Microbial Reduction Of Chlorite And Uranium Followed By Air Oxidation,
2011
Chinese Academy of Sciences
Microbial Reduction Of Chlorite And Uranium Followed By Air Oxidation, Gengxin Zhang, William D. Burgos, John M. Senko, Michael E. Bishop, Hailiang Dong, Maxim Boyanov, Kenneth M. Kemner
United States Department of Energy: Publications
To evaluate the stability of biogenic nanoparticulate U(IV) in the presence of an Fe(II)-rich iron-bearing phyllosilicate, we examined the reduction of structural Fe(III) in chlorite CCa-2 and uranium(VI) by Shewanella oneidensis MR-1, and the reoxidation of these minerals (after pasteurization) via the introduction of oxygen. Bioreduction experiments were conducted with combinations of chlorite, U(VI), and anthraquinone-2,6-disulfonate (AQDS). Abiotic experiments were conducted to quantify the reduction of U(VI) by chemically-reduced chlorite-associated Fe(II), the oxidation of nanoparticulate U(IV) by unaltered structural Fe(III) in chlorite, and the sorption of U(VI) to chlorite, to elucidate interactions between U(VI)/ U(IV) and Fe(II)/Fe(III)-chlorite. Solids were characterized …
Competitive Reduction Of
Pertechnetate (99tco4-) By
Dissimilatory Metal Reducing
Bacteria And Biogenic Fe(Ii),
2011
Pacific Northwest National Laboratory
Competitive Reduction Of Pertechnetate (99tco4-) By Dissimilatory Metal Reducing Bacteria And Biogenic Fe(Ii), Andrew Plymale, James K. Fredrickson, John M. Zachara, Alice Dohnalkova, Steve Heald, Dean Moore, David Kennedy, Matthew Marshall, Chongmin Wang, Charles Resch, Ponnusamy Nachimuthu
United States Department of Energy: Publications
The fate of pertechnetate (99Tc(VII)O4 -) during bioreduction was investigated in the presence of 2-line ferrihydrite (Fh) and various dissimilatory metal reducing bacteria (DMRB) (Geobacter, Anaeromyxobacter, Shewanella) in comparison with TcO4 - bioreduction in the absence of Fh. In the presence of Fh, Tc was present primarily as a fine-grained Tc(IV)/Fe precipitate that was distinct from the Tc(IV)O2 ·nH2O solids produced by direct biological Tc(VII) reduction. Aqueous Tc concentrations (<0.2 μm) in the bioreduced Fh suspensions (1.7 to 3.2 × 10-9 mol L-1) were over 1 order of magnitude lower than when TcO4 - …
Effect Of Grain Size On Uranium(Vi) Surface Complexation
Kinetics And Adsorption Additivity,
2011
Pacific Northwest National Laboratory
Effect Of Grain Size On Uranium(Vi) Surface Complexation Kinetics And Adsorption Additivity, Jianying Shang, Chongxuan Liu, Zheming Wang, John M. Zachara
United States Department of Energy: Publications
The contribution of variable grain sizes to uranium adsorption/ desorption was studied using a sediment from the US DOE Hanford site. The sediment was wet sieved into four size fractions: coarse sand (1−2 mm), medium sand (0.2−1 mm), fine sand (0.053−0.2 mm), and clay/silt fraction (<0.053 mm). For each size fraction and their composite (sediment), batch and flow-cell experiments were performed to determine uranium adsorption isotherms and kinetic uranium adsorption and subsequent desorption. The results showed that uranium adsorption isotherms and adsorption/desorption kinetics were size specific, reflecting the effects of size-specific adsorption site concentration and kinetic rate constants. The larger-size fraction had a larger mass percentage in the sediment but with a smaller adsorption site concentration and generally a slower uranium adsorption/desorption rate. The same equilibrium surface complexation reaction and reaction constant could describe uranium adsorption isotherms for all size fractions and the composite after accounting for the effect of adsorption site concentration. Mass-weighted, linear additivity was observed for both uranium adsorption isotherms and adsorption/desorption kinetics in the composite. One important implication of this study is that grain-size distribution may be used to estimate uranium adsorption site and adsorption/desorption kinetic rates in heterogeneous sediments from a common location.
Determining Individual Mineral Contributions To U(Vi)
Adsorption In A Contaminated Aquifer Sediment:
A Fluorescence Spectroscopy Study,
2011
Pacific Northwest National Laboratory
Determining Individual Mineral Contributions To U(Vi) Adsorption In A Contaminated Aquifer Sediment: A Fluorescence Spectroscopy Study, Zheming Wang, John M. Zachara, Jean-Francois Boily, Yuanxian Xia, Tom C. Resch, Dean A. Moore, Chongxuan Liu
United States Department of Energy: Publications
The adsorption and speciation of U(VI) was investigated on contaminated, fine grained sediment materials from the Hanford 300 area (SPP1 GWF) in simulated groundwater using cryogenic laser-induced U(VI) fluorescence spectroscopy combined with chemometric analysis. A series of reference minerals (montmorillonite, illite, Michigan chlorite, North Carolina chlorite, California clinochlore, quartz and synthetic 6-line ferrihydrite) was used for comparison that represents the mineralogical constituents of SPP1 GWF. Surface area-normalized Kd values were measured at U(VI) concentrations of 5 X 10−7 and 5 X 10−6 mol L−1 that displayed the following affinity series: 6-line-ferrihydrite > North Carolina chlorite ≈ California clinochlore …
The Mineralogic Transformation Of Ferrihydrite Induced By
Heterogeneous Reaction With Bioreduced Anthraquinone
Disulfonate (Aqds) And The Role Of Phosphate,
2011
Pacific Northwest National Laboratory
The Mineralogic Transformation Of Ferrihydrite Induced By Heterogeneous Reaction With Bioreduced Anthraquinone Disulfonate (Aqds) And The Role Of Phosphate, John M. Zachara, Ravi K. Kukkadapu, Tanya Peretyazhko, Mark Bowden, Chongmin Wang, David Kennedy, Dean Moore, Bruce Arey
United States Department of Energy: Publications
Bioreduced anthraquinone-2,6-disulfonate (AH2DS; dihydro-anthraquinone) was reacted with a 2-line, Si-substituted ferrihydrite under anoxic conditions at neutral pH in PIPES buffer. Phosphate (P) and bicarbonate (C); common adsorptive oxyanions and media/buffer components known to effect ferrihydrite mineralization; and Fe(II)aq (as a catalytic mineralization agent) were used in comparative experiments. Heterogeneous AH2DS oxidation coupled with Fe(III) reduction occurred within 0.13–1 day, with mineralogic transformation occurring thereafter. The product suite included lepidocrocite, goethite, and/or magnetite, with proportions varing with reductant:oxidant ratio (r:o) and the presence of P or C. Lepidocrocite was the primary product at low r:o in the absence of P …
Interfacial Reactivity Of Radionuclides:
Emerging Paradigms From Molecular-Level Observations,
2011
Pacific Northwest National Laboratory
Interfacial Reactivity Of Radionuclides: Emerging Paradigms From Molecular-Level Observations, A.R. Felmy, E.S. Ilton, K.M. Rosso, John M. Zachara
United States Department of Energy: Publications
Over the past few decades an increasing array of molecular-level analytical probes has provided new detailed insight into mineral and radionuclide interfacial reactivity in subsurface environments. This capability has not only helped change the way mineral surface reactivity is studied but also how field scale contaminant migration problems are addressed and ultimately resolved. Here we review relatively new interfacial reactivity paradigms and assess their implications for future research directions. Specific examples include understanding the following: the role of site-to-site electron conduction at mineral surfaces and through bulk mineral phases and the effects of local chemical environment on the stability of …
Structure Of A Bacterial Cell Surface
Decaheme Electron Conduit,
2011
University of East Anglia
Structure Of A Bacterial Cell Surface Decaheme Electron Conduit, Thomas A. Clarke, Marcus Edwards, Andrew J. Gates, Andrea Hall, Gaye F. White, Justin Bradley, Catherine L. Reardon, Liang Shi, Alexander Beliaev, Matthew Marshall, Zheming Wang, Nicholas Watmough, James K. Fredrickson, John M. Zachara, Julea Butt, David J. Richardson
United States Department of Energy: Publications
Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of transouter- membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to …
Sop For Pathway Inference In Integrated Microbial Genomes (Img),
2011
DOE Joint Genome Institute
Sop For Pathway Inference In Integrated Microbial Genomes (Img), Iain Anderson, Amy Chen, Victor Markowitz, Nikos Kyrpides, Natalia Ivanova
United States Department of Energy: Publications
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding …
Complete Genome Sequence Of The Cellulolytic Thermophile
Clostridium Thermocellum Dsm1313,
2011
Mascoma Corporation
Complete Genome Sequence Of The Cellulolytic Thermophile Clostridium Thermocellum Dsm1313, Lawrence Feinberg, Justine Foden, Trisha Barrett, Karen Walston Davenport, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Alla Lapidus, Susan Lucas, Jan-Fang Cheng, Samuel Pitluck, Tanja Woyke, Natalia Ivanova, Natalia Mikhailova, Miriam Land, Loren Hauser, D. Aaron Argyros, Lynne Goodwin, David Hogsett, Nicky Caiazza
United States Department of Energy: Publications
Clostridium thermocellum DSM1313 is a thermophilic, anaerobic bacterium with some of the highest rates of cellulose hydrolysis reported. The complete genome sequence reveals a suite of carbohydrate-active enzymes and demonstrates a level of diversity at the species level distinguishing it from the type strain ATCC 27405.
Img/M: The Integrated Metagenome Data
Management And Comparative Analysis System,
2011
Lawrence Berkeley National Laboratory
Img/M: The Integrated Metagenome Data Management And Comparative Analysis System, Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, Nikos C. Kyrpides
United States Department of Energy: Publications
The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M’s data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl
B-30929, A Novel Strain From A Commercial Ethanol Plant,
2011
National Center for Agricultural Utilization Research
Complete Genome Sequence Of Lactobacillus Buchneri Nrrl B-30929, A Novel Strain From A Commercial Ethanol Plant, Siqing Liu, Timothy D. Leathers, Alex Copeland, Olga Chertkov, Lynne Goodwin, David A. Mills
United States Department of Energy: Publications
Lactobacillus buchneri strain NRRL B-30929 was a contaminant obtained from a commercial ethanol fermentation. This facultative anaerobe is unique because of its rapid growth on xylose and simultaneous fermentation of xylose and glucose. The strain utilizes a broad range of carbohydrate substrates and possesses a high tolerance to ethanol and other stresses, making it an attractive candidate for bioconversion of biomass substrates to various bioproducts. The genome sequence of NRRL B-30929 will provide insight into the unique properties of this lactic acid bacterium.
Vista Region Viewer (Rviewer)—A Computational System For
Prioritizing Genomic Intervals For Biomedical Studies,
2011
Lawrence Berkeley National Laboratory
Vista Region Viewer (Rviewer)—A Computational System For Prioritizing Genomic Intervals For Biomedical Studies, Igor Lukashin, Pavel Novichkov, Dario Boffelli, Alex R. Paciorkowski, Simon Minovitsky, Song Yang, Inna Dubchak
United States Department of Energy: Publications
Summary:
Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (RViewer), an interactive online tool that allows for efficient screening and prioritization of regions of the human genome for follow-up studies. The tool takes as input genetic variation data from different biomedical studies, determines a number of various functional parameters for both coding …
Complete Genome Sequence Of The Plant Growth-Promoting
Endophyte Burkholderia Phytofirmans Strain Psjn,
2011
AIT Austrian Institute of Technology GmbH
Complete Genome Sequence Of The Plant Growth-Promoting Endophyte Burkholderia Phytofirmans Strain Psjn, Alexandra Weilharter, Birgit Mitter, Maria V. Shin, Patrick S. G. Chain, Jerzy Nowak, Angela Sessitsch
United States Department of Energy: Publications
Burkholderia phytofirmans PsJNT is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.
Characterization Of The Intragranular Water Regime Within
Subsurface Sediments: Pore Volume, Surface Area, And Mass
Transfer Limitations,
2011
U.S. Geological Survey
Characterization Of The Intragranular Water Regime Within Subsurface Sediments: Pore Volume, Surface Area, And Mass Transfer Limitations, Michael B. Hay, Deborah L. Stoliker, James A. Davis, John M. Zachara
United States Department of Energy: Publications
Although ‘‘intragranular’’ pore space within grain aggregates, grain fractures, and mineral surface coatings may contain a relatively small fraction of the total porosity within a porous medium, it often contains a significant fraction of the reactive surface area, and can thus strongly affect the transport of sorbing solutes. In this work, we demonstrate a batch experiment procedure using tritiated water as a high-resolution diffusive tracer to characterize the intragranular pore space. The method was tested using uranium contaminated sediments from the vadose and capillary fringe zones beneath the former 300A process ponds at the Hanford site (Washington). Sediments were contacted …
Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion,
2011
Pacific Northwest National Laboratory
Multispecies Diffusion Models: A Study Of Uranyl Species Diffusion, Chongxuan Liu, Jianying Shang, John M. Zachara
United States Department of Energy: Publications
Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found …
Transient Groundwater Chemistry Near A River: Effects On U(Vi)
Transport In Laboratory Column Experiments,
2011
Oregon State University
Transient Groundwater Chemistry Near A River: Effects On U(Vi) Transport In Laboratory Column Experiments, Jun Yin, Roy Haggerty, Deborah L. Stoliker, Douglas B. Kent, Jonathan D. Istok, Janek Greskowiak, John M. Zachara
United States Department of Energy: Publications
In the 300 Area of a U(VI)-contaminated aquifer at Hanford, Washington, USA, inorganic carbon and major cations, which have large impacts on U(VI) transport, change on an hourly and seasonal basis near the Columbia River. Batch and column experiments were conducted to investigate the factors controlling U(VI) adsorption/desorption by changing chemical conditions over time. Low alkalinity and low Ca concentrations (Columbia River water) enhanced adsorption and reduced aqueous concentrations. Conversely, high alkalinity and high Ca concentrations (Hanford groundwater) reduced adsorption and increased aqueous concentrations of U(VI). An equilibrium surface complexation model calibrated using laboratory batch experiments accounted for the decrease …
Simulating Adsorption Of U(Vi) Under Transient Groundwater
Flow And Hydrochemistry: Physical Versus Chemical
Nonequilibrium Model,
2011
CSIRO Land and Water
Simulating Adsorption Of U(Vi) Under Transient Groundwater Flow And Hydrochemistry: Physical Versus Chemical Nonequilibrium Model, Janek Greskowiak, Michael Hay, Henning Prommer, Chongxuan Liu, Vincent Post, Rui Ma, James Davis, Chunmiao Zheng, John M. Zachara
United States Department of Energy: Publications
Coupled intragrain diffusional mass transfer and nonlinear surface complexation processes play an important role in the transport behavior of U(VI) in contaminated aquifers. Two alternative model approaches for simulating these coupled processes were analyzed and compared: (1) the physical nonequilibrium approach that explicitly accounts for aqueous speciation and instantaneous surface complexation reactions in the intragrain regions and approximates the diffusive mass exchange between the immobile intragrain pore water and the advective pore water as multirate first-order mass transfer and (2) the chemical nonequilibrium approach that approximates the diffusion-limited intragrain surface complexation reactions by a set of multiple first-order surface complexation …
Transition Of Cellulose Crystalline Structure And Surface Morphology
Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation
To Enzymatic Hydrolysis,
2011
Joint BioEnergy Institute
Transition Of Cellulose Crystalline Structure And Surface Morphology Of Biomass As A Function Of Ionic Liquid Pretreatment And Its Relation To Enzymatic Hydrolysis, Gang Cheng, Patanjali Varanasi, Chenlin Li, Hanbin Liu, Yuri B. Melnichenko, Blake A. Simmons, Michael S. Kent, Seema Singh
United States Department of Energy: Publications
Cellulose is inherently resistant to breakdown, and the native crystalline structure (cellulose I) of cellulose is considered to be one of themajor factors limiting its potential in terms of cost-competitive lignocellulosic biofuel production. Here we report the impact of ionic liquid pretreatment on the cellulose crystalline structure in different feedstocks, including microcrystalline cellulose (Avicel), switchgrass (Panicum virgatum), pine (Pinus radiata), and eucalyptus (Eucalyptus globulus), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160°C for 1, 3, 6, and 12 …
Absolute High-Resolution Se+ Photoionization Cross-Section Measurements
With Rydberg-Series Analysis,
2011
University of Nevada - Reno
Absolute High-Resolution Se+ Photoionization Cross-Section Measurements With Rydberg-Series Analysis, D. A. Esteves, R. C. Bilodeau, N. C. Sterling, R. A. Phaneuf, A. L. D. Kilcoyne, E. C. Red, A. Aguilar
United States Department of Energy: Publications
Absolute single photoionization cross-section measurements for Se+ ions were performed at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory using the photo-ion merged-beams technique. Measurements were made at a photon energy resolution of 5.5 meV from 17.75 to 21.85 eV spanning the 4s24p34So3/2 ground-state ionization threshold and the 2Po3/2,2Po1/2,2Do5/2, and2Do3/2 metastable state thresholds. Extensive analysis of the complex resonant structure in this region identified numerous Rydberg series of resonances and …
Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+,
2011
University of Nevada - Reno
Photoionization Measurements For The Iron Isonuclear Sequence Fe3+, Fe5+, And Fe7+, M. F. Gharaibeh, A. Aguilar, A. M. Covington, E. D. Emmons, S. W. J. Scully, R. A. Phaneuf, A. Muller, J. D. Bozek, A. L. D. Kilcoyne, A. S. Schlachter, I. Alvarez, C. Cisneros, G. Hinojosa
United States Department of Energy: Publications
Cross sections for single photoionization of Fe3+, Fe5+, and Fe7+ ions were measured at spectral resolutions of 0.04, 0.15, and 0.13 eV, respectively, by merging mass- and charge-selected ion beams with a beam of monochromatized synchrotron undulator radiation. The measurements span photon energy ranges beginning at the ionization thresholds and extending several tens of electron volts to include the most important resonant contributions due to 3p–nd transitions to autoionizing states. The photoion yield spectra are characterized by narrow resonances and also broad features in Fe3+ and Fe5+ that are believed to result …
