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In situ groundwater bioremediation

Description: In situ groundwater bioremediation of hydrocarbons has been used for more than 40 years. Most strategies involve biostimulation; however, recently bioaugmentation have been used for dehalorespiration. Aquifer and contaminant profiles are critical to determining the feasibility and strategy for in situ groundwater bioremediation. Hydraulic conductivity and redox conditions, including concentrations of terminal electron acceptors are critical to determine the feasibility and strategy for potential bioremediation applications. Conceptual models followed by characterization and subsequent numerical models are critical for efficient and cost effective bioremediation. Critical research needs in this area include better modeling and integration of remediation strategies with natural attenuation.
Date: February 1, 2009
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Cometabolic bioremediation

Description: Cometabolic bioremediation is probably the most under appreciated bioremediation strategy currently available. Cometabolism strategies stimulate only indigenous microbes with the ability to degrade the contaminant and cosubstrate e.g. methane, propane, toluene and others. This highly targeted stimulation insures that only those microbes that can degrade the contaminant are targeted, thus reducing amendment costs, well and formation plugging, etc. Cometabolic bioremediation has been used on some of the most recalcitrant contaminants, e.g. PCE, TCE, MTBE, TNT, dioxane, atrazine, etc. Methanotrophs have been demonstrated to produce methane monooxygense, an oxidase that can degrade over 300 compounds. Cometabolic bioremediation also has the advantage of being able to degrade contaminants to trace concentrations, since the biodegrader is not dependent on the contaminant for carbon or energy. Increasingly we are finding that in order to protect human health and the environment that we must remediate to lower and lower concentrations, especially for compounds like endocrine disrupters, thus cometabolism may be the best and maybe the only possibility that we have to bioremediate some contaminants.
Date: February 15, 2009
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

4th Annual DOE-ERSP PI Meeting: Abstracts

Description: This contains abstracts from the 2009 Annual Environmental Remediation Sciences Program (ERSP) Principal Investigators (PI) Meeting. The ERSP seeks to advance fundamental science to understand, predict, and mitigate the impacts of environmental contamination from past nuclear weapons production and provide a scientific basis for the long-term stewardship of nuclear waste disposal. These ambitious goals cannot be achieved by any one project alone. Therefore, ERSP funds a combination of research programs at the DOE national laboratories, individual projects at universities and federal agencies, and large long(er)-term field site research. Integration of these activities to advance the ERSP goals is a constant challenge, but made significantly simpler by bringing together all funded ERSP researchers once a year to discuss the very latest research results. It is at these meetings where new ideas and/or scientific advancements in support of ERSP goals can be discussed and openly debated among all PIs in the program. The ERSP thrives, in part, on the new ideas, concepts, scientific connections, and collaborations generated as a result of these meetings. The annual PI Meeting is very much a working meeting with three major goals: (1) to provide opportunities for scientific interaction among the ERSP scientists, a critical element for the program; (2) to provide the ERSP program staff with an opportunity to evaluate the progress of each program and project; and (3) to showcase the ERSP to interested parties within DOE and within other federal agencies In addition to program managers from within OBER, there will be representatives from other offices within DOE and other federal agencies in attandance at the meeting.
Date: March 1, 2009
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

Description: Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in just a few hours is leading to similar breakthroughs in characterizing proteomes, metabolomes, phenotypes, and fluxes for organisms, populations, and communities. Understanding and modeling functional microbial community structure and stress responses in subsurface environments has tremendous implications for our fundamental understanding of biogeochemistry and the potential for making biofuel breakthroughs. Monitoring techniques that inventory and monitor terminal electron acceptors and electron donors, enzyme probes that measure functional activity in the environment, functional genomic microarrays, phylogenetic microarrays, metabolomics, proteomics, and quantitative PCR are also being rapidly adapted for studies in environmental biotechnology. Integration of all of these new high throughput techniques using the latest advances in bioinformatics and modeling will enable break-through science in environmental biotechnology. A review of these techniques with examples from field studies and lab simulations will be discussed.
Date: August 12, 2008
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Bioremediation Education Science and Technology (BEST) Program Annual Report 1999

Description: The Bioremediation, Education, Science and Technology (BEST) partnership provides a sustainable and contemporary approach to developing new bioremedial technologies for US Department of Defense (DoD) priority contaminants while increasing the representation of underrepresented minorities and women in an exciting new biotechnical field. This comprehensive and innovative bioremediation education program provides under-represented groups with a cross-disciplinary bioremediation cirruculum and financial support, coupled with relevant training experiences at advanced research laboratories and field sites. These programs are designed to provide a stream of highly trained minority and women professionals to meet national environmental needs.
Date: July 2000
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Multiphase Modeling of Flow, Transport, and Biodegradation in a Mesoscale Landfill Bioreactor

Description: The need to control gas and leachate production and minimize refuse volume in municipal solid waste landfills has motivated the development of landfill simulation models to predict and design optimal treatment processes. We have developed a multiphase and multicomponent nonisothermal module called T2LBM for the three-dimensional TOUGH2 flow and transport simulator. T2LBM can be used to simulate aerobic or anaerobic biodegradation of municipal solid waste and the associated flow and transport of gas and liquid through the refuse mass. Acetic acid is used as a proxy for all biodegradable substrates in the refuse. T2LBM incorporates a Monod kinetic rate law for the biodegradation of acetic acid by either aerobic or anaerobic microbes as controlled by the local oxygen concentration. We have verified the model against published data, and applied it to our own mesoscale laboratory aerobic landfill bioreactor experiments. We observe spatial variability of flow and biodegradation consistent with permeability heterogeneity and the geometry of the radial grid. The model is capable of matching results of a shut-in test where the respiration of the system is measured over time.
Date: February 1, 2002
Creator: Oldenburg, Curtis M.; Borglin, Sharon E. & Hazen, Terry C.
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

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

Fuzzy systems modeling of in situ bioremediation of chlorinatedsolve n ts

Description: A large-scale vadose zone-groundwater bioremediationdemonstration was conducted at the Savannah River Site (SRS) by injectingseveral types of gases (ambient air, methane, and nitrous oxide andtriethyl phosphate mixtures) through a horizontal well in the groundwaterat a 175 ft depth. Simultaneously, soil gas was extracted through aparallel horizontal well in the vadose zone at a 80 ft depth Monitoringrevealed a wide range of spatial and temporal variations ofconcentrations of VOCs, enzymes, and biomass in groundwater and vadosezone monitoring boreholes over the field site. One of the powerful modernapproaches to analyze uncertain and imprecise data chemical data is basedon the use of methods of fuzzy systems modeling. Using fuzzy modeling weanalyzed the spatio-temporal TCE and PCE concentrations and methanotrophdensities in groundwater to assess the effectiveness of differentcampaigns of air stripping and bioremediation, and to determine the fuzzyrelationship between these compounds. Our analysis revealed some detailsabout the processes involved in remediation, which were not identified inthe previous studies of the SRS demonstration. We also identified somefuture directions for using fuzzy systems modeling, such as theevaluation of the mass balance of the vadose zone - groundwater system,and the development of fuzzy-ruled methods for optimization of managingremediation activities, predictions, and risk assessment.
Date: September 5, 2001
Creator: Faybishenko, Boris & Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

2nd Annual DOE-ERSP PI Meeting: Abstracts

Description: Welcome to the annual 2007 Environmental Remediation Sciences Program (ERSP) Principal Investigators (PIs) meeting. The purpose of this meeting is to bring together all of the lead PIs and key Co-PIs in the program to share and review the results of funded research from the past year. This meeting allows program managers from the Environmental Remediation Sciences Division (ERSD) within the Office of Biological and Environmental Research (OBER) to gauge the progress and significance of the funded research, and it is also an important venue to showcase ERSP research to interested parties within DOE and other invited federal agency representatives. Additionally, these meetings should serve as an opportunity for funded PIs to view their research in the context of the entire ERSP portfolio. Past ERSP meetings have been very important venues for detailed discussion of research results among PIs, development of new research ideas, fostering new collaborations and discussion with ERSD program managers on future research efforts and/or initiatives within the program. In short, these meetings are an important resource for both program managers and PIs. There will be only one ERSP PI meeting for 2007. In years past, ERSD has sponsored two PI meetings, one in the spring and a separate meeting in the fall that focused primarily on field research. However, this format tends to insulate laboratory-based research from the field research sponsored in the program and is incompatible with the ERSD view that laboratory-based research should progress towards understanding the relevant processes in natural environments at the field scale. Therefore the agenda for this year's PI meeting is well integrated with both lab-based and field-based projects, to allow for detailed discussion between PIs involved in each area. In the agenda, you will notice a more relaxed format than in years past. This year's meeting spans four days, ...
Date: March 14, 2007
Creator: Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Overcoming the anaerobic hurdle in phenotypic microarrays: Generation andvisualization of growth curve data for Desulfovibrio vulgaris Hildenborough

Description: Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog(TM) system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.
Date: October 4, 2008
Creator: Borglin, Sharon E; Joyner, Dominique; Jacobsen, Janet; Mukhopadhyay, Aindrila & Hazen, Terry C.
Partner: UNT Libraries Government Documents Department

Visualization of Growth Curve Data from Phenotype Microarray Experiments

Description: Phenotype microarrays provide a technology to simultaneouslysurvey the response of an organism to nearly 2,000 substrates, includingcarbon, nitrogen and potassium sources; varying pH; varying saltconcentrations; and antibiotics. In order to more quickly and easily viewand compare the large number of growth curves produced by phenotypemicroarray experiments, we have developed software to produce and displaycolor images, each of which corresponds to a set of 96 growth curves.Using color images to represent growth curves data has proven to be avaluable way to assess experiment quality, compare replicates, facilitatecomparison of the responses of different organisms, and identifysignificant phenotypes. The color images are linked to traditional plotsof growth versus time, as well as to information about the experiment,organism, and substrate. In order to share and view information and dataproject-wide, all information, plots, and data are accessible using onlya Web browser.
Date: April 19, 2007
Creator: Jacobsen, Janet S.; Joyner, Dominique C.; Borglin, Sharon E.; Hazen, Terry C.; Arkin, Adam P. & Bethel, E. Wes
Partner: UNT Libraries Government Documents Department

Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using gaschromatography-mass spectrometry and fourier transform-ion cyclotronresonance mass spectrometry

Description: It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source witheither trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor.Analysis of cellular metabolites indicates that a large percentage(>75 percent) of lactate was partially oxidized to either acetate orpyruvate. The 13C isotope distributions in amino acids and other keymetabolites indicate that, under anaerobic conditions, a complete serinepathway is not present, and lactate is oxidized via a highly reversibleserine degradation pathway. The labeling data also suggest significantactivity in the anaplerotic (malic enzyme and phosphoenolpyruvatecarboxylase) and glyoxylate shunt (isocitrate lyase and malate synthase)reactions. Although the tricarboxylic acid (TCA) cycle is often observedto be incomplete in many other anaerobes (absence of 2-oxoglutaratedehydrogenase activity), isotopic labeling supports the existence of acomplete TCA cycle in S. oneidensis MR-1 under TMAO reductioncondition.
Date: July 11, 2006
Creator: Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C. & Keasling, Jay D.
Partner: UNT Libraries Government Documents Department

Flux analysis of central metabolic pathways in Geobactermetallireducens during reduction of solubleFe(III)-NTA

Description: We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were present under theseconditions, but enzymes in the glyoxylate shunt and malic enzyme wereabsent. Gluconeogenesis and the pentose phosphate pathway were mainlyemployed for biosynthesis and accounted for less than 3 percent of totalcarbon consumption. The model also indicated surprisingly highreversibility in the reaction between oxoglutarate and succinate. Thisstep operates close to the thermodynamic equilibrium possibly becausesuccinate is synthesized via a transferase reaction, and the conversionof oxoglutarate to succinate is a rate limiting step for carbonmetabolism. These findings enable a better understanding of therelationship between genome annotation and extant metabolic pathways inG. metallireducens.
Date: January 1, 2007
Creator: Tang, Yinjie J.; Chakraborty, Romy; Garcia-Martin, Hector; Chu,Jeannie; Hazen, Terry C. & Keasling, Jay D.
Partner: UNT Libraries Government Documents Department

Flux analysis of central metabolic pathways in the Fe(III)-reducing organism Geobacter metallireducens via 13C isotopiclabeling

Description: We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The model indicated that over 90 percent of the acetate wascompletely oxidized to CO2 via a complete tricarboxylic acid (TCA) cyclewhile reducing iron. Pyruvate carboxylase and phosphoenolpyruvatecarboxykinase were present under these conditions, but enzymes in theglyoxylate shunt and malic enzyme were absent. Gluconeogenesis and thepentose phosphate pathway were mainly employed for biosynthesis andaccounted for less than 3 percent of total carbon consumption. The modelalso indicated surprisingly high reversibility in the reaction betweenoxoglutarate and succinate. This step operates close to the thermodynamicequilibrium possibly because succinate is synthesized via a transferasereaction, and its product, acetyl-CoA, inhibits the conversion ofoxoglutarate to succinate. These findings enable a better understandingof the relationship between genome annotation and extant metabolicpathways in G. metallireducens.
Date: August 13, 2007
Creator: Tang, Yinjie J.; Chakraborty, Romy; Martin, Hector Garcia; Chu,Jeannie; Hazen, Terry C. & Keasling, Jay D.
Partner: UNT Libraries Government Documents Department

Large-Scale, Continuous-Flow Production of Stressed Biomass (Desulfovibrio vulgaris Hildenborough)

Description: The Protein Complex Analysis Project (PCAP, http://pcap.lbl.gov/), focuses on high-throughput analysis of microbial protein complexes in the anaerobic, sulfate-reducing organism, DesulfovibriovulgarisHildenborough(DvH).Interest in DvHas a model organism for bioremediation of contaminated groundwater sites arises from its ability to reduce heavy metals. D. vulgarishas been isolated from contaminated groundwater of sites in the DOE complex. To understand the effect of environmental changes on the organism, midlog-phase cultures are exposed to nitrate and salt stresses (at the minimum inhibitory concentration, which reduces growth rates by 50percent), and compared to controls of cultures at midlogand stationary phases. Large volumes of culture of consistent quality (up to 100 liters) are needed because of the relatively low cell density of DvHcultures (one order of magnitude lower than E. coli, for example) and PCAP's challenge to characterize low-abundance membrane proteins. Cultures are grown in continuous flow stirred tank reactors (CFSTRs) to produce consistent cell densities. Stressor is added to the outflow from the CFSTR, and the mixture is pumped through a plug flow reactor (PFR), to provide a stress exposure time of 2 hours. Effluent is chilled and held in large carboys until it is centrifuged. A variety of analyses -- including metabolites, total proteins, cell density and phospholipidfatty-acids -- track culture consistency within a production run, and differences due to stress exposure and growth phase for the different conditions used. With our system we are able to produce the requisite 100 L of culture for a given condition within a week.
Date: May 1, 2010
Creator: Geller, Jil T.; Borglin, Sharon E.; Fortney, Julian L.; Lam, Bonita R.; Hazen, Terry C. & Biggin, Mark D.
Partner: UNT Libraries Government Documents Department

Influences of Organic Carbon Supply Rate on Uranium Bioreduction in Initially Oxidizing, Contaminated Sediment

Description: Remediation of uranium (U) contaminated sediments through in-situ stimulation of bioreduction to insoluble UO{sub 2} is a potential treatment strategy under active investigation. Previously, we found that newly reduced U(IV) can be reoxidized under reducing conditions sustained by a continuous supply of organic carbon (OC) because of residual reactive Fe(III) and enhanced U(VI) solubility through complexation with carbonate generated through OC oxidation. That finding motivated this investigation directed at identifying a range of OC supply rates that is optimal for establishing U bioreduction and immobilization in initially oxidizing sediments. The effects of OC supply rate, from 0 to 580 mmol OC (kg sediment){sup -1} year{sup -1}, and OC form (lactate and acetate) on U bioreduction were tested in flow-through columns containing U-contaminated sediments. An intermediate supply rate on the order of 150 mmol OC (kg sediment){sup -1} year{sup -1} was determined to be most effective at immobilizing U. At lower OC supply rates, U bioreduction was not achieved, and U(VI) solubility was enhanced by complexation with carbonate (from OC oxidation). At the highest OC supply rate, resulting highly carbonate-enriched solutions also supported elevated levels of U(VI), even though strongly reducing conditions were established. Lactate and acetate were found to have very similar geochemical impacts on effluent U concentrations (and other measured chemical species), when compared at equivalent OC supply rates. While the catalysts of U(VI) reduction to U(IV) are presumably bacteria, the composition of the bacterial community, the Fe reducing community, and the sulfate reducing community had no direct relationship with effluent U concentrations. The OC supply rate has competing effects of driving reduction of U(VI) to low solubility U(IV) solids, as well as causing formation of highly soluble U(VI)-carbonato complexes. These offsetting influences will require careful control of OC supply rates in order to optimize bioreduction-based U stabilization.
Date: June 10, 2008
Creator: Tokunaga, Tetsu K.; Wan, Jiamin; Kim, Yongman; Daly, Rebecca A.; Brodie, Eoin L.; Hazen, Terry C. et al.
Partner: UNT Libraries Government Documents Department

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain

Description: A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.
Date: January 20, 2009
Creator: Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David et al.
Partner: UNT Libraries Government Documents Department

Energetic Consequences of nitrite stress in Desulfovibrio vulgarisHildenborough, inferred from global transcriptional analysis

Description: Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.
Date: November 3, 2005
Creator: He, Qiang; Huang, Katherine H.; He, Zhili; Alm, Eric J.; Fields,Matthew W.; Hazen, Terry C. et al.
Partner: UNT Libraries Government Documents Department

Mesoscale Biotransformations of Uranium: Identifying Sites and Strategies where Reductive Immobilization is Practical

Description: Bioreduction of U in contaminated sediments is an attractive strategy because of its low cost, and because of short-term studies supporting its feasibility. However, any in-situ immobilization approach for U will require assurance of either permanent fixation, or of very low release rates into the biosphere. Our previous long-term (2 years) laboratory experiments have shown that organic carbon (OC) based U(VI) bioreduction to UO2 can be transient even under sustained reducing (methanogenic) conditions. The biogeochemical processes underlying this finding urgently need to be understood. The current research is designed to identify mechanisms responsible for anaerobic U oxidation, and identify conditions that will support long-term stability of bioreduced U. We are investigating: (1) effects of OC concentration and supply rate on remobilization of bioreduced U, (2) the roles of Fe- and Mn-oxides as potential U oxidants in sediments, and (3) the role of microorganisms in U reoxidation, and (4) influences of pH on U(IV)/U(VI) redox equilibrium.
Date: June 1, 2006
Creator: Tokunaga, Tetsu K.; Wan, Jiamin; Hazen, Terry C.; Firestone, Mary K.; Brodie, Eoin; Kim, Yongman et al.
Partner: UNT Libraries Government Documents Department

Reoxidation of Bioreduced Uranium Under Reducing Conditions

Description: Uranium mining and processing for nuclear weapons and fuel have left thousands of sites with toxic levels of this actinide in soil and ground water. An emerging strategy for remediating such environments involves using organic carbon to promote microbially-mediated reduction and precipitation of insoluble U(IV) minerals. Although previous U bioreduction studies have shown promising results, they were of short duration (up to a few months). Our longer-term (20 months) laboratory study using historically contaminated sediment has alarmingly shown that microbial reduction of U was transient even under reducing (methanogenic) conditions. Uranium was reductively immobilized during the first 100 days, but later (150 to 600 days) reoxidized and mobilized, although a microbial community capable of reducing U(VI) remained through the end of the experiment. The formation of Ca{sub 2}UO{sub 2}(CO{sub 3}){sub 3} complexes (caused by the elevated carbonate concentration from microbial respiration and presence of calcium) drove the U(IV)/U(VI) reduction potential to much more reducing conditions. Fe(III) and Mn(IV) were found to be likely terminal electron acceptors (TEAs) for U reoxidation. Thus, U remediation by organic carbon based reductive precipitation is not sustainable in calcareous, neutral to alkaline soils and ground waters.
Date: February 5, 2005
Creator: Wan, Jiamin; Tokunaga, Tetsu K.; Larson, Joern; Zheng, Zuoping; Brodie, Eoin; Wang, Zheming et al.
Partner: UNT Libraries Government Documents Department