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Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

Description: The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.
Date: November 28, 2012
Creator: Lovley, Derek R
Partner: UNT Libraries Government Documents Department

MicrobeWorld Radio and Communications Initiative

Description: MicrobeWorld is a 90-second feature broadcast daily on more than 90 public radio stations and available from several sources as a podcast, including www.microbeworld.org. The feature has a strong focus on the use and adapatbility of microbes as alternative sources of energy, in bioremediation, their role in climate, and especially the many benefits and scientific advances that have resulting from decoding microbial genomes. These audio features are permanantly archived on an educational outreach site, microbeworld.org, where they are linked to the National Science Education Standards. They are also being used by instructors at all levels to introduce students to the multiple roles and potential of microbes, including a pilot curriculum program for middle-school students in New York.
Date: November 22, 2006
Creator: Hyde, Barbara
Partner: UNT Libraries Government Documents Department

Biodegradation of Certain Petroleum Product Contaminants in Soil and Water By Selected Bacteria

Description: Soil contamination by gasoline underground storage tanks is a critical environmental problem. The results herein show that in situ bioremediation using indigenous soil microorganisms is the method of choice. Five sites were selected for bioremediation based on the levels of benzene, toluene, ethylbenzene and xylene and the amount of total petroleum hydrocarbons in the soil. Bacteria capable of degrading these contaminants were selected from the contaminated sites and grown in 1,200 I mass cultures. These were added to the soil together with nutrients, water and air via PVC pipes.
Date: December 1995
Creator: Nevárez-Moorillón, Guadalupe Virginia
Partner: UNT Libraries

Dynamics of Coupled Microbial and Contaminant Transport.

Description: Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. This project's objective is to develop the understanding of the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases. In particular this interdisciplinary research project provides fundamental information on the attachment/detachment dynamics of anaerobic bacteria in heterogeneous porous media under growth and growth-limiting conditions. This is a critical requirement for designing and evaluating in situ bioremediation efforts.
Date: June 1, 2000
Creator: Ginn, Timothy R.; Murphy, Ellyn M.; Fletcher, Madilyn M. & Cushman, Jonh H.
Partner: UNT Libraries Government Documents Department

Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

Description: The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.
Date: November 28, 2012
Creator: Lovley, Derek R.
Partner: UNT Libraries Government Documents Department

Final report for DOE Grant No. DE-SC0006609 - Persistence of Microbially Facilitated Calcite Precipitation as an in situ Treatment for Strontium-90

Description: Subsurface radionuclide and metal contaminants throughout the U.S. Department of Energy (DOE) complex pose one of DOE?s greatest challenges for long-term stewardship. One promising stabilization mechanism for divalent ions, such as the short-lived radionuclide Sr-90, is co-precipitation in calcite. We have previously found that nutrient addition can stimulate microbial ureolytic activity, that this activity accelerates calcite precipitation and co-precipitation of Sr, and that higher calcite precipitation rates can result in increased Sr partitioning. We have conducted integrated field, laboratory, and computational research to evaluate the relationships between ureolysis and calcite precipitation rates and trace metal partitioning under environmentally relevant conditions, and investigated the coupling between flow/flux manipulations and precipitate distribution. A field experimental campaign conducted at the Integrated Field Research Challenge (IFRC) site located at Rifle, CO was based on a continuous recirculation design; water extracted from a down-gradient well was amended with urea and molasses (a carbon and electron donor) and re-injected into an up-gradient well. The goal of the recirculation design and simultaneous injection of urea and molasses was to uniformly accelerate the hydrolysis of urea and calcite precipitation over the entire inter-wellbore zone. The urea-molasses recirculation phase lasted, with brief interruptions for geophysical surveys, for 12 days and was followed by long-term monitoring which continued for 13 months. A post experiment core located within the inter-wellbore zone was collected on day 321 and characterized with respect to cation exchange capacity, mineral carbonate content, urease activity, ureC gene abundance, extractable ammonium (a urea hydrolysis product) content, and the C-13 isotopic composition of solid carbonates. It was also subjected to selective extractions for strontium and uranium. Result of the core characterization suggest that urea hydrolysis occurred primarily within the upper portion of the inter-wellbore zone and that strontium was mobilized from cation exchange sites and subsequently co-precipitated with new ...
Date: November 15, 2013
Creator: Smith, Robert W & Fujita, Yoshiko
Partner: UNT Libraries Government Documents Department

Microbial Oxidation and Demethylation Processes in the Environmental Mercury Cycle

Description: This project demonstrated that bacterial catalase enzymes can convert unreactive Hg(0) to highly reactive Hg(II) ion. It also demonstrated the mechanism of the organomercural lyase, a bacterial enzyme which degrades methylmercury and other organomercurials. Lastly, it demonstrated the 3-dimensional structure of this enzyme by both solution NMR and by x-ray crystallography. These structures provide insights into the catalytic mechanism of the lyase that will allow engineering of variants with improved ability to degrade methylmercury.
Date: October 30, 2000
Creator: Summers, Anne O.
Partner: UNT Libraries Government Documents Department

Integrating the Molecular Machines of Mercury Detoxification into Host Cell Biology

Description: Integrating the Molecular Machines of Mercury Detoxification into Host Cell Biology The bacterial mercury resistance (mer) operon, one of the most evolutionarily successful genetic loci in any defined organism, detoxifies organic and inorganic mercury compounds. Several major biotic processes in the global Hg(II) cycle are carried out by bacteria with this highly mobile detoxification locus that occurs in Gram negative and high and low GC Gram positive bacteria. The functions of many individual mer operon components are well described, so we aim to dissect the higher order interactions of the enzymes, transporters, and regulators of this paradigm metal metabolizing system with each other and with the larger metabolism of the host cell. Understanding how this ubiquitous detoxification system fits into the biology and ecology of its bacterial host is essential to guide interventions that support and enhance Hg remediation. Specifically, we will test the hypotheses that: (a) the organomercurial lyase, MerB, and the mercuric reductase, MerA, act synergistically together and with the membrane-bound Hg(II) transporters, MerT and MerC, to detoxify mercurials; (b) the interaction of the metalloregulator MerR with RNA polymerase (RNAP) and with its DNA binding site, MerO, modulates its metal response, and interaction with its antagonist, MerD, prevents RNA polymerase from binding to the structural gene promoter, P merT and (c) exposure of cells to Hg(II) makes specific demands on cellular resources and expression of the mer operon modulates those demands and is, in turn, modulated by them. To test these hypotheses we propose to: (a) use enzymology, NMR, fluorescence anisotropy, protein-crosslinking, crystallography, and calorimetry in vitro along with in vivo measurements of Hg(II) volatilization and HgR phenotyping to detect and define interactions between the mer enzymes, MerA and MerB, and the transporters, MerT and MerC,and their functional fragments and specific mutant variants; (b) use NMR, fluorescence anisotropy, ...
Date: March 11, 2010
Creator: Summers, Anne O
Partner: UNT Libraries Government Documents Department

Process Control Minitoring by Stress Response

Description: Environmental contamination with a variety of pollutants hasprompted the development of effective bioremediation strategies. But howcan these processes be best monitored and controlled? One avenue underinvestigation is the development of stress response systems as tools foreffective and general process control. Although the microbial stressresponse has been the subject of intensive laboratory investigation, theenvironmental reflection of the laboratory response to specific stresseshas been little explored. However, it is only within an environmentalcontext, in which microorganisms are constantly exposed to multiplechanging environmental stresses, that there will be full understanding ofmicrobial adaptive resiliency. Knowledge of the stress response in theenvironment will facilitate the control of bioremediation and otherprocesses mediated by complex microbial communities.
Date: April 17, 2006
Creator: Hazen, Terry C. & Stahl, David A.
Partner: UNT Libraries Government Documents Department

Comparison of Remediation Methods in Different Hydrogeologic Settings Using Bioplume II

Description: A contaminant fate and transport computer model, Bioplume II, which allows simulation of bioremediation in ground water systems, was used to compare the effects of 11 remediation scenarios on a benzene plume. The plume was created in three different hydrogeologic settings from the simulation of an underground gasoline storage tank leak.
Date: May 1996
Creator: White, Sherry A. (Sherry Anne)
Partner: UNT Libraries

Application of Proteomics and Lipid Studies in Environmental Biotechnology

Description: The overview of changes in protein levels or states in response to a growth condition, stress, mutation or metabolic engineering is invaluable in understanding the physiology of a microbial system. The lipid profile of the cell is similarly a valuable diagnostic of the cellular response and health, especially in context of survival in a fluctuating environment. To obtain comprehensive cellular models, post-transcriptional cell wide surveys at the levels of proteins and lipids are required. Both these fields have been greatly bolstered by the development of high throughput methods using mass spectrometry. Multiple strategies now exist for the identification of proteins, and numerous workflows to quantify protein abundance have also been developed. Cellular profiling such as these allows us to assess the potential of a microbial system for environmental applications such as bioremediation and bio-energy.
Date: August 12, 2008
Creator: Mukhopadhyay, Aindrila
Partner: UNT Libraries Government Documents Department

Mesoscale Tank Experiments for Investigating Carbon Tetrachloride Biodegradation

Description: Mesoscale tank experiments were performed to simulate bioremediation of saturated zone carbon tetrachloride (CCl4) originating from a vadose zone carbon tetrachloride source. The mesoscale tank is 2-m wide by 2-m high by 3-m long and was constructed of stainless steel, yielding a total volume of 12 m3. Simulated geology within the tank consisted of two unconsolidated sand layers separated by a clay layer containing variable-sized stainless steel tubes that represented fractures within a consolidated porous medium. The thickness of the upper sand layer was approximately 55 cm, the thickness of the virtual fracture layer was 25 cm, and the thickness of the lower sand layer was approximately 98 cm. The water table was located at an elevation of approximately 54 cm from the bottom of the tank. CCl4 was added to the sealed tank by pouring 500 ml of neat CCl4 into a beaker buried approximately 10 cm below the upper sand surface through a stainless steel tube. The CCl4 was then allowed to partition through the reactor over time, eventually coming to equilibrium. Once CCl4 equilibrium had occurred in the saturated zone (~500 ppb); the reactor was bioaugmented with a CCl4 degrading culture enriched from the Subsurface Disposal Area at the INEEL. The culture was grown to a cell density of ~ 1.0 x 108 cells/ml and injected into the simulated aquifer through a center sampling port. Following injection of the culture, an initial aliquot of lactate (1,000 g/L), nitrogen, and phosphorus were added to the reactor. Lactate was injected every 3 – 5 days for one month. After 1 month of operation, a continuous supply of lactate (1,000 g/L) was pumped into the reactor at an average rate of 50 mL/min. CCl4 concentrations in the unsaturated zone were measured using hollow fiber membrane samplers, while liquid samples were ...
Date: June 1, 2005
Creator: Lee, Brady D. & Lenhard, Robert J.
Partner: UNT Libraries Government Documents Department

Using a Consensus Conference to Characterize Regulatory Concerns Regarding Bioremediation of Radionuclides and Heavy Metals in Mixed Waste at DOE Sites

Description: A consensus workshop was developed and convened with ten state regulators to characterize concerns regarding emerging bioremediation technology to be used to clean-up radionuclides and heavy metals in mixed wastes at US DOE sites. Two questions were explored: integrated questions: (1) What impact does participation in a consensus workshop have on the knowledge, attitudes, and practices of state regulators regarding bioremediation technology? (2) How effective is a consensus workshop as a strategy for eliciting and articulating regulators’ concerns regarding the use of bioremediation to clean up radionuclides and heavy metals in mixed wastes at U.S. Department of Energy Sites around the county? State regulators met together for five days over two months to learn about bioremediation technology and develop a consensus report of their recommendations regarding state regulatory concerns. In summary we found that panel members: - quickly grasped the science related to bioremediation and were able to effectively interact with scientists working on complicated issues related to the development and implementation of the technology; - are generally accepting of in situ bioremediation, but concerned about costs, implementation (e.g., institutional controls), and long-term effectiveness of the technology; - are concerned equally about technological and implementation issues; and - believed that the consensus workshop approach to learning about bioremediation was appropriate and useful. Finally, regulators wanted decision makers at US DOE to know they are willing to work with DOE regarding innovative approaches to clean-up at their sites, and consider a strong relationship between states and the DOE as critical to any effective clean-up. They do not want perceive themselves to be and do not want others to perceive them as barriers to successful clean-up at their sites.
Date: September 1, 2006
Creator: Lach, Denise & Sanford, Stephanie
Partner: UNT Libraries Government Documents Department

Influence of Reactive Transport on the Reduction of U(VI) in the Presence of Fe(III) and Nitrate: Implications for U(VI) Immobilization by Bioremediation / Biobarriers- Final Report

Description: Subsurface contamination by metals and radionuclides represent some of the most challenging remediation problems confronting the Department of Energy (DOE) complex. In situ remediation of these contaminants by dissimilatory metal reducing bacteria (DMRB) has been proposed as a potential cost effective remediation strategy. The primary focus of this research is to determine the mechanisms by which the fluxes of electron acceptors, electron donors, and other species can be controlled to maximize the transfer of reductive equivalents to the aqueous and solid phases. The proposed research is unique in the NABIR portfolio in that it focuses on (i) the role of flow and transport in the initiation of biostimulation and the successful sequestration of metals and radionuclides [specifically U(VI)], (ii) the subsequent reductive capacity and stability of the reduced sediments produced by the biostimulation process, and (iii) the potential for altering the growth of biomass in the subsurface by the addition of specific metabolic uncoupling compounds. A scientifically-based understanding of these phenomena are critical to the ability to design successful bioremediation schemes. The laboratory research will employ Shewanella putrefaciens (CN32), a facultative DMRB that can use Fe(III) oxides as a terminal electron acceptor. Sediment-packed columns will be inoculated with this organism, and the reduction of U(VI) by the DMRB will be stimulated by the addition of a carbon and energy source in the presence of Fe(III). Separate column experiments will be conducted to independently examine: (1) the importance of the abiotic reduction of U(VI) by biogenic Fe(II); (2) the influence of the transport process on Fe(III) reduction and U(VI) immobilization, with emphasis on methods for controlling the fluxes of aqueous species to maximize uranium reduction; (3) the reductive capacity of biologically-reduced sediments (with respect to re-oxidation by convective fluxes of O2 and NO3-) and the long-term stability of immobilized uranium mineral ...
Date: January 1, 2007
Creator: Wood, B.D.
Partner: UNT Libraries Government Documents Department

Guidelines A Primer for Communicating Effectively with NABIR Stakeholders

Description: The purpose of this report is to help scientists communicate with stakeholders and the public (primarily nonscientists) about fundamental science research. The primary audience for this report is scientists involved in the Natural and Accelerated Bioremediation Research (NABIR) program of the U.S. Department of Energy. However, the information and insights in the report that are not program-specific should be helpful to scientists in other fundamental science research programs. The report first discusses why scientists should talk to stakeholders and the public, and the challenges associated with discussing the NABIR program. It is observed that communication initiatives can be characterized by three factors: relationships in the social environment, views of what constitutes communication, and accepted forms of communication practices and products. With a focus on informal science communication, recent efforts to gauge public understanding of science and the factors that affect public trust of science institutions are discussed. The social bases for scientist-nonscientist interactions are then examined, including possible sources of distrust and difficulties in transferring discussions of fundamental science from classrooms (where most of the public first learns about science) to public forums. Finally, the report contains specific suggestions for preparing, meeting, and following up on public interactions with stakeholders and the public, including themes common to public discussions of NABIR science and features of scientist-nonscientist interactions observed in interpersonal, small group, and large group interactions between NABIR scientists and stakeholders. A Quick Preparation Guide for Meeting NABIR Stakeholders is provided immediately following the Summary. It condenses some of the information and advice found in the text of the report.
Date: March 15, 2002
Creator: Weber, James R.; Word, Charlotte J. & Bilyard, Gordon R.
Partner: UNT Libraries Government Documents Department

in situ Calcite Precipitation for Contaminant Immobilization

Description: in situ Calcite Precipitation for Contaminant Immobilization Yoshiko Fujita (Yoshiko.fujita@inl.gov) (Idaho National Laboratory, Idaho Falls, Idaho, USA) Robert W. Smith (University of Idaho-Idaho Falls, Idaho Falls, Idaho, USA) Subsurface radionuclide and trace metal contaminants throughout the U.S. Department of Energy (DOE) complex pose one of DOE’s greatest challenges for long-term stewardship. One promising stabilization mechanism for divalent trace ions, such as the short-lived radionuclide strontium-90, is co-precipitation in calcite. Calcite, a common mineral in the arid western U.S., can form solid solutions with trace metals. The rate of trace metal incorporation is susceptible to manipulation using either abiotic or biotic means. We have previously demonstrated that increasing the calcite precipitation rate by stimulating the activity of urea hydrolyzing microorganisms can result in significantly enhanced Sr uptake. Urea hydrolysis causes the acceleration of calcium carbonate precipitation (and trace metal co-precipitation) by increasing pH and alkalinity, and also by liberating the reactive cations from the aquifer matrix via exchange reactions involving the ammonium ion derived from urea: H2NCONH2 + 3H2O ? 2NH4+ + HCO3- + OH- urea hydrolysis >X:2Ca + 2NH4+ ? 2>X:NH4 + Ca2+ ion exchange Ca2+ + HCO3- + OH- ? CaCO3(s) + H2O calcite precipitation where >X: is a cation exchange site on the aquifer matrix. This contaminant immobilization approach has several attractive features. Urea hydrolysis is catalyzed by the urease enzyme, which is produced by many indigenous subsurface microorganisms. Addition of foreign microbes is unnecessary. In turn the involvement of the native microbes and the consequent in situ generation of reactive components in the aqueous phase (e.g., carbonate and Ca or Sr) can allow dissemination of the reaction over a larger volume and/or farther away from an amendment injection point, as compared to direct addition of the reactants at a well (which can lead to clogging). A final ...
Date: August 1, 2009
Creator: Fujita, Yoshiko & Smith, Robert W.
Partner: UNT Libraries Government Documents Department

Two Component Signal Transduction in Desulfovibrio Species

Description: The environmentally relevant Desulfovibrio species are sulfate-reducing bacteria that are of interest in the bioremediation of heavy metal contaminated water. Among these, the genome of D. vulgaris Hildenborough encodes a large number of two component systems consisting of 72 putative response regulators (RR) and 64 putative histidinekinases (HK), the majority of which are uncharacterized. We classified the D. vulgaris Hildenborough RRs based on their output domains and compared the distribution of RRs in other sequenced Desulfovibrio species. We have successfully purified most RRs and several HKs as His-tagged proteins. We performed phospho-transfer experiments to verify relationships between cognate pairs of HK and RR, and we have also mapped a few non-cognate HK-RR pairs. Presented here are our discoveries from the Desulfovibrio RR categorization and results from the in vitro studies using purified His tagged D. vulgaris HKs and RRs.
Date: May 17, 2010
Creator: Luning, Eric; Rajeev, Lara; Ray, Jayashree & Mukhopadhyay, Aindrila
Partner: UNT Libraries Government Documents Department

Developments in Bioremediation of Soils and Sediments Polluted with Metals and Radionuclides: 2. Field Research on Bioremediation of Metals and Radionuclides

Description: Bioremediation of metals and radionuclides has had manyfield tests, demonstrations, and full-scale implementations in recentyears. Field research in this area has occurred for many different metalsand radionuclides using a wide array of strategies. These strategies canbe generally characterized in six major categories: biotransformation,bioaccumulation/bisorption, biodegradation of chelators, volatilization,treatment trains, and natural attenuation. For all field applicationsthere are a number of critical biogeochemical issues that most beaddressed for the successful field application. Monitoring andcharacterization parameters that are enabling to bioremediation of metalsand radionuclides are presented here. For each of the strategies a casestudy is presented to demonstrate a field application that uses thisstrategy.
Date: March 15, 2007
Creator: Hazen, Terry C. & Tabak, Henry H.
Partner: UNT Libraries Government Documents Department

Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

Description: The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirements of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.
Date: June 9, 2005
Creator: Sun, Y & Glascoe, L
Partner: UNT Libraries Government Documents Department

Bioremediation of Petroleum Hydrocarbons in Heterogeneous Soils

Description: Western Research Institute (WRI) in conjunction with the University of Wyoming, Department of Renewable Resources and the U.S. Department of Energy, under Task 35, conducted a laboratory-scale study of hydrocarbon biodegradation rates versus a variety of physical and chemical parameters to develop a base model. By using this model, biodegradation of Petroleum hydrocarbons in heterogeneous soils can be predicted. The base model, as developed in this study, have been tested by both field and laboratory data. Temperature, pH, and nutrients appear to be the key parameters that can be incorporate into the model to predict biodegradation rates. Results to date show the effect of soil texture and source on the role of each parameter in the rates of hydrocarbon biodegradation. Derived from the existing study, an alternative approach of using CO{sub 2} accumulation data has been attempted by our collaborators at the University of Wyoming. The model has been modified and fine tuned by incorporating these data to provide more information on biodegradation.
Date: March 2, 2006
Creator: Jin, Song; Fallgren, Paul & Brown, Terry
Partner: UNT Libraries Government Documents Department