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  • 1
    Language: English
    In: Biochemistry, 19 July 2011, Vol.50(28), pp.6217-24
    Description: In the model microbe Shewanella oneidensis, multi-heme proteins are utilized for respiratory metabolism where metals serve as the terminal electron acceptor. Among those is the periplasm-localized small tetraheme cytochrome (STC). STC has been extensively characterized structurally and electrochemically to which electron flow in and out of the protein has been modeled. However, until the present work, no kinetic studies have been performed to probe the route of electron flow or to determine the iron-binding site on STC. Using iron chelated by EDTA, NTA, or citrate, we have used chemical modification, site-directed mutagenesis along with isothermal titration calorimetry (ITC), and stopped-flow measurements to identify the iron binding site of STC. Chemical modifications of STC revealed that carboxyl groups on STC are involved in binding of EDTA-Fe(3+). Scanning mutagenesis was performed on Asp and Glu to probe the putative iron-binding site on STC. Two STC mutants (D21N; D80N) showed ∼70% decrease in observed electron transfer rate constant with EDTA-Fe(3+) from transient-state kinetic measurements. The impaired reactivity of STC (D80N/D21N) with EDTA-Fe(3+) was further confirmed by a significant decrease (〉10-fold) in iron binding affinity.
    Keywords: Bacterial Proteins -- Chemistry ; Cytochromes -- Chemistry ; Heme -- Chemistry ; Iron-Binding Proteins -- Chemistry ; Shewanella -- Enzymology
    ISSN: 00062960
    E-ISSN: 1520-4995
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  • 2
    Language: English
    In: Geochimica et Cosmochimica Acta, 2011, Vol.75(2), pp.337-351
    Description: We have compiled time-series concentration data for the biological reduction of manganese(III/IV) published between 1985 and 2004 and fit these data with a simple hyperbolic rate expression or, when appropriate, one of its limiting forms. The compiled data and rate constants are available in . The zero- and first-order rate constants appear to follow a log–normal distribution that could be used, for example, in predictive modeling of Mn-oxide reduction in a reactive transport scenario. We have also included details of the experimental procedures used to generate each time-series data-set in our compilation. These meta-data—mostly pertaining to the type and concentration of micro-organism, electron donor, and electron acceptor—enable us to examine the rate data for trends. We have computed a number of rudimentary, mono-variate statistics on the compiled data with the hope of stimulating both more detailed statistical analyses of the data and new experiments to fill gaps in the existing data-set. We have also analyzed the data with parametric models based on the log–normal distribution and rate equations that are hyperbolic in the concentration of cells and Mn available for reduction. This parametric analysis allows us to provide best estimates of zero- and first-order rate constants both ignoring and accounting for the meta-data.
    Keywords: Geology
    ISSN: 0016-7037
    E-ISSN: 1872-9533
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2016, Vol.11(3), p.e0151214
    Description: Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: Applied and Environmental Microbiology, Dec 1, 2012, Vol.78(23), p.8412(9)
    Description: The article discusses the simultaneous electrosynthesis of three commodity chemicals namely methane, acetate and hydrogen by a microbial community, dominated by Methanobacterium. The bacteria is analyzed using 16 S rRNA sequencing and the results show that the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, which could help in economic feasibility.
    Keywords: Methanogens – Research ; Methanogens – Genetic Aspects ; Methanogens – Physiological Aspects ; Chemical Compounds – Physiological Aspects ; Chemical Compounds – Economic Aspects ; Chemical Compounds – Research ; RNA Sequencing – Usage
    ISSN: 0099-2240
    Source: Cengage Learning, Inc.
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  • 5
    Language: English
    In: Applied and environmental microbiology, December 2012, Vol.78(23), pp.8412-20
    Description: A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at -590 mV versus the standard hydrogen electrode (SHE) with CO(2) as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from 4 mM day(-1) (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to 〉11 mM day(-1) (versus 0.045 mM day(-1) abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of -460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.
    Keywords: Acetates -- Metabolism ; Archaea -- Isolation & Purification ; Bacteria -- Isolation & Purification ; Electrodes -- Microbiology ; Hydrogen -- Metabolism ; Methane -- Metabolism ; Microbial Consortia -- Physiology
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 6
    Language: English
    In: PLoS ONE, 01 February 2011, Vol.6(2), p.e16649
    Description: Bioelectrochemical systems rely on microorganisms to link complex oxidation/reduction reactions to electrodes. For example, in Shewanella oneidensis strain MR-1, an electron transfer conduit consisting of cytochromes and structural proteins, known as the Mtr respiratory pathway, catalyzes electron flow from cytoplasmic oxidative reactions to electrodes. Reversing this electron flow to drive microbial reductive metabolism offers a possible route for electrosynthesis of high value fuels and chemicals. We examined electron flow from electrodes into Shewanella to determine the feasibility of this process, the molecular components of reductive electron flow, and what driving forces were required. Addition of fumarate to a film of S. oneidensis adhering to a graphite electrode poised at -0.36 V versus standard hydrogen electrode (SHE) immediately led to electron uptake, while a mutant lacking the periplasmic fumarate reductase FccA was unable to utilize electrodes for fumarate reduction. Deletion of the gene encoding the outer membrane cytochrome-anchoring protein MtrB eliminated 88% of fumarate reduction. A mutant lacking the periplasmic cytochrome MtrA demonstrated more severe defects. Surprisingly, disruption of menC, which prevents menaquinone biosynthesis, eliminated 85% of electron flux. Deletion of the gene encoding the quinone-linked cytochrome CymA had a similar negative effect, which showed that electrons primarily flowed from outer membrane cytochromes into the quinone pool, and back to periplasmic FccA. Soluble redox mediators only partially restored electron transfer in mutants, suggesting that soluble shuttles could not replace periplasmic protein-protein interactions. This work demonstrates that the Mtr pathway can power reductive reactions, shows this conduit is functionally reversible, and provides new evidence for distinct CymA:MtrA and CymA:FccA respiratory units.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 7
    Language: English
    In: Genome Announcements, 06 October 2016, Vol.4(5)
    Description: The draft genome sequence ofPseudomonas stutzeristrain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. The genome encodes a complete nitrogen fixation pathway and the upper and lower naphthalene degradation pathways.
    Keywords: Basic Biological Sciences ; Draft Genome ; Coalbed Methane ; Microbiology ; Biology
    ISSN: 2169-8287
    E-ISSN: 2169-8287
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  • 8
    Language: English
    In: Genome announcements, 03 November 2016, Vol.4(6)
    Description: A near-complete Pseudomonas stutzeri draft genome was extracted from a coalbed metagenome. The draft genome described herein provides insight into the functional pathways encoded by this bacterium and its potential role in coalbed methane environments.
    Keywords: Biology;
    ISSN: 2169-8287
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  • 9
    Language: English
    In: Genome announcements, 01 September 2016, Vol.4(5)
    Description: We report here the 1,882,100-bp draft genome sequence of Methanohalophilus mahii strain DAL1, recovered from Marcellus Shale hydraulic fracturing-produced water using metagenomic contig binning. Genome annotation revealed several key methanogenesis genes and provides valuable information on archaeal activity associated with hydraulic fracturing-produced water environments.
    Keywords: Biology;
    ISSN: 2169-8287
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  • 10
    Language: English
    In: genome Announcements, 15 January 2015, Vol.3(1)
    Description: A draft genome of Sulfurospirillum sp. strain MES was isolated through taxonomic binning of a metagenome sequenced from a microbial electrosynthesis system (MES) actively producing acetate and hydrogen. The genome contains the nosZDFLY genes, which are involved in nitrous oxide reduction, suggesting the potential role of this strain in denitrification.
    Keywords: Basic Biological Sciences ; Biology
    ISSN: 2169-8287
    E-ISSN: 2169-8287
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