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1	Electron transfer in multiheme cytochromes of Shewanella oneidensis MR-1: CymA and the dissimilatory metal reduction pathway Sherwood, Mackenzie A. Firer January 2012 (has links) Thesis (Ph.D.)--Boston University / PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / Shewanella oneidensis is a facultative, gram-negative microbe that, in the absence of oxygen, can use a wide variety of terminal electron acceptors including iron, manganese, uranium, nitrite, nitrate, sulfate, fumarate, and DMSO. The anaerobic versatility is believed to be the result of a highly branched electron transfer pathway involving many redox-active proteins. Shewanella is capable of dissimilatory metal reduction (DMR) of insoluble iron and manganese oxides, in which electrons are transferred from the cell's interior to its exterior. Several multiheme c -type cytochromes comprise a pathway for this electron transfer. These cytochromes, specifically the tetraheme protein, CymA, and the decaheme protein, MtrA, are the primary focus of this thesis. The current model of electron transfer indicates that electrons originate in the cytoplasmic membrane from the menaquinol pool, and are transferred into the periplasm by CymA. From here the pathway branches and electrons are transferred into several potential periplasmic targets, including MtrA. MtrA may then transfer electrons directly or indirectly to MtrC and OmcA, which have been shown to reduce exogenous electron acceptors such as iron oxides. Recently, it has been suggested that MtrA and MtrC dock with 13-barrel protein, MtrB and transfer electrons through the porin sheath. Here, the DMR pathway has been studied with respect to four aims: (1) purification and characterization of the multiheme cytochromes through the use of non-catalytic protein film voltammetry (PFV), (2) structural analysis of MtrA by small angle X-ray scattering (SAXS), (3) investigation of protein-protein interactions via catalytic PFV and anaerobic affinity chromatography, and (4) exploration of heme cofactor function within the tetraheme cytochrome, CymA and MtrA by characterizing heme knockout mutants of the two proteins. We demonstrate that these proteins interact to form an electron transfer pathway from the cytoplasm to terminal electron acceptors on the outside of the cell through a "wire" of heme cofactors. Additionally, the data support the model that MtrA can span a large portion of the peri plasmic space to act as an intermediary by accepting electrons from CymA and subsequently docking with MtrB to transfer electrons to MtrC. / 2031-01-02 Shewanella oneidensis Dissimilatory metal reduction
2	Role of microbial manganese respiration in the anaerobic cycling of nitrogen Szeinbaum, Nadia Heliana 08 June 2015 (has links) Despite the environmental significance of microbial manganese reduction, the molecular mechanism of microbial manganese respiration remains poorly understood. Soluble Mn(III) has been recently found to be a dominant soluble species in aquatic systems, yet little is known about the identity of microbial populations catalyzing Mn(III) reduction in the environment nor the molecular mechanism of Mn(III) respiration. In this research, a suite of Mn(III) reduction-deficient mutant strains were isolated, including Mn(III) reduction-deficient mutant strain Mn3-1 that also displayed the ability to reduce soluble organic-Fe(III), but not solid Fe(III) oxides, demonstrating for the first time that the reduction of soluble organic-Fe(III) and solid Fe(III) oxides proceed through electron transport pathways with at least one distinct component. This work also shows that the electron transport pathway for Mn(III) reduction in S. oneidensis shares many of the electron transport components of Fe(III) and Mn(IV) reduction pathways and that Mn(IV) reduction to Mn(II) proceeds step-wise through two one-electron transfer reactions with Mn(III) as a transient intermediate. Finally, sediment incubations were carried out to enrich for NH4+ oxidizing- Mn(III) reducing consortia. The Mn(III) reducing consortium was found to be dominated by an electrogenic Ochrobactrum sp. and a Shewanella sp. The isolated Shewanella strain is able to oxidize acetate with Mn(III) as electron acceptor, an activity never observed before in a metal-reducing member of the Shewanella genus. Shewanella Metal reduction Manganese Anaerobic ammonium oxidation
3	Bacterial iron and manganese reduction driven by organic sulfur electron shuttles Cooper, Rebecca Elizabeth 27 May 2016 (has links) Dissimilatory metal-reducing bacteria (DMRB) play an important role in the biogeochemical cycling of metals. DMRB are unique in that they possess the ability to couple metal reduction with their metabolism. Microbial Fe(III) respiration is a central component of a variety of environmentally important processes, including the biogeochemical cycling of iron and carbon in redox stratified water and sediments, the bioremediation of radionuclide-contaminated water, the degradation of toxic hazardous pollutants, and the generation of electricity in microbial fuel cells. Despite this environmental and evolutionary importance, the molecular mechanism of microbial Fe(III) respiration is poorly understood. Current models of the molecular mechanism of microbial metal respiration are based on direct enzymatic, Fe(III) solubilization, and electron shuttling pathways. Fe(III) oxides are solid at circumneutral pH and therefore unable to come into direct contact with the microbial inner membrane, these bacteria must utilize an alternative strategy for iron reduction. Reduced organic compounds such as thiols are prominent in natural environments where DMRB are found. These thiol compounds are redox reactive and are capable of abiotically reducing Fe(III) oxides at high rates S. oneidensis wild-type and ΔluxS anaerobic biofilm formation phenotypes were examined under a variety of electron donor-electron acceptor pairs, including lactate or formate as the electron donor and fumarate, thiosulfate, or Fe(III) oxide-coated silica surfaces as the terminal electron acceptor. The rates of biofilm formation under the aforementioned growth conditions as well as in the presence of exogenous thiol compounds indicate that ∆luxS formed biofilms at rates only 5-10% of the wild-type strain and ∆luxS biofilm formation rates were restored to wild-type levels by addition of a variety of exogenous compounds including cysteine, glutathione, homocysteine, methionine, serine, and homoserine. Cell adsorption isotherm analyses results indicate that wild-type is can attach to the surface of hematite particles attachment , but ΔluxS is unable to attach the hematite surfaces. These results indicate that biofilm formation is not required for Fe(III) oxide reduction by S. oneidensis ∆luxS anaerobic biofilm formation rates were restored to wild-type levels by addition of exogenous auntoinducer-2 (AI-2), a by-product of homocysteine production in the Activated Methyl Cycle. This discovery led to subsequent experiments performed to detect the production and utilization of AI-2 by wild-type and ∆luxS strains under aerobic and anaerobic conditions. AI-2 production experiments showed wild-type, but not ΔluxS, was capable of producing AI-2. The addition of exogenous S. oneidensis and Vibrio harveyi-produced AI-2 to wild-type and ∆luxS resulted in the swift depletion of AI-2 from the media. These results provide evidence that S. oneidensis can produce AI-2 and subsequently utilize its’ own AI-2 as well as AI-2 produced by other bacteria as a carbon and electron source in the absence of preferred carbon sources. S. oneidensis produces and secretes a suite of extracellular thiols under anaerobic Fe(III)-reducing and Mn(III) and Mn(IV)-reducing conditions including cysteine, homocysteine, glutathione, and cyteamine. Exogenous thiols produced by S. oneidensis are intermediates of the Activated Methyl Cycle (AMC) and Transulfurylation Pathway (TSP). Reduced and oxidized thiols were detected, indicating that the thiols are in a constant state of flux between the reduced and oxidized forms and that the concentration of reduced thiols to its’ oxidized counterpart is indicative of the state of metal reduction by the microorganisms. Respiratory phenotypes Based on Fe(III) and Mn(IV) respiratory phenotypes observed in the AMC and TSP pathway mutants (∆luxS, ∆metB, ∆metC and ∆metY) we can infer that cysteine, glutathione, and cysteamine contribute to metal reduction by serving as efficient electron shuttling molecules, while homocysteine is critical for maintenance of the AMC, propagation of thiol biosynthesis, and maintenance of cellular metabolism via the AMC intermediate SAM. Furthermore, these findings suggest that all metal-reducing bacteria require thiol formation to reduce solid metal oxides. Direct contact mechanism is not the dominant means through electrons are transferred and metals are reduced, instead electron shuttles are the maid reduction mechanism. Shewanella oneidensis Metal reduction Organic sulfur Electron shuttles
4	Molecular mechanisms of microbial iron respiration by Shewanella oneidensis MR-1 Burns, Justin Lee 05 April 2010 (has links) Metal-respiring bacteria occupy a central position in a variety of environmentally important processes including the biogeochemical cycling of metals and carbon, biocorrosion of steel surfaces, bioremediation of radionuclide-contaminated aquifers, and electricity generation in microbial fuel cells. Metal-respiring bacteria are presented, however, with a unique physiological challenge: they are required to respire anaerobically on electron acceptors (e.g., Fe(III) oxides, elemental sulfur) that are highly insoluble at circumneutral pH and unable to enter the cell and contact inner membrane-localized respiratory systems. To overcome these physiological problems, metal-respiring bacteria are postulated to employ a variety of novel respiratory strategies not found in other bacteria, including 1) direct enzymatic reduction at the cell surface, 2) electron shuttling between the cell and metal surfaces, and 3) metal solubilization by bacterially-produced organic ligands followed by respiration of the soluble organic-metal complexes. This work highlights my latest findings on the genetic and enzymatic mechanism of metal respiration by Shewanella oneidensis, a facultative anaerobe ubiquitous to redox-stratified natural waters and sediments. Metal reduction Iron Metal respiration Shewanella Microbial respiration
5	The geomicrobiology of cementitious radioactive waste Williamson, Adam John January 2014 (has links) It is government policy that the UK’s intermediate level radioactive wastes (ILW) will be disposed of in a deep geological disposal facility (GDF), where cementitious materials will be ubiquitous. After ILW disposal, groundwater ingress through the engineered facility is expected, forming a hyperalkaline plume from the cementitious materials into the surrounding host rock. This will form a persistent, high pH, “chemically disturbed zone” over timescales of 105 - 106 years, that will evolve from pH >13 to pH 10 over time. In the deep subsurface, microbial processes, particularly metal reduction may immobilise redox active radioactive contaminants in the waste, yet these reactions remain poorly characterised under these extreme conditions. In this project, microbiologically-mediated Fe(III) reduction was explored under alkaline conditions in sediment from a lime workings site in Buxton, UK, as an analogue for an ILW impacted subsurface environment. In addition, the impact of these processes on radionuclide (U, Tc and Np) behaviour was considered. Microcosms were set up using sediments taken from the site, adjusted to pH 10, augmented with electron donor (organic acids with yeast extract) and Fe(III), U(VI), Tc(VII) or Np(V) as electron acceptors. Biogeochemical processes were monitored using geochemistry, microbial ecology and X-ray absorption spectroscopy (XAS) techniques. A cascade of microbial reduction processes occurred at pH 10 – 10.5 in all microbially active systems. In Fe(III) enriched systems, the dominant post-reduction mineral phase was magnetite and the rate and extent of Fe(III) reduction was increased in the presence of extracellular (AQDS, Aldrich humic acid) and endogenous (riboflavin) electron shuttles. In U(VI) supplemented sediment systems, partial U(VI) reduction occurred to a non-uraninite phase, which was susceptible to reoxidation by air (O2) and nitrate. By contrast, in Fe(III)-augmented microcosms, more complete U removal to solids was noted, with uraninite identified as the end product, which was also reoxidised by air (O2) and nitrate. In these experiments there was, however, evidence to suggest that uranium was associated with the reoxidised Fe(III) mineral. In Tc supplemented microcosm experiments, complete Tc(VII) reduction occurred in systems with and without added Fe(III). In the microcosms with no added Fe(III) however, only partial Tc removal from solution occurred, despite evidence for complete reduction, suggesting that soluble or colloidal Tc(IV) may be present. Moderate Tc reoxidation occurred with air (O2) in both systems with and without added Fe(III) however no Tc remobilisation occurred during reoxidation with added nitrate. XAS on Fe(III) enriched sediments that had been microbially reduced and then re-oxidised by air, indicated that Tc may be associated with the reoxidised Fe mineral phase in these experiments. In the Np experiments, significant Np(V) sorption to sediments with and without added Fe(III) occurred initially, followed by Np(V) bioreduction to Np(IV). In all experiments, microbial (16S rRNA gene) profiling suggested a role for novel Gram-positive bacteria in Fe(III) and radionuclide reduction. These results highlight the significance of microorganisms on radionuclide biogeochemistry at high pH and have implications for the safe disposal of intermediate level nuclear wastes. 551.9
6	Reduction of selenium by Pseudomonas Stutzeri NT-l; Growth reduction and kinetics Wessels, Charlotte Elize January 2017 (has links) Bioremediation of seleniferous water is gaining more momentum, especially when it comes to bacterial reduction of the selenium oxyanions. More and more bacterial strains that are able to reduce selenium are being isolated. These bacteria need to be studied further to determine whether they are suited for industrial application. In this study, the reduction of Se(VI) to Se(0) by Pseudomonas stutzeri NT-I was examined using batch experiments with the bacteria suspended in MSM. For the determination of the optimum conditions for the growth of the bacteria, the linearized rate during the exponential phase for different conditions were compared. A pH of 7, temperature of 37 ⁰C, salinity of 20 g.L-1 NaCl and initial concentration of 5 mM selenate were found to be the best at promoting growth. To determine the optimum conditions for the reduction of selenium, the amount of Se(0) recovered from the plug after 16 hours of incubation was measured. A pH of 8, temperature of 37 ⁰C and salinity of 5 g.L-1 resulted in the most Se(0) recovered. The kinetics of the reduction of Se(VI) to Se(0) was found to follow the adapted Monod equation. An increase in the initial Se(VI) concentration positively affected the reduction rate indicating that substrate saturation had not yet been reached. One kmax could be fitted to each of the two reactions but not one Ks. It was found that Ks decreased with increasing initial selenate concentration. Visually it can be deduced that inhibition starts playing a role in the reduction of selenate at a concentration of 4 mM. Pseudomonas stutzeri NT-I is an exemplary selenium reducing agent and deserves more attention, not only for industrial application but also in the research world, for further understanding of the complex mechanism behind metal reduction in bacteria. / Dissertation (MEng)--University of Pretoria, 2017. / Chemical Engineering / MEng / Unrestricted Pseudomonas stutzeri NT-I Reduction kinetics Metal reduction Bacterial growth UCTD
7	An Investigation Correlating Bioluminescence and Metal Ruduction Utilizing <i>Shewanella woodyi</i> Theberge, Allison Lindsey 30 May 2019 (has links) No description available. Chemistry Microbiology Shewanella woodyi extracellular electron transfer EET microbial metal reduction microbial electrochemical systems bioluminescence
8	Anoxygenic photosynthetic communities and heavy element transformations in extreme environments: hydrothermal and hypersaline ecosystems Csotonyi, Julius Thomas 20 January 2011 (has links) The current research project investigated the anoxygenic phototrophic and metal(loid) transforming bacteria of hypersaline and deep ocean hydrothermal environments. The East German Creek brine springs, an unusual flowing hypersaline system, was enumerated using classical techniques. Subterranean sulfide supported purple sulfur and nonsulfur bacteria, but at the highly oxygenated surface, aerobic anoxygenic phototrophs (AAP) were numerically dominant (up to 16-36% of cultivable bacteria). Strains (EG8, EG13, EG17, EG19) with unusual phylogenetic affiliation and novel photosynthetic and metal(loid) reducing traits were described taxonomically. Chromocurvus halotolerans gen. nov., sp. nov. was proposed as a second example of a gammaproteobacterial AAP. It exhibited bent rod-shaped cells, unusual among AAP. Facultatively anaerobic Charonomicrobium ambiphototrophicum gen. nov., sp. nov. was capable of both aerobic and anaerobic anoxygenic photosynthesis, and incapable of photoautotrophy, distinguishing it from both AAP and purple nonsulfur bacteria. Roseovarius vanadiphilum sp. nov. surprisingly produced 4.5 times more biomass and 2 times more bacteriochlorophyll (BChl) at extremely high NaVO3 concentration (7.5 g/l) than in metal-free medium. A second novel metabolic mode, anaerobic respiration on the toxic metalloid tellurate, was described for a relative of non-phototrophic Shewanella frigidimarina (ER-Te-48), from deep ocean hydrothermal vent Paralvinella worms at Explorer Ridge in the Pacific Ocean. Other strains respired on SeO32- (ER-Se-17L), VO3- (ER-V-6), and VO43- (AV-V-25). These organisms provided the first examples of anaerobic respiration on Te, Se and V at hydrothermal vents. High level resistance of AAP to metal(loid)s prompted investigation of the influence of TeO32- on photosynthetic pigment production in species including Erythromicrobium ramosum (from a terrestrial hydrothermal system) and Erythrobacter litoralis (from a hypersaline supralittoral system). Tellurite enhanced photosynthetic pigment production up to 3.4 times, consistent with an antioxidant carotenoid-based defense mechanism. However, in E. litoralis BChl precursors such as Mg protoporphyrin or its monomethyl ester also accumulated, indicating biosynthetic pathway interruption. In hydrothermal and hypersaline ecosystems, largely devoid of eukaryotic phototrophs but often enriched in metal(loid)s, AAP and metal(loid) reducers are key modulators of nutrient and toxin availability. The presented results on their ecology, physiology and biochemistry have important implications for theoretical understanding of extreme environments and hold potential for biotechnological applications. extreme environments aerobic anoxygenic phototrophs microbial photosynthesis bacteriochlorophyll carotenoids microbial ecology hypersaline springs hydrothermal vents tellurium microbial metal reduction bioremediation microbial mats purple nonsulfur bacteria selenite metavanadate Roseovarius tellurite metalloids
9	Anoxygenic photosynthetic communities and heavy element transformations in extreme environments: hydrothermal and hypersaline ecosystems Csotonyi, Julius Thomas 20 January 2011 (has links) The current research project investigated the anoxygenic phototrophic and metal(loid) transforming bacteria of hypersaline and deep ocean hydrothermal environments. The East German Creek brine springs, an unusual flowing hypersaline system, was enumerated using classical techniques. Subterranean sulfide supported purple sulfur and nonsulfur bacteria, but at the highly oxygenated surface, aerobic anoxygenic phototrophs (AAP) were numerically dominant (up to 16-36% of cultivable bacteria). Strains (EG8, EG13, EG17, EG19) with unusual phylogenetic affiliation and novel photosynthetic and metal(loid) reducing traits were described taxonomically. Chromocurvus halotolerans gen. nov., sp. nov. was proposed as a second example of a gammaproteobacterial AAP. It exhibited bent rod-shaped cells, unusual among AAP. Facultatively anaerobic Charonomicrobium ambiphototrophicum gen. nov., sp. nov. was capable of both aerobic and anaerobic anoxygenic photosynthesis, and incapable of photoautotrophy, distinguishing it from both AAP and purple nonsulfur bacteria. Roseovarius vanadiphilum sp. nov. surprisingly produced 4.5 times more biomass and 2 times more bacteriochlorophyll (BChl) at extremely high NaVO3 concentration (7.5 g/l) than in metal-free medium. A second novel metabolic mode, anaerobic respiration on the toxic metalloid tellurate, was described for a relative of non-phototrophic Shewanella frigidimarina (ER-Te-48), from deep ocean hydrothermal vent Paralvinella worms at Explorer Ridge in the Pacific Ocean. Other strains respired on SeO32- (ER-Se-17L), VO3- (ER-V-6), and VO43- (AV-V-25). These organisms provided the first examples of anaerobic respiration on Te, Se and V at hydrothermal vents. High level resistance of AAP to metal(loid)s prompted investigation of the influence of TeO32- on photosynthetic pigment production in species including Erythromicrobium ramosum (from a terrestrial hydrothermal system) and Erythrobacter litoralis (from a hypersaline supralittoral system). Tellurite enhanced photosynthetic pigment production up to 3.4 times, consistent with an antioxidant carotenoid-based defense mechanism. However, in E. litoralis BChl precursors such as Mg protoporphyrin or its monomethyl ester also accumulated, indicating biosynthetic pathway interruption. In hydrothermal and hypersaline ecosystems, largely devoid of eukaryotic phototrophs but often enriched in metal(loid)s, AAP and metal(loid) reducers are key modulators of nutrient and toxin availability. The presented results on their ecology, physiology and biochemistry have important implications for theoretical understanding of extreme environments and hold potential for biotechnological applications. extreme environments aerobic anoxygenic phototrophs microbial photosynthesis bacteriochlorophyll carotenoids microbial ecology hypersaline springs hydrothermal vents tellurium microbial metal reduction bioremediation microbial mats purple nonsulfur bacteria selenite metavanadate Roseovarius tellurite metalloids
10	Identifikation von Genen und Mikroorganismen, die an der dissimilatorischen Fe(III)-Reduktion beteiligt sind / Isolation of Genes and Microorganisms Involved in Dissimilatory Fe(III)-Reduction Özyurt, Baris 21 January 2009 (has links) No description available. 500 Naturwissenschaften allgemein Mathematics and Computer Science Metagenomik dissimilatorische Fe(III)-Reduktion Dissimilatory iron reduction DIR dissimilatory oxido-reduction of iron dissimilatory iron(III) reduction metal reduction ferricironreduction microbial iron respiration bacterial respiration microorganisms for energy production dissimilatory iron reducing bacteria dissimilatory metal reducing bacteria DMRB energy production electricity energy transduction microbial electricity electron donor electron acceptor electron transfer carbon source carbohydrate mannit mannitol biofilm mineral mineral formation microbial degradation ribosomal proteins cytochromes hypothetical proteins enzymes oxidation reduction ferric iron iron oxide Fe(II) Fe(III) soluble iron insoluble iron ferric reductase activity iron mineral formation mineralisation <i>E. coli</i> Escherichia coli environmental microorganisms life in extreme environments uncultivable bacteria soil microbial ecology anaerobic growth anaerobic incubation environmental sequences environmental DNA DNA extraction functional screening metagenomic metagenome meta-genome microbial ecology environmental genomics soil metagenome BACs sequencing bioinformatics microbial communities 16S rRNA phylogenetics 30 42.30 42.30 58.30 42.49 58.30 42.13 RA W

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