates and severe pathogenicity to zebrafish. We found that V. alginolyticus 178 motility was significantly suppressed by another marine bacterium, Bacillus sp. strain 176, isolated from the same niche. We isolated, purified, and characterized two different cyclic lipopeptides (CLPs) from Bacillus sp. 176 using high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The two related CLPs have a pumilacidin-like structure and were both effective inhibitors of V. alginolyticus 178 motility. The CLPs differ by only one methylene group in their fatty acid chains. In addition to motility suppression, the CLPs also induced cell aggregation in the medium and reduced adherence of V. alginolyticus 178 to glass substrates. Notably, upon CLP treatment, the expression levels of two V. alginolyticus flagellar assembly genes ( flgA and flgP ) dropped dramatically. Moreover, the CLPs inhibited biofilm formation in several other strains of pathogenic bacteria without inducing cell death. This study indicates that CLPs from Bacillus sp. 176 show promise as antimicrobial lead compounds targeting bacterial motility and biofilm formation with a low potential for eliciting antibiotic resistance. IMPORTANCE Pathogenic bacteria often require motility to establish infections and subsequently spread within host organisms. Thus, motility is an attractive therapeutic target for the development of novel antibiotics. We found that cyclic lipopeptides (CLPs) produced by marine bacterium Bacillus sp. strain 176 dramatically suppress the motility of the pathogenic bacterium Vibrio alginolyticus strain 178, reduce biofilm formation, and promote

Thermally activated charge transport in microbial protein nanowires

PubMed Central

Lampa-Pastirk, Sanela; Veazey, Joshua P.; Walsh, Kathleen A.; Feliciano, Gustavo T.; Steidl, Rebecca J.; Tessmer, Stuart H.; Reguera, Gemma

2016-01-01

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. PMID:27009596

Thermally activated charge transport in microbial protein nanowires

NASA Astrophysics Data System (ADS)

Lampa-Pastirk, Sanela; Veazey, Joshua P.; Walsh, Kathleen A.; Feliciano, Gustavo T.; Steidl, Rebecca J.; Tessmer, Stuart H.; Reguera, Gemma

2016-03-01

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.

Thermally activated charge transport in microbial protein nanowires.

PubMed

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.

Alkaline Fe(III) reduction by a novel alkali-tolerant Serratia sp. isolated from surface sediments close to Sellafield nuclear facility, UK.

PubMed

Thorpe, Clare L; Morris, Katherine; Boothman, Christopher; Lloyd, Jonathan R

2012-02-01

Extensive denitrification resulted in a dramatic increase in pH (from 6.8 to 9.5) in nitrate-impacted, acetate-amended sediment microcosms containing sediment representative of the Sellafield nuclear facility, UK. Denitrification was followed by Fe(III) reduction, indicating the presence of alkali-tolerant, metal-reducing bacteria. A close relative (99% 16S rRNA gene sequence homology) to Serratia liquefaciens dominated progressive enrichment cultures containing Fe(III)-citrate as the sole electron acceptor at pH 9 and was isolated aerobically using solid media. The optimum growth conditions for this facultatively anaerobic Serratia species were investigated, and it was capable of metabolizing a wide range of electron acceptors including oxygen, nitrate, FeGel, Fe-NTA and Fe-citrate and electron donors including acetate, lactate, formate, ethanol, glucose, glycerol and yeast extract at an optimum pH of c. 6.5 at 20 °C. The alkali tolerance of this strain extends the pH range of highly adaptable Fe(III)-reducing Serratia species from mildly acidic pH values associated with acid mine drainage conditions to alkali conditions representative of subsurface sediments stimulated for extensive denitrification and metal reduction. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Desulfovibrio tunisiensis sp. nov., a novel weakly halotolerant, sulfate-reducing bacterium isolated from exhaust water of a Tunisian oil refinery.

PubMed

Ben Ali Gam, Zouhaier; Oueslati, Ridha; Abdelkafi, Slim; Casalot, Laurence; Tholozan, Jean Luc; Labat, Marc

2009-05-01

A novel weakly halotolerant, sulfate-reducing bacterium, designated strain RB22(T), was isolated from exhaust water of a Tunisian oil refinery. Cells of strain RB22(T) were Gram-negative, motile, vibrio-shaped or sigmoid and non-spore-forming, and occurred singly or in chains. Strain RB22(T) grew between 15 and 45 degrees C (optimum, 37 degrees C) and at pH 4.5 to 9 (optimum, pH 7). NaCl was not required for growth, but the strain tolerated high NaCl concentrations (up to 70 g l(-1)) with an optimum of 40 g l(-1). Sulfate, thiosulfate, sulfite and elemental sulfur served as electron acceptors, but not fumarate. Nitrate and nitrite were not reduced. Strain RB22(T) utilized lactate, formate, fumarate, succinate, glycerol, H(2)+CO(2) and methanol as substrates. The DNA G+C content was found to be 59.6 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the isolate was a member of the genus Desulfovibrio, with no close relatives at the species level (16S rRNA gene sequence similarity of less than 95 %). Strain RB22(T) exhibited levels of 16S rRNA gene sequence similarity of 94.6 and 94.12 % to the type strains of the closely related species Desulfovibrio aespoeensis and Desulfovibrio dechloracetivorans, respectively. On the basis of genotypic and phylogenetic characteristics, and significant phenotypic differences, we suggest that strain RB22(T) represents a novel species, for which the name Desulfovibrio tunisiensis sp. nov. is proposed. The type strain is RB22(T) (=NCIMB 14400(T)=JCM 15076(T)=DSM 19275(T)).

Diversity in bacterium-host interactions within the species Helicobacter heilmannii sensu stricto

PubMed Central

2013-01-01

Helicobacter (H.) heilmannii sensu stricto (s.s.) is a zoonotic bacterium that naturally colonizes the stomach of dogs and cats. In humans, this microorganism has been associated with gastritis, peptic ulcer disease and mucosa associated lymphoid tissue (MALT) lymphoma. Little information is available about the pathogenesis of H. heilmannii s.s. infections in humans and it is unknown whether differences in virulence exist within this species. Therefore, a Mongolian gerbil model was used to study bacterium-host interactions of 9 H. heilmannii s.s. strains. The colonization ability of the strains, the intensity of gastritis and gene expression of various inflammatory cytokines in the stomach were determined at 9 weeks after experimental infection. The induction of an antrum-dominant chronic active gastritis with formation of lymphocytic aggregates was shown for 7 strains. High-level antral colonization was seen for 4 strains, while colonization of 4 other strains was more restricted and one strain was not detected in the stomach at 9 weeks post infection. All strains inducing a chronic active gastritis caused an up-regulation of the pro-inflammatory cytokine IL-1β in the antrum. A reduced antral expression of H+/K+ ATPase was seen in the stomach after infection with 3 highly colonizing strains and 2 highly colonizing strains caused an increased gastrin expression in the fundus. In none of the H. heilmannii s.s.-infected groups, IFN-γ expression was up-regulated. This study demonstrates diversity in bacterium-host interactions within the species H. heilmannii s.s. and that the pathogenesis of gastric infections with this microorganism is not identical to that of an H. pylori infection. PMID:23895283

Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost.

PubMed

Guo, Junhui; Wang, Yue Qiang; Yang, Guiqin; Chen, Yunqi; Zhou, Shungui; Zhao, Yong; Zhuang, Li

2016-05-01

A Gram-staining-positive, facultative anaerobic, motile and rod-shaped bacterium, designated GSS08(T), was isolated from a windrow compost pile and characterized by means of a polyphasic approach. Growth occurred with 0-4 % (w/v) NaCl (optimum 1 %), at pH 6.5-9.5 (optimum pH 7.5) and at 20-45 °C (optimum 37 °C). Anaerobic growth occurred with anthraquinone-2,6-disulphonate, fumarate and NO3 (-) as electron acceptor. The main respiratory quinone was MK-7. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5 %) were iso-C15:0 (43.1 %), anteiso-C15:0 (27.4 %) and iso-C16:0 (8.3 %). The DNA G + C content was 39.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSS08(T) formed a phyletic lineage with the type strain of Bacillus humi DSM 16318(T) with a high sequence similarity of 97.5 %, but it displayed low sequence similarity with other valid species in the genus Bacillus (<96.0 %). The DNA-DNA relatedness between strains GSS08(T) and B. humi DSM 16318(T) was 50.8 %. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS08(T) represents a novel species, for which the name Bacillus nitroreducens sp. nov. is proposed. The type strain is GSS08(T) (=KCTC 33699(T) = MCCC 1K01091(T)).

Gut bacterium of Dendrobaena veneta (Annelida: Oligochaeta) possesses antimycobacterial activity.

PubMed

Fiołka, Marta J; Zagaja, Mirosław P; Piersiak, Tomasz D; Wróbel, Marek; Pawelec, Jarosław

2010-09-01

The new bacterial strain with antimycobacterial activity has been isolated from the midgut of Dendrobaena veneta (Annelida). Biochemical and molecular characterization of isolates from 18 individuals identified all as Raoultella ornithinolytica genus with 99% similarity. The bacterium is a possible symbiont of the earthworm D. veneta. The isolated microorganism has shown the activity against four strains of fast-growing mycobacteria: Mycobacterium butiricum, Mycobacterium jucho, Mycobacterium smegmatis and Mycobacterium phlei. The multiplication of the gut bacterium on plates with Sauton medium containing mycobacteria has caused a lytic effect. After the incubation of the cell free extract prepared from the gut bacterium with four strains of mycobacteria in liquid Sauton medium, the cells of all tested strains were deformed and divided to small oval forms and sometimes created long filaments. The effect was observed by the use of light, transmission and scanning microscopy. Viability of all examined species of mycobacteria was significantly decreased. The antimycobacterial effect was probably the result of the antibiotic action produced by the gut bacterium of the earthworm. The application of ultrafiltration procedure allowed to demonstrate that antimicrobial substance with strong antimycobacterial activity from bacterial culture supernatant, is a protein with the molecular mass above 100 kDa. Copyright 2010 Elsevier Inc. All rights reserved.

Rates of cuticular penetration of chelated Fe(III): role of humidity, concentration, adjuvants, temperature, and type of chelate.

PubMed

Schönherr, Jörg; Fernández, Victoria; Schreiber, Lukas

2005-06-01

Time courses of cuticular penetration of FeCl3 and Fe(III) complexes of citric acid, EDTA, EDDHA (Sequestrene 138Fe), imidodisuccinic acid (IDHA), and ligninsulfonic acid (Natrel) were studied using astomatous cuticular membranes (CMs) isolated from Populus x canescens leaves. At 100% relative humidity, the Fe(III) chelates disappeared exponentially with time from the surface of the CMs; that is, penetration was a first-order process that can be described using rate constants or half-times of penetration (t(1/2)). Half-times ranged from 20 to 30 h. At 90% humidity, penetration rates were insignificant with the exception of Natrel, for which t(1/2) amounted to 58 h. Rate constants were independent of temperature (15, 25, and 35 degrees C). Permeability decreased with increasing Fe chelate concentration (IDHA and EDTA). At 100% humidity, half-times measured with FeIDHA were 11 h (2 mmol L(-1)), 17 h (10 mmol L(-1)) and 36 h (20 mmol L(-1)), respectively. In the presence of FeEDTA, penetration of CaCl2 was slowed greatly. Half-times for penetration of CaCl2, which were 1.9 h in the absence of FeEDTA, rose to 3.12 h in the presence of an equimolar concentration of EDTA and 13.3 h when the FeEDTA concentration was doubled. Hence, Fe chelates reduced permeability of CMs to CaCl2 and to the Fe chelates themselves. It is suggested that Fe chelates reduced the size of aqueous pores. This view is supported by the fact that rate constants for calcium salts were about 5 times higher than for Fe chelates with the same molecular weights. Adding Tween 20 (5 g L(-1)) as a humectant did not increase permeability to FeIDHA at 90% humidity and below, while addition of glycine betaine did. Penetration of FeCl3 applied at 5 g L(-1) (pH 1.5) was not a first order process as rate constants decreased rapidly with time. Only 2% of the dose penetrated during the first 2 h and less than that in the subsequent 8 h. Recovery was only 70%. This was attributed to the formation of insoluble Fe

Protozoan grazing reduces the current output of microbial fuel cells.

PubMed

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. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Characterization of the promising poly(3-hydroxybutyrate) producing halophilic bacterium Halomonas halophila.

PubMed

Kucera, Dan; Pernicová, Iva; Kovalcik, Adriana; Koller, Martin; Mullerova, Lucie; Sedlacek, Petr; Mravec, Filip; Nebesarova, Jana; Kalina, Michal; Marova, Ivana; Krzyzanek, Vladislav; Obruca, Stanislav

2018-05-01

This work explores molecular, morphological as well as biotechnological features of the highly promising polyhydroxyalkanoates (PHA) producer Halomonas halophila. Unlike many other halophiles, this bacterium does not require expensive complex media components and it is capable to accumulate high intracellular poly(3-hydroxybutyrate) (PHB) fractions up to 82% of cell dry mass. Most remarkably, regulating the concentration of NaCl apart from PHB yields influences also the polymer's molecular mass and polydispersity. The bacterium metabolizes various carbohydrates including sugars predominant in lignocelluloses and other inexpensive substrates. Therefore, the bacterium was employed for PHB production on hydrolysates of cheese whey, spent coffee grounds, sawdust and corn stover, which were hydrolyzed by HCl; required salinity of cultivation media was set up during neutralization by NaOH. The bacterium was capable to use all the tested hydrolysates as well as sugar beet molasses for PHB biosynthesis, indicating its potential for industrial PHB production. Copyright © 2018 Elsevier Ltd. All rights reserved.

Purification and Characterization of Active-Site Components of the Putative p-Cresol Methylhydroxylase Membrane Complex from Geobacter metallireducens▿

PubMed Central

Johannes, Jörg; Bluschke, Alexander; Jehmlich, Nico; von Bergen, Martin; Boll, Matthias

2008-01-01

p-Cresol methylhydroxylases (PCMH) from aerobic and facultatively anaerobic bacteria are soluble, periplasmic flavocytochromes that catalyze the first step in biological p-cresol degradation, the hydroxylation of the substrate with water. Recent results suggested that p-cresol degradation in the strictly anaerobic Geobacter metallireducens involves a tightly membrane-bound PCMH complex. In this work, the soluble components of this complex were purified and characterized. The data obtained suggest a molecular mass of 124 ± 15 kDa and a unique αα′β2 subunit composition, with α and α′ representing isoforms of the flavin adenine dinucleotide (FAD)-containing subunit and β representing a c-type cytochrome. Fluorescence and mass spectrometric analysis suggested that one FAD was covalently linked to Tyr394 of the α subunit. In contrast, the α′ subunit did not contain any FAD cofactor and is therefore considered to be catalytically inactive. The UV/visible spectrum was typical for a flavocytochrome with two heme c cofactors and one FAD cofactor. p-Cresol reduced the FAD but only one of the two heme cofactors. PCMH catalyzed both the hydroxylation of p-cresol to p-hydroxybenzyl alcohol and the subsequent oxidation of the latter to p-hydroxybenzaldehyde in the presence of artificial electron acceptors. The very low Km values (1.7 and 2.7 μM, respectively) suggest that the in vivo function of PCMH is to oxidize both p-cresol and p-hydroxybenzyl alcohol. The latter was a mixed inhibitor of p-cresol oxidation, with inhibition constants of a Kic (competitive inhibition) value of 18 ± 9 μM and a Kiu (uncompetitive inhibition) value of 235 ± 20 μM. A putative functional model for an unusual PCMH enzyme is presented. PMID:18658262

Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the N2 -fixing community depending on depth and agricultural use of soil.

PubMed

Calderoli, Priscila A; Collavino, Mónica M; Behrends Kraemer, Filipe; Morrás, Héctor J M; Aguilar, O Mario

2017-10-01

In this survey, a total of 80 787 reads and 28 171 unique NifH protein sequences were retrieved from soil RNA. This dataset extends our knowledge about the structure and diversity of the functional diazotrophic communities in agricultural soils from Argentinean Pampas. Operational taxonomic unit (OTU)-based analyses showed that nifH phylotypes related to Geobacter and Anaeromyxobacter (44.8%), Rhizobiales (29%), Cyanobacteria (16.7%), and Verrucomicrobiales (8%) are key microbial components of N 2 fixation in soils associated with no-till management and soil depth. In addition, quantification of nifH gene copies related to Geobacter and Cyanobacteria revealed that these groups are abundant in soils under maize-soybean rotation and soybean monoculture, respectively. The correlation of physicochemical soil parameters with the diazotrophic diversity and composition showed that soil stability and organic carbon might contribute to the functional signatures of particular nifH phylotypes in fields under no-till management. Because crop production relies on soil-borne microorganism's activities, such as free N 2 fixation, the information provided by our study on the diazotrophic population dynamics, associated with the edaphic properties and land-use practices, represents a major contribution to gain insight into soil biology, in which functionally active components are identified. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Formation of Light Absorbing Soluble Secondary Organics and Insoluble Polymeric Particles from the Dark Reaction of Catechol and Guaiacol with Fe(III).

PubMed

Slikboer, Samantha; Grandy, Lindsay; Blair, Sandra L; Nizkorodov, Sergey A; Smith, Richard W; Al-Abadleh, Hind A

2015-07-07

Transition metals such as iron are reactive components of environmentally relevant surfaces. Here, dark reaction of Fe(III) with catechol and guaiacol was investigated in an aqueous solution at pH 3 under experimental conditions that mimic reactions in the adsorbed phase of water. Using UV-vis spectroscopy, liquid chromatography, mass spectrometry, elemental analysis, dynamic light scattering, and electron microscopy techniques, we characterized the reactants, intermediates, and products as a function of reaction time. The reactions of Fe(III) with catechol and guaiacol produced significant changes in the optical spectra of the solutions due to the formation of light absorbing secondary organics and colloidal organic particles. The primary steps in the reaction mechanism were shown to include oxidation of catechol and guaiacol to hydroxy- and methoxy-quinones. The particles formed within a few minutes of reaction and grew to micron-size aggregates after half an hour reaction. The mass-normalized absorption coefficients of the particles were comparable to those of strongly absorbing brown carbon compounds produced by biomass burning. These results could account for new pathways that lead to atmospheric secondary organic aerosol formation and abiotic polymer formation on environmental surfaces mediated by transition metals.

Enhanced Production of Bioethanol by Fermentation of Autohydrolyzed and C4mimOAc-Treated Sugarcane Bagasse Employing Various Yeast Strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hashmi, Muzna; Shah, Aamer; Hameed, Abdul

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Our observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

Enhanced Production of Bioethanol by Fermentation of Autohydrolyzed and C4mimOAc-Treated Sugarcane Bagasse Employing Various Yeast Strains

DOE PAGES

Hashmi, Muzna; Shah, Aamer; Hameed, Abdul; ...

2017-08-01

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hgmore » via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Our observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.« less

[Study on anti-bacterium activity of ginkgolic acids and their momomers].

PubMed

Yang, Xiaoming; Zhu, Wei; Chen, Jun; Qian, Zhiyu; Xie, Jimin

2004-09-01

Ginkgolic acids and their three monomers were separated from ginkgo sarcotestas. The anti-bacterium activity of ginkgolic acids were tested. The relation between the anti-bacterium activity and side chain of ginkgolic acid were studied. The MIC of ginkgolic acids and their three monomers and salicylic acid were tested. Ginkgolic acid has strong inhibitive effect on G+-bacterium. Salicylic acid has no side chain, so no anti-bacterial activity. When the length of gingkolic acid side chain is C13:0, it has the strongest anti-bacterial activity in three monomers. The side chain of ginkgolic acid is the key functional group that possessed anti-bacterial activity. The length of Ginkgolic acid was the main effective factor of anti-bacterial activity.

Growth of a Strictly Anaerobic Bacterium on Furfural (2-Furaldehyde)

PubMed Central

Brune, Gerhard; Schoberth, Siegfried M.; Sahm, Hermann

1983-01-01

A strictly anaerobic bacterium was isolated from a continuous fermentor culture which converted the organic constituents of sulfite evaporator condensate to methane and carbon dioxide. Furfural is one of the major components of this condensate. This furfural isolate could degrade furfural as the sole source of carbon and energy in a defined mineral-vitamin-sulfate medium. Acetic acid was the major fermentation product. This organism could also use ethanol, lactate, pyruvate, or fumarate and contained cytochrome c3 and desulfoviridin. Except for furfural degradation, the characteristics of the furfural isolate were remarkably similar to those of the sulfate reducer Desulfovibrio gigas. The furfural isolate has been tentatively identified as Desulfovibrio sp. strain F-1. Images PMID:16346423

Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae.

PubMed

Podosokorskaya, Olga A; Kadnikov, Vitaly V; Gavrilov, Sergey N; Mardanov, Andrey V; Merkel, Alexander Y; Karnachuk, Olga V; Ravin, Nikolay V; Bonch-Osmolovskaya, Elizaveta A; Kublanov, Ilya V

2013-06-01

A novel moderately thermophilic, facultatively anaerobic chemoorganotrophic bacterium strain P3M-2(T) was isolated from a microbial mat developing on the wooden surface of a chute under the flow of hot water (46°C) coming out of a 2775-m-deep oil exploration well (Tomsk region, Russia). Strain P3M-2(T) is a moderate thermophile and facultative anaerobe growing on mono-, di- or polysaccharides by aerobic respiration, fermentation or by reducing diverse electron acceptors [nitrite, Fe(III), As(V)]. Its closest cultivated relative (90.8% rRNA gene sequence identity) is Ignavibacterium album, the only chemoorganotrophic member of the phylum Chlorobi. New genus and species Melioribacter roseus are proposed for isolate P3M-2(T) . Together with I. album, the new organism represents the class Ignavibacteria assigned to the phylum Chlorobi. The revealed group includes a variety of uncultured environmental clones, the 16S rRNA gene sequences of some of which have been previously attributed to the candidate division ZB1. Phylogenetic analysis of M. roseus and I. album based on their 23S rRNA and RecA sequences confirmed that these two organisms could represent an even deeper, phylum-level lineage. Hence, we propose a new phylum Ignavibacteriae within the Bacteroidetes-Chlorobi group with a sole class Ignavibacteria, two families Ignavibacteriaceae and Melioribacteraceae and two species I. album and M. roseus. This proposal correlates with chemotaxonomic data and phenotypic differences of both organisms from other cultured representatives of Chlorobi. The most essential differences, supported by the analyses of complete genomes of both organisms, are motility, facultatively anaerobic and obligately organotrophic mode of life, the absence of chlorosomes and the apparent inability to grow phototrophically. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Crystal structure of K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, an open-framework iron phosphite with mixed-valent Fe(II)/Fe(III) ions.

PubMed

Larrea, Edurne S; Mesa, José Luis; Legarra, Estibaliz; Aguayo, Andrés Tomás; Arriortua, Maria Isabel

2016-01-01

Single crystals of the title compound, potassium hexa-phosphito-penta-ferrate(II,III) hemihydrate, K0.75[Fe(II) 3.75Fe(III) 1.25(HPO3)6]·0.5H2O, were grown under mild hydro-thermal conditions. The crystal structure is isotypic with Li1.43[Fe(II) 4.43Fe(III) 0.57(HPO3)6]·1.5H2O and (NH4)2[Fe(II) 5(HPO3)6] and exhibits a [Fe(II) 3.75Fe(III) 1.25(HPO3)6](0.75-) open framework with disordered K(+) (occupancy 3/4) as counter-cations. The anionic framework is based on (001) sheets of two [FeO6] octa-hedra (one with point group symmetry 3.. and one with point group symmetry .2.) linked along [001] through [HPO3](2-) oxoanions. Each sheet is constructed from 12-membered rings of edge-sharing [FeO6] octa-hedra, giving rise to channels with a radius of ca 3.1 Å where the K(+) cations and likewise disordered water mol-ecules (occupancy 1/4) are located. O⋯O contacts between the water mol-ecule and framework O atoms of 2.864 (5) Å indicate hydrogen-bonding inter-actions of medium strength. The infrared spectrum of the compound shows vibrational bands typical for phosphite and water groups. The Mössbauer spectrum is in accordance with the presence of Fe(II) and Fe(III) ions.

Enhanced biosynthesis of dihydrodaidzein and dihydrogenistein by a newly isolated bovine rumen anaerobic bacterium.

PubMed

Wang, Xiu-Ling; Shin, Kwang-Hee; Hur, Hor-Gil; Kim, Su-Il

2005-02-09

A rod-shaped and Gram-positive anaerobic bacterium, named Niu-O16, which was isolated from bovine rumen contents, was found to be capable of anaerobically converting isoflavones daidzein and genistein to dihydrodaidzein (DHD) and dihydrogenistein (DHG), respectively. The metabolites DHD and DHG were identified using EI-MS and NMR spectrometric analyses. Stereoisomeric metabolites, which were separated on chiral stationary phase HPLC, were formed in equal amounts by the strain Niu-O16. Tautomerization reaction occurred on the B-ring of DHD and DHG seems to be attributed to the equal production of stereoisomeric metabolites. For the synthesis of DHD, the strain Niu-O16 showed an optimal pH range from 6.0 to 7.0 and completely reduced up to 800 microM of daidzein to DHD with the initial OD600nm=1.0 and pH 7.0 for 3 days incubation. The strain Niu-O16, showed relatively faster reduction activity toward daidzein to produce DHD than the previously isolated human intestinal bacterium Clostridium sp. HGH6.

Beta-resorcylic acid reduces Campylobacter jejuni in post-harvest poultry

USDA-ARS?s Scientific Manuscript database

Human Campylobacter infections, a leading food borne illnesses globally, has been linked with high prevalence of this bacterium in retail chicken meat. Reduction of Campylobacter in poultry will greatly reduce the risk of this disease. Unfortunately, strategies employed to reduce Campylobacter in li...

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

PubMed Central

Zhou, Aifen; Lau, Rebecca; Baran, Richard; Ma, Jincai; von Netzer, Frederick; Shi, Weiling; Gorman-Lewis, Drew; Kempher, Megan L.; He, Zhili; Qin, Yujia; Shi, Zhou; Zane, Grant M.; Wu, Liyou; Bowen, Benjamin P.; Northen, Trent R.; Hillesland, Kristina L.; Stahl, David A.; Wall, Judy D.; Arkin, Adam P.

2017-01-01

ABSTRACT Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. PMID:29138306

Synthesis, magnetic, spectral, and antimicrobial studies of Cu(II), Ni(II) Co(II), Fe(III), and UO 2(II) complexes of a new Schiff base hydrazone derived from 7-chloro-4-hydrazinoquinoline

NASA Astrophysics Data System (ADS)

El-Behery, Mostafa; El-Twigry, Haifaa

2007-01-01

A new hydrazone ligand, HL, was prepared by the reaction of 7-chloro-4-hydrazinoquinoline with o-hydroxybenzaldehyde. The ligand behaves as monoprotic bidentate. This was accounted for as the ligand contains a phenolic group and its hydrogen atom is reluctant to be replaced by a metal ion. The ligand reacted with Cu(II), Ni(II), Co(II), Fe(III), and UO 2(II) ions to yield mononuclear complexes. In the case of Fe(III) ion two complexes, mono- and binuclear complexes, were obtained in the absence and presence of LiOH, respectively. Also, mixed ligand complexes were obtained from the reaction of the metal cations Cu(II), Ni(II) and Fe(III) with the ligand (HL) and 8-hydroxyquinoline (8-OHqu) in the presence of LiOH, in the molar ratio 1:1:1:1. It is clear that 8-OHqu behaves as monoprotic bidentate ligand in such mixed ligand complexes. The ligand, HL, and its metal complexes were characterized by elemental analyses, IR, UV-vis, mass, and 1H NMR spectra, as well as magnetic moment, conductance measurements, and thermal analyses. All complexes have octahedral configurations except Cu(II) complex which has an extra square-planar geometry, while Ni(II) mixed complex has also formed a tetrahedral configuration and UO 2(II) complex which formed a favorable pentagonal biprymidial geometry. Magnetic moment of the binuclear Fe(III) complex is quite low compared to calculated value for two iron ions complex and thus shows antiferromagnetic interactions between the two adjacent ferric ions. The HL and metal complexes were tested against one stain Gram positive bacteria ( Staphylococcus aureus), Gram negative bacteria ( Escherichia coli), and fungi ( Candida albicans). The tested compounds exhibited higher antibacterial acivities.

Development of a C3-symmetric benzohydroxamate tripod: Trimetallic complexation with Fe(III), Cr(III) and Al(III)

NASA Astrophysics Data System (ADS)

Baral, Minati; Gupta, Amit; Kanungo, B. K.

2016-06-01

The design, synthesis and physicochemical characterization of a C3-symmetry Benzene-1,3,5-tricarbonylhydroxamate tripod, noted here as BTHA, are described. The chelator was built from a benzene as an anchor, symmetrically extended by three hydroxamate as ligating moieties, each bearing O, O donor sites. A combination of absorption spectrophotometry, potentiometry and theoretical investigations are used to explore the complexation behavior of the ligand with some trivalent metal ions: Fe(III), Cr(III), and Al(III). Three protonation constants were calculated for the ligand in a pH range of 2-11 in a highly aqueous medium (9:1 H2O: DMSO). A high rigidity in the molecular structure restricts the formation of 1:1 (M/L) metal encapsulation but shows a high binding efficiency for a 3:1 metal ligand stoichiometry giving formation constant (in β unit) 28.73, 26.13 and 19.69 for [M3L]; Mdbnd Fe(III), Al(III) and Cr(III) respectively, and may be considered as an efficient Fe-carrier. The spectrophotometric study reveals of interesting electronic transitions occurred during the complexation. BTHA exhibits a peak at 238 nm in acidic pH and with the increase of pH, a new peak appeared at 270 nm. A substantial shifting in both of the peaks in presence of the metal ions implicates a s coordination between ligand and metal ions. Moreover, complexation of BTHA with iron shows three distinct colors, violet, reddish orange and yellow in different pH, enables the ligand to be considered for the use as colorimetric sensor.

The formation of light absorbing insoluble organic compounds from the reaction of biomass burning precursors and Fe(III)

NASA Astrophysics Data System (ADS)

Lavi, Avi; Lin, Peng; Bhaduri, Bhaskar; Laskin, Alexander; Rudich, Yinon

2017-04-01

Dust particles and volatile organic compounds from fuel or biomass burning are two major components that affect air quality in urban polluted areas. We characterized the products from the reaction of soluble Fe(III), a reactive transition metal originating from dust particles dissolution processes, with phenolic compounds , namely, guaiacol, syringol, catechol, o- and p- cresol that are known products of incomplete fuel and biomass combustion but also from other natural sources such as humic compounds degradation. We found that under acidic conditions comparable to those expected on a dust particle surface, phenolic compounds readily react with dissolved Fe(III), leading to the formation of insoluble polymeric compounds. We characterized the insoluble products by x-ray photoelectron microscopy, UV-Vis spectroscopy, mass spectrometry, elemental analysis and thermo-gravimetric analysis. We found that the major chromophores formed are oligomers (from dimers to pentamers) of the reaction precursors that efficiently absorb light between 300nm and 500nm. High variability of the mass absorption coefficient of the reaction products was observed with catechol and guaiacol showing high absorption at the 300-500nm range that is comparable to that of brown carbon (BrC) from biomass burning studies. The studied reaction is a potential source for the in-situ production of secondary BrC material under dark conditions. Our results suggest a reaction path for the formation of bio-available iron in coastal polluted areas where dust particles mix with biomass burning pollution plumes. Such mixing can occur, for instance in the coast of West Africa or North Africa during dust and biomass burning seasons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Tao; Kukkadapu, Ravi K.; Griffin, Aron M.

Fe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies of microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area goethite. Cryogenic (12K) 57Fe Mössbauermore » spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II)-phyllosilicate) in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl22H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicatesilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26-87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe

Spectroscopic studies of Fe(III) ion-exchanged ETS-10 and ETAS-10 molecular sieves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sommerfeld, D.A.; Ellis, W.R. Jr.; Eyring, E.M.

1992-11-26

Two new titanium silicate molecular sieves, designated ETS-10 and ETAS-10, have been ion-exchanged with Fe(III). Both products exhibit prominent EPR signals, at g = 6.0 and 4.3, that are assigned to populations of ferric iron on the surface and in the interior cavities, respectively, of the molecular sieve microcrystals. Corollary XPS measurements on these samples indicate that a substantial fraction of the surface iron is present as Fe(II). Chemical modification procedures have been explored in an effort to produce ion-exchanged materials containing no exterior iron. Acid treatment (pH 1.0) proved to be an effective means of achieving this goal inmore » the case of ETS-10-based materials. ETAS-10-based samples do not retain their crystallinity under these conditions. 35 refs., 4 figs., 2 tabs.« less

Synthesis, characterization and physicochemical studies of new chelating resin 1, 8-(3, 6-dithiaoctyl)-4-polyvinylbenzenesulphonate (dpvbs) and its metallopolymer Cu(II), Ni(II), Co(II) and Fe(III) complexes

NASA Astrophysics Data System (ADS)

Khalil, Tarek E.; Elbadawy, Hemmat A.; El-Dissouky, Ali

2018-02-01

A new chelating resin, 1,8-(3,6-dithiaoctyl)-4-polyvinylbenzenesulphonate (dpvbs) has been synthesized by coupling Amberlite XAD-16 with (2,2‧-ethylenedithio) diethanol using pyridine/CH2Cl2 mixture as a solvent. The chelating resin and its metallopolymer Cu(II), Ni(II), Co(II) and Fe(III) complexes have been synthesized and characterized by EDS, SEM, XPS, elemental analysis, spectral (IR, UV/Vis, EPR). The thermal analysis of the resin and its metallopolymer complexes indicated an endothermic spontaneous sorption mechanism with the liberation of water of hydration of the metal ions and that adsorbed by the free resin. At the solid liquid interface, the degrees of freedom increased during the sorption of the metal ions onto the resin. The surface area of polymer support and its metallopolymer complexes are estimated by (BJH) method. The batch equilibrium method was used for studying the metal sorption and selectivity at different pH values and different contact times at room temperature. ICP-AES was used to estimate the metal capacity of the resin for sorption of Cu(II), Ni(II), Co(II) and Fe(III) from aqueous solutions utilizing the batch equilibrium method. The sorption tendency of the metal ions by the resin was found to be: Cu(II) > Fe(III) > Co(II) > Ni(II). Adsorption kinetics was found to be fit the pseudo-second order model.

Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

PubMed Central

Hoffman, Michele T.; Gunatilaka, Malkanthi K.; Wijeratne, Kithsiri; Gunatilaka, Leslie; Arnold, A. Elizabeth

2013-01-01

Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA), often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria) have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales), but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales). Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions. PMID:24086270

Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring.

PubMed

Baena, Sandra; Perdomo, Natalia; Carvajal, Catalina; Díaz, Carolina; Patel, Bharat K C

2011-04-01

A thermophilic, sulfate-reducing bacterium, designated strain USBA-053(T), was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45' 33.29″ N 73° 6' 49.89″ W), Colombia. Cells of strain USBA-053(T) were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H(2) as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO(2) and H(2)S. Strain USBA-053(T) fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l(-1), with an optimum at 25 g l(-1) NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053(T) was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96(T) as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053(T) represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053(T) ( = KCTC 5670(T) = DSM 22027(T)).

The sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 as a model for understanding bacterial mercury methylation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilmour, C C; Elias, Dwayne A; Kucken, A M

2010-01-01

We propose the use of Desulfovibrio sp. ND132 as a model species for understanding the genetics and biochemistry of microbial Hg methylation. ND132 is a dissimilatory sulfate-reducing bacterium (DSRB) that exhibits exceptionally high rates of Hg methylation in culture, but is otherwise a characteristically typical Desulfovibrio strain. The full genome sequence of ND132 will be available soon. ND132 is very similar to other DSRB that are sequenced but do not methylate Hg, allowing comparison for potential methylation genes. Here, we describe the physiological characteristics of the strain, examine its MeHg production capability, and place the strain within the phylogeny ofmore » the Desulfovibrionales using 16S rRNA. We also examine Hg toxicity and the inducibility of MeHg production amongst the DSRB by comparing ND132 to non-methylating DSRB. The optimal growth medium for Hg methylation is pyruvate/fumarate, which supports strong respiratory growth without sulfide production. At moderate Hg concentrations (10 ng/ml), and using TiNTA as a reductant, ND132 methylates about 30% of added HgCl2 during batch culture growth on 40 mM pyruvate/fumarate. Under constant culture conditions, MeHg production is an exponential function of Hg concentration, probably reflecting Hg partitioning between aqueous and solid phases. To help understand how Hg is taken up by this organism, we examined the influence of a variety of small thiol-bearing ligands, as well as select amino acids, on methylation by D. desulfuricans ND132. All thiol bearing ligands tested affected methylation in similar ways, suggesting that Hg uptake by ND132 is not associated with uptake of a specific amino acid. To identify enzymes for the methylation activity, a genetic approach is being pursued. Conjugation from E. coli donors works well that allows the generation of a transposon library of random ND132 mutants. These mutants will be screened for affects on mercury methylation.« less

Isolation and Genomic Characterization of ‘Desulfuromonas soudanensis WTL’, a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine

PubMed Central

Badalamenti, Jonathan P.; Summers, Zarath M.; Chan, Chi Ho; Gralnick, Jeffrey A.; Bond, Daniel R.

2016-01-01

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. ‘D. soudanensis’ contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of ‘D. soudanensis’ underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats. PMID:27445996

Garciella nitratireducens gen. nov., sp. nov., an anaerobic, thermophilic, nitrate- and thiosulfate-reducing bacterium isolated from an oilfield separator in the Gulf of Mexico.

PubMed

Miranda-Tello, Elizabeth; Fardeau, Marie-Laure; Sepúlveda, José; Fernández, Luis; Cayol, Jean-Luc; Thomas, Pierre; Ollivier, Bernard

2003-09-01

A novel Gram-positive, anaerobic and thermophilic bacterium, strain MET79(T), was isolated from an oil well located in the Gulf of Mexico. Cells were straight rods, motile by a subpolar flagellum. Spores were formed in old cultures. Inner gas vacuoles swelled the cells when exposed to air. The optimum growth conditions were 55 degrees C, pH 7.5 and 1 % NaCl. Yeast extract was required for growth. Strain MET79(T) fermented several sugars, some organic acids and Casamino acids. Glucose was fermented into lactate, acetate, butyrate, H(2) and CO(2). Strain MET79(T) reduced thiosulfate to hydrogen sulfide and nitrate to ammonium. The DNA G+C content was 30.9 mol%. The closest phylogenetic relative of strain MET79(T) was Caloranaerobacter azorensis (88.7 % 16S rDNA sequence similarity). As strain MET79(T) (=DSM 15102(T)=CIP 107615(T)) was physiologically and phylogenetically different from its closest relatives, it is assigned as the type strain of a novel species of a new genus, Garciella nitratireducens gen. nov., sp. nov.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dantas, Joana M.; Simões, Telma; Morgado, Leonor

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 conservedmore » 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.« less

Direct measurement of interaction forces between a single bacterium and a flat plate.

PubMed

Klein, Jonah D; Clapp, Aaron R; Dickinson, Richard B

2003-05-15

A technique for precisely measuring the equilibrium and viscous interaction forces between a single bacterium and a flat surface as functions of separation distance is described. A single-beam gradient optical trap was used to micromanipulate the bacterium against a flat surface while evanescent wave light scattering was used to measure separation distances. Calibrating the optical trap far from the surface allowed the trapped bacterium to be used as a force probe. Equilibrium force-distance profiles were determined by measuring the deflection of the cell from the center of the optical trap at various trap positions. Simultaneously, viscous forces were determined by measuring the relaxation time for the fluctuating bacterium. Absolute distances were determined using a best-fit approximation to the theoretical prediction for the hindered mobility of a diffusing sphere near a wall. Using this approach, forces in the range from 0.01 to 4 pN were measured at near-nanometer resolution between Staphylococcus aureus and glass that was bare or coated with adsorbed protein.

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments

NASA Astrophysics Data System (ADS)

Nixon, Sophie L.; Telling, Jon P.; Wadham, Jemma L.; Cockell, Charles S.

2017-03-01

Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent.

PubMed

Zeng, Xiang; Zhang, Zhao; Li, Xi; Zhang, Xiaobo; Cao, Junwei; Jebbar, Mohamed; Alain, Karine; Shao, Zongze

2015-02-01

A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter

STRUCTURE AND FUNCTION OF SUBSURFACE MICROBIAL COMMUNITIES AFFECTING RADIONUCLIDE TRANSPORT AND BIOIMMOBILIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joel E. Kostka; Lee Kerkhof; Kuk-Jeong Chin

2011-06-15

The objectives of this project were to: (1) isolate and characterize novel anaerobic prokaryotes from subsurface environments exposed to high levels of mixed contaminants (U(VI), nitrate, sulfate), (2) elucidate the diversity and distribution of metabolically active metal- and nitrate-reducing prokaryotes in subsurface sediments, and (3) determine the biotic and abiotic mechanisms linking electron transport processes (nitrate, Fe(III), and sulfate reduction) to radionuclide reduction and immobilization. Mechanisms of electron transport and U(VI) transformation were examined under near in situ conditions in sediment microcosms and in field investigations at the Oak Ridge Field Research Center (ORFRC), in Oak Ridge, Tennessee, where themore » subsurface is exposed to mixed contamination predominated by uranium and nitrate. A total of 20 publications (16 published or 'in press' and 4 in review), 10 invited talks, and 43 contributed seminars/ meeting presentations were completed during the past four years of the project. PI Kostka served on one proposal review panel each year for the U.S. DOE Office of Science during the four year project period. The PI leveraged funds from the state of Florida to purchase new instrumentation that aided the project. Support was also leveraged by the PI from the Joint Genome Institute in the form of two successful proposals for genome sequencing. Draft genomes are now available for two novel species isolated during our studies and 5 more genomes are in the pipeline. We effectively addressed each of the three project objectives and research highlights are provided. Task I - Isolation and characterization of novel anaerobes: (1) A wide range of pure cultures of metal-reducing bacteria, sulfate-reducing bacteria, and denitrifying bacteria (32 strains) were isolated from subsurface sediments of the Oak Ridge Field Research Center (ORFRC), where the subsurface is exposed to mixed contamination of uranium and nitrate. These isolates which

Photoinduced electron transfer between Fe(III) and adenosine triphosphate-BODIPY conjugates: Application to alkaline-phosphatase-linked immunoassay.

PubMed

Lin, Jia-Hui; Yang, Ya-Chun; Shih, Ya-Chen; Hung, Szu-Ying; Lu, Chi-Yu; Tseng, Wei-Lung

2016-03-15

Fluorescent boron dipyrromethene (BODIPY) analogs are often used as sensors for detecting various species because of their relatively high extinction coefficients, outstanding fluorescence quantum yields, photostability, and pH-independent fluorescence. However, there is little-to-no information in the literature that describes the use of BODIPY analogs for detecting alkaline phosphatase (ALP) activity and inhibition. This study discovered that the fluorescence of BODIPY-conjugated adenosine triphosphate (BODIPY-ATP) was quenched by Fe(III) ions through photoinduced electron transfer. The ALP-catalyzed hydrolysis of BODIPY-ATP resulted in the formation of BODIPY-adenosine and phosphate ions. The fluorescence of the generated BODIPY-adenosine was insensitive to the change in the concentration of Fe(III) ions. Thus, the Fe(III)-induced fluorescence quenching of BODIPY-ATP can be paired with its ALP-mediated dephosphorylation to design a turn-on fluorescence probe for ALP sensing. A method detection limit at a signal-to-noise ratio of 3 for ALP was estimated to be 0.02 units/L (~6 pM; 1 ng/mL). This probe was used for the screening of ALP inhibitors, including Na3VO4, imidazole, and arginine. Because ALP is widely used in enzyme-linked immunosorbent assays, the probe was coupled to an ALP-linked immunosorbent assay for the sensitive and selective detection of immunoglobulin G (IgG). The lowest detectable concentration for IgG in this system was 5 ng/mL. Compared with the use of 3,6-fluorescein diphosphate as a signal reporter in an ALP-linked immunosorbent assay, the proposed system provided comparable sensitivity, large linear range, and high stability over temperature and pH changes. Copyright © 2015 Elsevier B.V. All rights reserved.

Combination of a recombinant bacterium with organonitrile-degrading and biofilm-forming capability and a positively charged carrier for organonitriles removal.

PubMed

Li, Chunyan; Sun, Yueling; Yue, Zhenlei; Huang, Mingyan; Wang, Jinming; Chen, Xi; An, Xuejiao; Zang, Hailian; Li, Dapeng; Hou, Ning

2018-04-10

The immobilization of organonitrile-degrading bacteria via the addition of biofilm-forming bacteria represents a promising technology for the treatment of organonitrile-containing wastewater, but biofilm-forming bacteria simply mixed with degrading bacteria may reduce the biodegradation efficiency. Nitrile hydratase and amidase genes, which play critical roles in organonitriles degradation, were cloned and transformed into the biofilm-forming bacterium Bacillus subtilis N4 to construct a recombinant bacterium B. subtilis N4/pHTnha-ami. Modified polyethylene carriers with positive charge was applied to promote bacterial adherence and biofilm formation. The immobilized B. subtilis N4/pHTnha-ami was resistant to organonitriles loading shocks and could remove organic cyanide ion with a initial concentration of 392.6 mg/L for 24 h in a moving bed biofilm reactor. The imputed quorum-sensing signal and the high-throughput sequencing analysis of the biofilm indicated that B. subtilis N4/pHTnha-ami was successfully immobilized and became dominant. The successful application of the immobilized recombinant bacterium offers a novel strategy for the biodegradation of recalcitrant compounds. Copyright © 2018 Elsevier B.V. All rights reserved.

The construction of an engineered bacterium to remove cadmium from wastewater.

PubMed

Chang, S; Shu, H

2014-01-01

The removal of cadmium (Cd) from wastewater before it is released from factories is important for protecting human health. Although some researchers have developed engineered bacteria, the resistance of these engineered bacteria to Cd have not been improved. In this study, two key genes involved in glutathione synthesis (gshA and gshB), a serine acetyltransferase gene (cysE), a Thlaspi caerulescens phytochelatin synthase gene (TcPCS1), and a heavy metal ATPase gene (TcHMA3) were transformed into Escherichia coli BL21. The resistance of the engineered bacterium to Cd was significantly greater than that of the initial bacterium and the Cd accumulation in the engineered bacterium was much higher than in the initial bacterium. In addition, the Cd resistance of the bacteria harboring gshB, gshA, cysE, and TcPCS1 was higher than that of the bacteria harboring gshA, cysE, and TcPCS1. This finding demonstrated that gshB played an important role in glutathione synthesis and that the reaction catalyzed by glutathione synthase was the limiting step for producing phytochelatins. Furthermore, TcPCS1 had a greater specificity and a higher capacity for removing Cd than SpPCS1, and TcHMA3 not only played a role in T. caerulescens but also functioned in E. coli.

In vitro antiplasmodial activity of bacterium RJAUTHB 14 associated with marine sponge Haliclona Grant against Plasmodium falciparum.

PubMed

Jacob Inbaneson, Samuel; Ravikumar, Sundaram

2012-06-01

Malaria is the most important parasitic disease, leading to annual death of about one million people, and the Plasmodium falciparum develops resistance to well-established antimalarial drugs. The newest antiplasmodial drug from a marine microorganism helps in addressing this problem. In the present study, Haliclona Grant were collected and subjected for enumeration and isolation of associated bacteria. The count of bacterial isolates was maximum in November 2007 (18 × 10(4) colony-forming units (CFU) g(-1), and the average count was maximum during the monsoon season (117 × 10(3) CFU g(-1)). Thirty-three morphologically different bacterial isolates were isolated from Haliclona Grant, and the extracellular ethyl acetate extracts were screened for antiplasmodial activity against P. falciparum. The antiplasmodial activity of bacterium RJAUTHB 14 (11.98 μg[Symbol: see text]ml(-1)) is highly comparable with the positive control chloroquine (IC(50) 19.59 μg[Symbol: see text]ml(-1)), but the other 21 bacterial extracts showed an IC(50) value of more than 100 μg[Symbol: see text]ml(-1). Statistical analysis reveals that significant in vitro antiplasmodial activity (P < 0.05) was observed between the concentrations and time of exposure. The chemical injury to erythrocytes showed no morphological changes in erythrocytes by the ethyl acetate extract of bacterial isolates after 48 h of incubation. The in vitro antiplasmodial activity might be due to the presence of reducing sugars and alkaloids in the ethyl acetate extracts of bacterium RJAUTHB 14. The 16S rRNA gene partial sequence of bacterium RJAUTHB 14 is deposited in NCBI (GenBank accession no. GU269569). It is concluded from the present study that the ethyl acetate extracts of bacterium RJAUTHB 14 possess lead compounds for the development of antiplasmodial drugs.

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena

PubMed Central

Sun, Jinchun; Jin, Jinshan; Beger, Richard D.; Cerniglia, Carl E.; Yang, Maocheng; Chen, Huizhong

2017-01-01

The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the argininenitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine. PMID:27480511

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena.

PubMed

Sun, Jinchun; Jin, Jinshan; Beger, Richard D; Cerniglia, Carl E; Yang, Maocheng; Chen, Huizhong

2016-10-01

The association between exposure to smokeless tobacco products (STP) and oral diseases is partially due to the physiological and pathological changes in the composition of the oral microbiome and its metabolic profile. However, it is not clear how STPs affect the physiology and ecology of oral microbiota. A UPLC/QTof-MS-based metabolomics study was employed to analyze metabolic alterations in oral bacterium, Capnocytophaga sputigena as a result of smokeless tobacco exposure and to assess the capability of the bacterium to metabolize nicotine. Pathway analysis of the metabolome profiles indicated that smokeless tobacco extracts caused oxidative stress in the bacterium. The metabolomics data also showed that the arginine-nitric oxide pathway was perturbed by the smokeless tobacco treatment. Results also showed that LC/MS was useful in identifying STP constituents and additives, including caffeine and many flavoring compounds. No significant changes in levels of nicotine and its major metabolites were found when C. sputigena was cultured in a nutrient rich medium, although hydroxylnicotine and cotinine N-oxide were detected in the bacterial metabolites suggesting that nicotine metabolism might be present as a minor degradation pathway in the bacterium. Study results provide new insights regarding the physiological and toxicological effects of smokeless tobacco on oral bacterium C. sputigena and associated oral health as well as measuring the ability of the oral bacterium to metabolize nicotine. Published by Elsevier Ltd.

Near-complete genome sequence of the cellulolytic Bacterium Bacteroides ( Pseudobacteroides) cellulosolvens ATCC 35603

DOE PAGES

Dassa, Bareket; Utturkar, Sagar M.; Hurt, Richard A.; ...

2015-09-24

We report the single-contig genome sequence of the anaerobic, mesophilic, cellulolytic bacterium, Bacteroides cellulosolvens. The bacterium produces a particularly elaborate cellulosome system, whereas the types of cohesin-dockerin interactions are opposite of other known cellulosome systems: cell-surface attachment is thus mediated via type-I interactions whereas enzymes are integrated via type-II interactions.

[A rarely isolated bacterium in microbiology laboratories: Streptococcus uberis].

PubMed

Eryıldız, Canan; Bukavaz, Şebnem; Gürcan, Şaban; Hatipoğlu, Osman

2017-04-01

Streptococcus uberis is a gram-positive bacterium that is mostly responsible for mastitis in cattle. The bacterium rarely has been associated with human infections. Conventional phenotyphic methods can be inadequate for the identification of S.uberis; and in microbiology laboratories S.uberis is confused with the other streptococci and enterococci isolates. Recently, molecular methods are recommended for the accurate identification of S.uberis isolates. The aim of this report is to present a lower respiratory tract infection case caused by S.uberis and the microbiological methods for identification of this bacterium. A 66-year-old male patient with squamous cell lung cancer who received radiotherapy was admitted in our hospital for the control. According to the chest X-Ray, patient was hospitalized with the prediagnosis of ''cavitary tumor, pulmonary abscess''. In the first day of the hospitalization, blood and sputum cultures were drawn. Blood culture was negative, however, Candida albicans was isolated in the sputum culture and it was estimated to be due to oral lesions. After two weeks from the hospitalization, sputum sample was taken from the patient since he had abnormal respiratory sounds and cough complaint. In the Gram stained smear of the sputum there were abundant leucocytes and gram-positive cocci, and S.uberis was isolated in both 5% sheep blood and chocolate agar media. Bacterial identification and antibiotic susceptibility tests were performed by VITEK 2 (Biomerieux, France) and also, the bacterium was identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) based VITEK MS system as S.uberis. The isolate was determined susceptible to ampicillin, erythromycin, clindamycin, levofloxacin, linezolid, penicillin, cefotaxime, ceftriaxone, tetracycline and vancomycin. 16S, 23S ribosomal RNA and 16S-23S intergenic spacer gene regions were amplified with specific primers and partial DNA sequence analysis of 16S

Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium †

PubMed Central

Little, C. Deane; Palumbo, Anthony V.; Herbes, Stephen E.; Lidstrom, Mary E.; Tyndall, Richard L.; Gilmer, Penny J.

1988-01-01

Trichloroethylene (TCE), a common groundwater contaminant, is a suspected carcinogen that is highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a type I methanotrophic bacterium, degraded TCE if grown on methane or methanol, producing CO2 and water-soluble products. Gas chromatography and 14C radiotracer techniques were used to determine the rate, methane dependence, and mechanism of TCE biodegradation. TCE biodegradation by strain 46-1 appears to be a cometabolic process that occurs when the organism is actively metabolizing a suitable growth substrate such as methane or methanol. It is proposed that TCE biodegradation by methanotrophs occurs by formation of TCE epoxide, which breaks down spontaneously in water to form dichloroacetic and glyoxylic acids and one-carbon products. Images PMID:16347616

Stoichiometry of mercury-thiol complexes on bacterial cell envelopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Bhoopesh; Shoenfelt, Elizabeth; Yu, Qiang

We have examined the speciation of Hg(II) complexed with intact cell suspensions (1013 cells L- 1) of Bacillus subtilis, a common gram-positive soil bacterium, Shewanella oneidensis MR-1, a facultative gram-negative aquatic organism, and Geobacter sulfurreducens, a gram-negative anaerobic bacterium capable of Hg-methylation at Hg(II) loadings spanning four orders of magnitude (120 nM to 350 μM) at pH 5.5 (± 0.2). The coordination environments of Hg on bacterial cells were analyzed using synchrotron based X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy at the Hg LIII edge. The abundance of thiols on intact cells wasmore » determined by a fluorescence-spectroscopy based method using a soluble bromobimane, monobromo(trimethylammonio)bimane (qBBr) to block thiol sites, and potentiometric titrations of biomass with and without qBBr treatment. The chemical forms of S on intact bacterial cells were determined using S k-edge XANES spectroscopy.« less

Desulfomicrobium thermophilum sp. nov., a novel thermophilic sulphate-reducing bacterium isolated from a terrestrial hot spring in Colombia.

PubMed

Thevenieau, France; Fardeau, Marie-Laure; Ollivier, Bernard; Joulian, Catherine; Baena, Sandra

2007-03-01

A moderately thermophilic, sulphate-reducing bacterium, designated strain P6-2(T), was isolated from a terrestrial hot spring located at a height of 2,500 m in the Andean region, Colombia (5 degrees 43'69''N, 73 degrees 6'10''W). Cells of strain P6-2(T) were rod-shaped, stained Gram-negative and were motile by means of a single polar flagellum. The strain grew lithotrophically with H(2) as the electron donor and organotrophically on lactate, pyruvate, ethanol, malate, fumarate, n-propanol and succinate in the presence of sulphate as the terminal electron acceptor. Fumarate and pyruvate was fermented. Strain P6-2(T) grew optimally at 55 degrees C (range 37-60 degrees C), pH 6.6 (range 5.8-8.8) in the presence of 0.5% NaCl (range 0-4.5%) with lactate and sulphate and produced acetate, CO(2) and H(2)S as the major end-products. Sulphate, sulphite and thiosulphate could be used as electron acceptors but not elemental sulphur or nitrate. The G + C content of the genomic DNA was 58.7 mol%. The 16S rRNA sequence analysis indicated that strain P6-2(T) was a member of the class Deltaproteobacteria, domain Bacteria with Desulfomicrobium baculatum being the closest relative (similarity value of 94%). Phylogeny of genes encoding alpha- and beta-subunits of the dissimilatory sulphite reductase (dsrAB genes) supported its affiliation to members of the genus Desulfomicrobium. On the basis of this evidence, we propose to assign strain P6-2(T) as new species of the genus Desulfomicrobium, D. thermophilum sp. nov., with strain P6-2(T) as the type strain (= DSM 16697(T) = CCUG 49732(T)).

Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings.

PubMed

Min, Ui-Gi; Kim, So-Jeong; Hong, Heeji; Kim, Song-Gun; Gwak, Joo-Han; Jung, Man-Young; Kim, Jong-Geol; Na, Jeong-Geol; Rhee, Sung-Keun

2016-06-01

A strictly anaerobic bacterium, strain B5(T), was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5(T) were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5-7.5 and 25-45°C, respectively. Growth of strain B5(T) was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0-4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5(T) grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone-2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5(T) did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5(T) is most closely related to the genus Tepidibacillus (T. fermentans STGH(T); 96.3%) and Vulcanibacillus (V. modesticaldus BR(T); 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5(T) was higher than those of T. fermentans STGH(T) (34.8 mol%) and V. modesticaldus BR(T) (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5(T) (=KCTC 15397(T) =JCM 19989(T)), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

Draft Genome Sequence of the Cellulolytic Bacterium Clostridium papyrosolvens C7 (ATCC 700395).