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  1. Article ; Online: Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes.

    Long, Philip E / Williams, Kenneth H / Hubbard, Susan S / Banfield, Jillian F

    Trends in microbiology

    2016  Volume 24, Issue 8, Page(s) 600–610

    Abstract: Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA ... ...

    Abstract Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes-such as the nitrogen cycle-that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.
    Language English
    Publishing date 2016-08
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1158963-2
    ISSN 1878-4380 ; 0966-842X
    ISSN (online) 1878-4380
    ISSN 0966-842X
    DOI 10.1016/j.tim.2016.04.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes

    Long, Philip E / Jillian F. Banfield / Kenneth H. Williams / Susan S. Hubbard

    Elsevier Ltd Trends in microbiology. 2016 Aug., v. 24, no. 8

    2016  

    Abstract: Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA ... ...

    Abstract Microorganisms play key roles in terrestrial system processes, including the turnover of natural organic carbon, such as leaf litter and woody debris that accumulate in soils and subsurface sediments. What has emerged from a series of recent DNA sequencing-based studies is recognition of the enormous variety of little known and previously unknown microorganisms that mediate recycling of these vast stores of buried carbon in subsoil compartments of the terrestrial system. More importantly, the genome resolution achieved in these studies has enabled association of specific members of these microbial communities with carbon compound transformations and other linked biogeochemical processes–such as the nitrogen cycle–that can impact the quality of groundwater, surface water, and atmospheric trace gas concentrations. The emerging view also emphasizes the importance of organism interactions through exchange of metabolic byproducts (e.g., within the carbon, nitrogen, and sulfur cycles) and via symbioses since many novel organisms exhibit restricted metabolic capabilities and an associated extremely small cell size. New, genome-resolved information reshapes our view of subsurface microbial communities and provides critical new inputs for advanced reactive transport models. These inputs are needed for accurate prediction of feedbacks in watershed biogeochemical functioning and their influence on the climate via the fluxes of greenhouse gases, CO2, CH4, and N2O.
    Keywords byproducts ; carbon ; carbon dioxide ; climate ; DNA ; genome ; greenhouse gases ; groundwater ; metagenomics ; methane ; microbial communities ; microorganisms ; models ; nitrogen ; nitrous oxide ; plant litter ; prediction ; recycling ; sediments ; sulfur ; surface water ; watersheds
    Language English
    Dates of publication 2016-08
    Size p. 600-610.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1158963-2
    ISSN 1878-4380 ; 0966-842X
    ISSN (online) 1878-4380
    ISSN 0966-842X
    DOI 10.1016/j.tim.2016.04.006
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Dying for Good: Virus-Bacterium Biofilm Co-evolution Enhances Environmental Fitness.

    Jin, Hongjun / Squier, Thomas C / Long, Philip E

    Biochemistry insights

    2012  Volume 5, Page(s) 1–9

    Abstract: Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for ... ...

    Abstract Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. Using the E. coli strain TG1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the reductive immobilization of chromate (ie, M13-phageGh-ChrR). In the absence of a selective pressure, M13-phage infection results in a reduction in bacterial growth rate; in comparison, in the presence of chromate there are substantial increases in both cellular killing and biomass formation following infection of E. coli strain TG1with M13-phageGh-ChrR that is dependent on chromate-reductase activity. These results are discussed in terms of community structures that facilitate lateral gene transfer of beneficial traits that enhance phage replication, infectivity, and stability against environmental change.
    Language English
    Publishing date 2012-07-03
    Publishing country England
    Document type Journal Article
    ISSN 1178-6264
    ISSN 1178-6264
    DOI 10.4137/BCI.S9553
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Field Application of

    Jemison, Noah E / Shiel, Alyssa E / Johnson, Thomas M / Lundstrom, Craig C / Long, Philip E / Williams, Kenneth H

    Environmental science & technology

    2018  Volume 52, Issue 6, Page(s) 3422–3430

    Abstract: Biostimulation to induce reduction of soluble U(VI) to relatively immobile U(IV) is an effective strategy for decreasing aqueous U(VI) concentrations in contaminated groundwater systems. If oxidation of U(IV) occurs following the biostimulation phase, U( ... ...

    Abstract Biostimulation to induce reduction of soluble U(VI) to relatively immobile U(IV) is an effective strategy for decreasing aqueous U(VI) concentrations in contaminated groundwater systems. If oxidation of U(IV) occurs following the biostimulation phase, U(VI) concentrations increase, challenging the long-term effectiveness of this technique. However, detecting U(IV) oxidation through dissolved U concentrations alone can prove difficult in locations with few groundwater wells to track the addition of U to a mass of groundwater. We propose the
    MeSH term(s) Biodegradation, Environmental ; Groundwater ; Nitrates ; Oxidation-Reduction ; Uranium ; Water Pollutants, Radioactive
    Chemical Substances Nitrates ; Water Pollutants, Radioactive ; Uranium (4OC371KSTK)
    Language English
    Publishing date 2018-03-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5851
    ISSN (online) 1520-5851
    DOI 10.1021/acs.est.7b05162
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site.

    McGuinness, Lora R / Wilkins, Michael J / Williams, Kenneth H / Long, Philip E / Kerkhof, Lee J

    PloS one

    2015  Volume 10, Issue 9, Page(s) e0137270

    Abstract: Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to ... ...

    Abstract Understanding which organisms are capable of reducing uranium at historically contaminated sites provides crucial information needed to evaluate treatment options and outcomes. One approach is determination of the bacteria which directly respond to uranium addition. In this study, uranium amendments were made to groundwater samples from a site of ongoing biostimulation with acetate. The active microbes in the planktonic phase were deduced by monitoring ribosomes production via RT-PCR. The results indicated several microorganisms were synthesizing ribosomes in proportion with uranium amendment up to 2 μM. Concentrations of U (VI) >2 μM were generally found to inhibit ribosome synthesis. Two active bacteria responding to uranium addition in the field were close relatives of Desulfobacter postgateii and Geobacter bemidjiensis. Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites.
    MeSH term(s) Biodegradation, Environmental ; Colorado ; Deltaproteobacteria/genetics ; Deltaproteobacteria/metabolism ; Geobacter/genetics ; Geobacter/metabolism ; Groundwater/analysis ; Groundwater/microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Ribosomal/genetics ; RNA, Ribosomal/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; Uranium/analysis ; Uranium/metabolism ; Water Pollutants, Radioactive/analysis ; Water Pollutants, Radioactive/metabolism
    Chemical Substances RNA, Bacterial ; RNA, Ribosomal ; Water Pollutants, Radioactive ; Uranium (4OC371KSTK)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0137270
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Uranium Bioreduction Rates across Scales: Biogeochemical Hot Moments and Hot Spots during a Biostimulation Experiment at Rifle, Colorado

    Bao, Chen / Li Li / Long Philip E / Newcomer Darrell / Williams Kenneth H / Wu Hongfei

    Environmental Science & Technology. 2014 Sept. 02, v. 48, no. 17

    2014  

    Abstract: We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to ... ...

    Abstract We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to insoluble U(IV). Bicarbonate was coinjected in half of the domain to mobilize sorbed U(VI). We used reactive transport modeling to integrate hydraulic and geochemical data and to quantify rates at the grid block (0.25 m) and experimental field scale (tens of meters). Although local rates varied by orders of magnitude in conjunction with biostimulation fronts propagating downstream, field-scale rates were dominated by those orders of magnitude higher rates at a few selected hot spots where Fe(III), U(VI), and FeRB were at their maxima in the vicinity of the injection wells. At particular locations, the hot moments with maximum rates negatively corresponded to their distance from the injection wells. Although bicarbonate injection enhanced local rates near the injection wells by a maximum of 39.4%, its effect at the field scale was limited to a maximum of 10.0%. We propose a rate-versus-measurement-length relationship (log R′ = −0.63 log L – 2.20, with R′ in μmol/mg cell protein/day and L in meters) for orders-of-magnitude estimation of uranium bioreduction rates across scales.
    Keywords acetates ; bacteria ; bicarbonates ; field experimentation ; iron ; models ; uranium ; wells ; Colorado
    Language English
    Dates of publication 2014-0902
    Size p. 10116-10127.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5851
    DOI 10.1021%2Fes501060d
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Uranium bioreduction rates across scales: biogeochemical hot moments and hot spots during a biostimulation experiment at Rifle, Colorado.

    Bao, Chen / Wu, Hongfei / Li, Li / Newcomer, Darrell / Long, Philip E / Williams, Kenneth H

    Environmental science & technology

    2014  Volume 48, Issue 17, Page(s) 10116–10127

    Abstract: We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to ... ...

    Abstract We aim to understand the scale-dependent evolution of uranium bioreduction during a field experiment at a former uranium mill site near Rifle, Colorado. Acetate was injected to stimulate Fe-reducing bacteria (FeRB) and to immobilize aqueous U(VI) to insoluble U(IV). Bicarbonate was coinjected in half of the domain to mobilize sorbed U(VI). We used reactive transport modeling to integrate hydraulic and geochemical data and to quantify rates at the grid block (0.25 m) and experimental field scale (tens of meters). Although local rates varied by orders of magnitude in conjunction with biostimulation fronts propagating downstream, field-scale rates were dominated by those orders of magnitude higher rates at a few selected hot spots where Fe(III), U(VI), and FeRB were at their maxima in the vicinity of the injection wells. At particular locations, the hot moments with maximum rates negatively corresponded to their distance from the injection wells. Although bicarbonate injection enhanced local rates near the injection wells by a maximum of 39.4%, its effect at the field scale was limited to a maximum of 10.0%. We propose a rate-versus-measurement-length relationship (log R' = -0.63 log L - 2.20, with R' in μmol/mg cell protein/day and L in meters) for orders-of-magnitude estimation of uranium bioreduction rates across scales.
    MeSH term(s) Bacteria/metabolism ; Biodegradation, Environmental ; Colorado ; Models, Theoretical ; Time Factors ; Uranium/isolation & purification ; Water/chemistry ; Water Pollutants, Radioactive/isolation & purification
    Chemical Substances Water Pollutants, Radioactive ; Water (059QF0KO0R) ; Uranium (4OC371KSTK)
    Language English
    Publishing date 2014-09-02
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5851
    ISSN (online) 1520-5851
    DOI 10.1021/es501060d
    Database MEDical Literature Analysis and Retrieval System OnLINE

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

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

    Applied and environmental microbiology

    2012  Volume 78, Issue 24, Page(s) 8735–8742

    Abstract: 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 ... ...

    Abstract 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.
    MeSH term(s) Bacterial Proteins/analysis ; Biomass ; Geobacter/genetics ; Geobacter/growth & development ; Geobacter/metabolism ; Metabolic Networks and Pathways/genetics ; Metals/metabolism ; Oxidation-Reduction ; Proteome/analysis ; Proteomics
    Chemical Substances Bacterial Proteins ; Metals ; Proteome
    Language English
    Publishing date 2012-10-05
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 223011-2
    ISSN 1098-5336 ; 0099-2240
    ISSN (online) 1098-5336
    ISSN 0099-2240
    DOI 10.1128/AEM.01795-12
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: No Measurable Changes in 238U/235U due to Desorption–Adsorption of U(VI) from Groundwater at the Rifle, Colorado, Integrated Field Research Challenge Site

    Shiel, Alyssa E / Johnson Thomas M / Laubach Parker G / Long Philip E / Lundstrom Craig C / Williams Kenneth H

    Environmental Science & Technology. 2013 Mar. 19, v. 47, no. 6

    2013  

    Abstract: Groundwater samples were collected from the Integrated Field Research Challenge field site in Rifle, Colorado, over the course of a bicarbonate-induced U desorption–adsorption experiment. Uranium concentrations and high precision U isotopic ... ...

    Abstract Groundwater samples were collected from the Integrated Field Research Challenge field site in Rifle, Colorado, over the course of a bicarbonate-induced U desorption–adsorption experiment. Uranium concentrations and high precision U isotopic compositions (²³⁸U/²³⁵U) of these groundwater samples were determined and used to assess the impact of bicarbonate-induced U(VI) desorption from contaminated sediments on the ²³⁸U/²³⁵U of groundwater. The ²³⁸U/²³⁵U of groundwater was not significantly impacted by bicarbonate-induced desorption of U(VI) from mineral surfaces or by adsorption of advecting U(VI) from upgradient locations onto those surfaces after the treatment. Assuming this absence of a significant shift in U isotopic composition associated with desorption–adsorption applies to other systems, reduction of U(VI) to U(IV) is expected to be the dominant source of U isotopic fractionation associated with removal of U(VI) from pore water as a result of natural and stimulated reductive pathways. Thus, changes in the ²³⁸U/²³⁵U composition of uranium-bearing fluids should be useful in quantifying the extent of reduction.
    Keywords adsorption ; desorption ; groundwater ; isotope fractionation ; sediment contamination ; uranium ; Colorado
    Language English
    Dates of publication 2013-0319
    Size p. 2535-2541.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5851
    DOI 10.1021%2Fes303913y
    Database NAL-Catalogue (AGRICOLA)

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  10. Book ; Online: (Table 1) Results of core-NCR (Non-Contact Resistivity) data analyses from ODP Leg 204, supplementary data to: Riedel, Michael; Long, Philip E; Collett, Tim S (2006): Estimates of in situ gas hydrate concentration from resistivity monitoring of gas hydrate bearing sediments during temperature equilibration. Marine Geology, 227(3-4), 215-225

    Riedel, Michael / Collett, Tim S / Long, Philip E

    2006  

    Abstract: As part of Ocean Drilling Program Leg 204 at southern Hydrate Ridge off Oregon we have monitored changes in sediment electrical resistivity during controlled gas hydrate dissociation experiments. Two cores were used, each filled with gas hydrate bearing ... ...

    Abstract As part of Ocean Drilling Program Leg 204 at southern Hydrate Ridge off Oregon we have monitored changes in sediment electrical resistivity during controlled gas hydrate dissociation experiments. Two cores were used, each filled with gas hydrate bearing sediments(predominantly mud/silty mud). One core was from Site 1249 (1249F-9H3), 42.1 m below seafloor (mbsf) and the other from Site 1248 (1248C-4X1), 28.8 mbsf. At Site 1247, a third experiment was conducted on a core without gas hydrate (1247B-2H1, 3.6 mbsf). First, the cores were imaged using an infra-red (IR) camera upon recovery to map the gas hydrate occurrence through dissociation cooling. Over a period of several hours, successive runs on the multi-sensor track (includes sensors for P-wave velocity, resistivity, magnetic susceptibility and gamma-ray density) were carried out complemented by X-ray imaging on core 1249F-9H3. After complete equilibration to room temperature (17-18 8C) and complete gas hydrate dissociation, the final measurement of electrical resistivity was used to calculate pore-water resistivity and salinities. The calculated pore-water freshening after dissociation is equivalent to a gas hydrate concentration in situ of 35-70% along core 1249F-9H3 and 20-35% for core 1248C-4X1 assuming seawater salinity of in situ pore fluid. Detailed analysis of the IR scan, X-ray images and split-core photographs showed the hydrate mainly occurred disseminated throughout the core. Additionally, in core 1249F-9H3, a single hydrate filled vein, approximately 10 cm long and dipping at about 658, was identified. Analyses of the logging-while-drilling (LWD) resistivity data revealed a structural dip of 40-808 in the interval between 40 and 44 mbsf. We further analyzed all resistivity data measured on the recovered core during Leg 204. Generally poor data quality due to gas cracks allowed analyses to be carried out only at selected intervals at Sites 1244, 1245, 1246, 1247, 1248, 1249, and 1252. With a few exceptions, data from these intervals yield low to no gas hydrate concentration, which corresponds to estimates from downhole resistivity logs. However, since the gas cracking may be the result of gas hydrate dissociation, this is a biased sampling. Cores that had contained some gas hydrate may have been excluded.
    Language English
    Dates of publication 2006-9999
    Size Online-Ressource
    Publisher PANGAEA - Data Publisher for Earth & Environmental Science
    Publishing place Bremen/Bremerhaven
    Document type Book ; Online
    Note This dataset is supplement to doi:10.1016/j.margeo.2005.10.007
    DOI 10.1594/PANGAEA.726488
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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