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1.
Environ Sci Technol ; 52(6): 3422-3430, 2018 03 20.
Artigo em Inglês | MEDLINE | ID: mdl-29464949

RESUMO

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 238U/235U ratio of aqueous U as an independent, reliable tracer of U(IV) remobilization via oxidation or mobilization of colloids. Reduction of U(VI) produces 238U-enriched U(IV), whereas remobilization of solid U(IV) should not induce isotopic fractionation. The incorporation of remobilized U(IV) with a high 238U/235U ratio into the aqueous U(VI) pool produces an increase in 238U/235U of aqueous U(VI). During several injections of nitrate to induce U(IV) oxidation, 238U/235U consistently increased, suggesting 238U/235U is broadly applicable for detecting mobilization of U(IV).


Assuntos
Água Subterrânea , Urânio , Poluentes Radioativos da Água , Biodegradação Ambiental , Nitratos , Oxirredução
2.
Environ Sci Technol ; 50(1): 46-53, 2016 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-26651843

RESUMO

The Rifle alluvial aquifer along the Colorado River in west central Colorado contains fine-grained, diffusion-limited sediment lenses that are substantially enriched in organic carbon and sulfides, as well as uranium, from previous milling operations. These naturally reduced zones (NRZs) coincide spatially with a persistent uranium groundwater plume. There is concern that uranium release from NRZs is contributing to plume persistence or will do so in the future. To better define the physical extent, heterogeneity and biogeochemistry of these NRZs, we investigated sediment cores from five neighboring wells. The main NRZ body exhibited uranium concentrations up to 100 mg/kg U as U(IV) and contains ca. 286 g of U in total. Uranium accumulated only in areas where organic carbon and reduced sulfur (as iron sulfides) were present, emphasizing the importance of sulfate-reducing conditions to uranium retention and the essential role of organic matter. NRZs further exhibited centimeter-scale variations in both redox status and particle size. Mackinawite, greigite, pyrite and sulfate coexist in the sediments, indicating that dynamic redox cycling occurs within NRZs and that their internal portions can be seasonally oxidized. We show that oxidative U(VI) release to the aquifer has the potential to sustain a groundwater contaminant plume for centuries. NRZs, known to exist in other uranium-contaminated aquifers, may be regionally important to uranium persistence.


Assuntos
Sedimentos Geológicos/química , Água Subterrânea/química , Compostos Orgânicos/análise , Urânio/química , Poluentes Radioativos da Água/análise , Carbono/análise , Cor , Colorado , Oxirredução , Tamanho da Partícula , Enxofre/análise , Urânio/análise , Espectroscopia por Absorção de Raios X
3.
Environ Microbiol ; 17(3): 622-36, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24674078

RESUMO

Microbial community structure, and niche and neutral processes can all influence response to disturbance. Here, we provide experimental evidence for niche versus neutral and founding community effects during a bioremediation-related organic carbon disturbance. Subsurface sediment, partitioned into 22 flow-through columns, was stimulated in situ by the addition of acetate as a carbon and electron donor source. This drove the system into a new transient biogeochemical state characterized by iron reduction and enriched Desulfuromonadales, Comamonadaceae and Bacteroidetes lineages. After approximately 1 month conditions favoured sulfate reduction, and were accompanied by a substantial increase in the relative abundance of Desulfobulbus, Desulfosporosinus, Desulfitobacterium and Desulfotomaculum. Two subsets of four to five columns each were switched from acetate to lactate amendment during either iron (earlier) or sulfate (later) reduction. Hence, subsets had significantly different founding communities. All lactate treatments exhibited lower relative abundances of Desulfotomaculum and Bacteroidetes, enrichments of Clostridiales and Psychrosinus species, and a temporal succession from highly abundant Clostridium sensu stricto to Psychrosinus. Regardless of starting point, lactate-switch communities followed comparable structural trajectories, whereby convergence was evident 9 to 16 days after each switch, and significant after 29 to 34 days of lactate addition. Results imply that neither the founding community nor neutral processes influenced succession following perturbation.


Assuntos
Ácido Acético/metabolismo , Carbono/metabolismo , Sedimentos Geológicos/microbiologia , Ferro/metabolismo , Consórcios Microbianos , Sulfatos/metabolismo , Bacteroidetes/genética , Bacteroidetes/metabolismo , Biodegradação Ambiental , Biodiversidade , Clostridium/genética , Clostridium/metabolismo , Comamonadaceae/classificação , Comamonadaceae/genética , Comamonadaceae/metabolismo , Deltaproteobacteria/genética , Desulfotomaculum/genética , Desulfotomaculum/metabolismo , Ecossistema , Oxirredução , Filogenia
4.
Environ Sci Technol ; 49(12): 7340-7, 2015 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-26001126

RESUMO

Oxidative dissolution controls uranium release to (sub)oxic pore waters from biogenic uraninite produced by natural or engineered processes, such as bioremediation. Laboratory studies show that uraninite dissolution is profoundly influenced by dissolved oxygen (DO), carbonate, and solutes such as Ca(2+). In complex and heterogeneous subsurface environments, the concentrations of these solutes vary in time and space. Knowledge of dissolution processes and kinetics occurring over the long-term under such conditions is needed to predict subsurface uranium behavior and optimize the selection and performance of uraninite-based remediation technologies over multiyear periods. We have assessed dissolution of biogenic uraninite deployed in wells at the Rifle, CO, DOE research site over a 22 month period. Uraninite loss rates were highly sensitive to DO, with near-complete loss at >0.6 mg/L over this period but no measurable loss at lower DO. We conclude that uraninite can be stable over decadal time scales in aquifers under low DO conditions. U(VI) solid products were absent over a wide range of DO values, suggesting that dissolution proceeded through complexation and removal of oxidized surface uranium atoms by carbonate. Moreover, under the groundwater conditions present, Ca(2+) binds strongly to uraninite surfaces at structural uranium sites, impacting uranium fate.


Assuntos
Cálcio/química , Água Subterrânea/química , Oxigênio/química , Urânio/química , Biodegradação Ambiental , Carbonatos/química , Análise de Fourier , Cinética , Oxirredução , Solubilidade , Poluentes Radioativos da Água/análise , Espectroscopia por Absorção de Raios X
5.
Environ Sci Technol ; 48(17): 10116-27, 2014 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-25079237

RESUMO

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.


Assuntos
Urânio/isolamento & purificação , Bactérias/metabolismo , Biodegradação Ambiental , Colorado , Modelos Teóricos , Fatores de Tempo , Água/química , Poluentes Radioativos da Água/isolamento & purificação
6.
Environ Sci Technol ; 48(21): 12842-50, 2014 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-25265543

RESUMO

In this study, we report the results of in situ U(VI) bioreduction experiments at the Integrated Field Research Challenge site in Rifle, Colorado, USA. Columns filled with sediments were deployed into a groundwater well at the site and, after a period of conditioning with groundwater, were amended with a mixture of groundwater, soluble U(VI), and acetate to stimulate the growth of indigenous microorganisms. Individual reactors were collected as various redox regimes in the column sediments were achieved: (i) during iron reduction, (ii) just after the onset of sulfate reduction, and (iii) later into sulfate reduction. The speciation of U retained in the sediments was studied using X-ray absorption spectroscopy, electron microscopy, and chemical extractions. Circa 90% of the total uranium was reduced to U(IV) in each reactor. Noncrystalline U(IV) comprised about two-thirds of the U(IV) pool, across large changes in microbial community structure, redox regime, total uranium accumulation, and reaction time. A significant body of recent research has demonstrated that noncrystalline U(IV) species are more suceptible to remobilization and reoxidation than crystalline U(IV) phases such as uraninite. Our results highlight the importance of considering noncrystalline U(IV) formation across a wide range of aquifer parameters when designing in situ remediation plans.


Assuntos
Sedimentos Geológicos/química , Água Subterrânea/química , Urânio/química , Poluentes Radioativos da Água/química , Bactérias/metabolismo , Biodegradação Ambiental , Colorado , Metais/metabolismo , Dados de Sequência Molecular , Oxirredução , Espectrometria por Raios X , Sulfatos/metabolismo , Espectroscopia por Absorção de Raios X
7.
Appl Environ Microbiol ; 79(3): 799-807, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23160129

RESUMO

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO(3)(-)) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO(3), but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.


Assuntos
Bactérias/classificação , Bactérias/genética , Biota , Água Subterrânea/microbiologia , Metagenômica/métodos , Análise em Microsséries/métodos , Acetatos/metabolismo , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Sensibilidade e Especificidade , Bicarbonato de Sódio/metabolismo
8.
Environ Sci Technol ; 47(6): 2535-41, 2013 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-23379698

RESUMO

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 ((238)U/(235)U) of these groundwater samples were determined and used to assess the impact of bicarbonate-induced U(VI) desorption from contaminated sediments on the (238)U/(235)U of groundwater. The (238)U/(235)U 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 (238)U/(235)U composition of uranium-bearing fluids should be useful in quantifying the extent of reduction.


Assuntos
Bicarbonatos/química , Sedimentos Geológicos/análise , Água Subterrânea/análise , Urânio/análise , Poluentes Radioativos da Água/análise , Adsorção , Colorado
9.
Appl Environ Microbiol ; 78(24): 8735-42, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23042184

RESUMO

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.


Assuntos
Geobacter/crescimento & desenvolvimento , Geobacter/metabolismo , Redes e Vias Metabólicas/genética , Proteômica , Proteínas de Bactérias/análise , Biomassa , Geobacter/genética , Metais/metabolismo , Oxirredução , Proteoma/análise
10.
Appl Environ Microbiol ; 78(8): 2966-72, 2012 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22327592

RESUMO

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (E(h)) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.


Assuntos
Biota , Microbiologia Ambiental , Variação Genética , Urânio/metabolismo , Biodegradação Ambiental , Poluentes Ambientais/metabolismo , Análise em Microsséries , Oxirredução
11.
Biodegradation ; 23(4): 535-46, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22270689

RESUMO

Stimulating microbial reduction of soluble U(VI) to less soluble U(IV) shows promise as an in situ bioremediation strategy for uranium contaminated groundwater, but the optimal electron donors for promoting this process have yet to be identified. The purpose of this study was to better understand how the addition of various electron donors to uranium-contaminated subsurface sediments affected U(VI) reduction and the composition of the microbial community. The simple electron donors, acetate or lactate, or the more complex donors, hydrogen-release compound (HRC) or vegetable oil, were added to the sediments incubated in flow-through columns. The composition of the microbial communities was evaluated with quantitative PCR probing specific 16S rRNA genes and functional genes, phospholipid fatty acid analysis, and clone libraries. All the electron donors promoted U(VI) removal, even though the composition of the microbial communities was different with each donor. In general, the overall biomass, rather than the specific bacterial species, was the factor most related to U(VI) removal. Vegetable oil and HRC were more effective in stimulating U(VI) removal than acetate. These results suggest that the addition of more complex organic electron donors could be an excellent option for in situ bioremediation of uranium-contaminated groundwater.


Assuntos
Bactérias/isolamento & purificação , Bactérias/metabolismo , Urânio/metabolismo , Bactérias/classificação , Bactérias/genética , Biodegradação Ambiental , Elétrons , Sedimentos Geológicos/microbiologia , Água Subterrânea/microbiologia , Dados de Sequência Molecular , Oxirredução
12.
Environ Sci Technol ; 45(4): 1250-6, 2011 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-21226528

RESUMO

Previous experiments at the Rifle, Colorado Integrated Field Research Challenge (IFRC) site demonstrated that field-scale addition of acetate to groundwater reduced the ambient soluble uranium concentration. In this report, sediment samples collected before and after acetate field addition were used to assess the active microbes via (13)C acetate stable isotope probing on 3 phases [coarse sand, fines (8-approximately 150 µm), groundwater (0.2-8 µm)] over a 24-day time frame. TRFLP results generally indicated a stronger signal in (13)C-DNA in the "fines" fraction compared to the sand and groundwater. Before the field-scale acetate addition, a Geobacter-like group primarily synthesized (13)C-DNA in the groundwater phase, an alpha Proteobacterium primarily grew on the fines/sands, and an Acinetobacter sp. and Decholoromonas-like OTU utilized much of the (13)C acetate in both groundwater and particle-associated phases. At the termination of the field-scale acetate addition, the Geobacter-like species was active on the solid phases rather than the groundwater, while the other bacterial groups had very reduced newly synthesized DNA signal. These findings will help to delineate the acetate utilization patterns of bacteria in the field and can lead to improved methods for stimulating distinct microbial populations in situ.


Assuntos
Acetatos/metabolismo , Bactérias/metabolismo , Poluentes Radioativos do Solo/metabolismo , Bactérias/isolamento & purificação , Biodegradação Ambiental , Colorado , Água Subterrânea/microbiologia , Microbiologia do Solo , Urânio
13.
Environ Sci Technol ; 45(20): 8748-54, 2011 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-21910475

RESUMO

Reductive bioremediation is currently being explored as a possible strategy for uranium-contaminated aquifers such as the Old Rifle site (Colorado). The stability of U(IV) phases under oxidizing conditions is key to the performance of this procedure. An in situ method was developed to study oxidative dissolution of biogenic uraninite (UO2), a desirable U(VI) bioreduction product, in the Old Rifle, CO, aquifer under different variable oxygen conditions. Overall uranium loss rates were 50-100 times slower than laboratory rates. After accounting for molecular diffusion through the sample holders, a reactive transport model using laboratory dissolution rates was able to predict overall uranium loss. The presence of biomass further retarded diffusion and oxidation rates. These results confirm the importance of diffusion in controlling in-aquifer U(IV) oxidation rates. Upon retrieval, uraninite was found to be free of U(VI), indicating dissolution occurred via oxidation and removal of surface atoms. Interaction of groundwater solutes such as Ca²âº or silicate with uraninite surfaces also may retard in-aquifer U loss rates. These results indicate that the prolonged stability of U(IV) species in aquifers is strongly influenced by permeability, the presence of bacterial cells and cell exudates, and groundwater geochemistry.


Assuntos
Água Subterrânea/química , Urânio/química , Urânio/metabolismo , Poluentes Radioativos da Água/química , Poluentes Radioativos da Água/metabolismo , Biodegradação Ambiental , Colorado , Oxirredução
14.
Environ Sci Technol ; 44(15): 5927-33, 2010 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-20597538

RESUMO

The attenuation of groundwater contamination via chemical reaction is traditionally evaluated by monitoring contaminant concentration through time. However, this method can be confounded by common transport processes (e.g., dilution, sorption). Isotopic techniques bypass the limits of concentration methods, and so may provide improved accuracy in determining the extent of reaction. We apply measurements of 238U/235U to a U bioremediation field experiment at the Rifle Integrated Field Research Challenge Site in Rifle, Colorado. An array of monitoring and injection wells was installed on a 100 m2 plot where U(VI) contamination was present in the groundwater. Acetate-amended groundwater was injected along an up-gradient gallery to encourage the growth of dissimilatory metal reducing bacteria (e.g., Geobacter species). During amendment, U concentration dropped by an order of magnitude in the experiment plot. We measured 238U/235U in samples from one monitoring well by MC-ICP-MS using a double isotope tracer method. A significant approximately 1.00 per thousand decrease in 238U/235U occurred in the groundwater as U(VI) concentration decreased. The relationship between 238U/235U and concentration corresponds approximately to a Rayleigh distillation curve with an effective fractionation factor (alpha) of 1.00046. We attribute the observed U isotope fractionation to a nuclear field shift effect during enzymatic reduction of U(VI)(aq) to U(IV)(s).


Assuntos
Monitoramento de Radiação/métodos , Urânio/análise , Poluentes Radioativos da Água/análise , Biodegradação Ambiental , Colorado , Traçadores Radioativos
15.
Environ Sci Technol ; 44(23): 8897-903, 2010 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-21058662

RESUMO

Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or "pseudo-metagenomes", for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.


Assuntos
Bactérias/metabolismo , Água Doce/microbiologia , Plâncton/metabolismo , Proteoma/metabolismo , Bactérias/classificação , Bactérias/genética , Biodiversidade , Biomassa , Plâncton/classificação , Plâncton/genética , Microbiologia da Água
16.
Appl Environ Microbiol ; 75(20): 6591-9, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19717633

RESUMO

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.


Assuntos
Geobacter/genética , Geobacter/fisiologia , Urânio/metabolismo , Poluentes Radioativos da Água/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Genômica , Geobacter/classificação , Geobacter/isolamento & purificação , Dados de Sequência Molecular , Oxirredução , Mapeamento de Peptídeos , Plâncton/classificação , Plâncton/genética , Plâncton/isolamento & purificação , Plâncton/fisiologia , Proteômica , Microbiologia da Água
17.
J Contam Hydrol ; 93(1-4): 216-35, 2007 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-17442451

RESUMO

During 2002 and 2003, bioremediation experiments in the unconfined aquifer of the Old Rifle UMTRA field site in western Colorado provided evidence for the immobilization of hexavalent uranium in groundwater by iron-reducing Geobacter sp. stimulated by acetate amendment. As the bioavailable Fe(III) terminal electron acceptor was depleted in the zone just downgradient of the acetate injection gallery, sulfate-reducing organisms came to dominate the microbial community. In the present study, we use multicomponent reactive transport modeling to analyze data from the 2002 field experiment to identify the dominant transport and biological processes controlling uranium mobility during biostimulation, and determine field-scale parameters for these modeled processes. The coupled process simulation approach was able to establish a quantitative characterization of the principal flow, transport, and reaction processes based on the 2002 field experiment, that could be applied without modification to describe the 2003 field experiment. Insights gained from this analysis include field-scale estimates of the bioavailable Fe(III) mineral threshold for the onset of sulfate reduction, and rates for the Fe(III), U(VI), and sulfate terminal electron accepting processes.


Assuntos
Urânio/química , Poluentes Químicos da Água/análise , Purificação da Água/métodos , Acetatos/química , Biodegradação Ambiental , Brometos/química , Calibragem , Elétrons , Geologia/métodos , Ferro/química , Modelos Químicos , Modelos Estatísticos , Sulfatos/química , Fatores de Tempo , Água/química
18.
Trends Microbiol ; 24(8): 600-610, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27156744

RESUMO

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.


Assuntos
Clima , Ecossistema , Metagenômica , Consórcios Microbianos/fisiologia , Microbiologia do Solo , Atmosfera , Biodiversidade , Carbono/metabolismo , Gases , Genoma Microbiano , Sedimentos Geológicos , Efeito Estufa , Água Subterrânea , Redes e Vias Metabólicas/fisiologia , Consórcios Microbianos/genética , Interações Microbianas/fisiologia , Nitrogênio/metabolismo , Ciclo do Nitrogênio , Solo/química , Enxofre/metabolismo , Simbiose/fisiologia
19.
PLoS One ; 10(9): e0137270, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26382047

RESUMO

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.


Assuntos
Deltaproteobacteria/metabolismo , Geobacter/metabolismo , Água Subterrânea/microbiologia , RNA Bacteriano/metabolismo , RNA Ribossômico/metabolismo , Urânio/metabolismo , Poluentes Radioativos da Água/metabolismo , Biodegradação Ambiental , Colorado , Deltaproteobacteria/genética , Geobacter/genética , Água Subterrânea/análise , Filogenia , RNA Bacteriano/genética , RNA Ribossômico/genética , Ribossomos/genética , Ribossomos/metabolismo , Urânio/análise , Poluentes Radioativos da Água/análise
20.
PLoS One ; 10(4): e0123378, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25874721

RESUMO

The Department of Energy's Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.


Assuntos
Betaproteobacteria/isolamento & purificação , Microbiologia do Solo , Urânio/química , Acetatos/química , Betaproteobacteria/genética , Biodegradação Ambiental , Burkholderia/genética , Colorado , Elétrons , Sedimentos Geológicos/microbiologia , Água Subterrânea , Funções Verossimilhança , Espectrometria de Massas , Microbiota , Dados de Sequência Molecular , Compostos Organometálicos/química , Oxigênio/química , Filogenia , RNA Ribossômico 16S/química , Radioisótopos/química
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