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Rapid Determination of Microbial Pathways for Pollutant Degradation

EPA Grant Number: R831276C011
Subproject: this is subproject number 011 , established and managed by the Center Director under grant CR831276
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).

Center: Gulf Coast HSRC (Lamar)
Center Director: Ho, Tho C.
Title: Rapid Determination of Microbial Pathways for Pollutant Degradation
Investigators: Kinney, Kerry A. , Whitman, Christian
Current Investigators: Kinney, Kerry A. , Kirisits, Mary Jo , Whitman, Christian
Institution: University of Texas at Austin
EPA Project Officer: Krishnan, Bala S.
Project Period: December 1, 2003 through November 30, 2004
Project Amount: Refer to main center abstract for funding details.
RFA: Gulf Coast Hazardous Substance Research Center (Lamar University) (1996)
Research Category: Targeted Research , Hazardous Waste/Remediation

Description:

Objective:

Significant quantities of organic pollutants are released into the air, soils and waterways of the Gulf Coast Region posing a potential health risk to nearby communities. These pollutants are a drain on our economy as investigation and clean up costs can be prohibitive. Both in situ and ex situ biological treatment processes are an attractive control option for organic pollutants because they are cost effective, consume little energy, and can convert organic pollutants into benign products. Despite the promise of these methods, controlling and optimizing these systems to the field can be difficult due to their inherent complexity. In addition, current microbiological and analytical methods for determining biodegradation pathways are cumbersome and time consuming for the poorly characterized microorganisms usually found in treatment systems. A diagnostic tool that would allow engineers to more rapidly determine how the design and operation of their biotreatment system affects key biodegradation pathways would greatly enhance our ability to quickly optimize pollutant biodegradation rates.

The objective of the proposed research is therefore to develop a molecular tool, complementary DNA (cDNA) subtraction, in a novel way that allows rapid and efficient determination of the metabolic pathways used by microorganisms to degrade organic pollutants. The cDNA subtraction technique is well suited for environmental applications since it can identify specifically those genes that are expressed for pollutant degradation and does not require a priori knowledge of a microorganism's metabolism.

Approach:

Specific tasks of the proposed project include the following:

  • Develop the cDNA subtraction tool for application to environmentally relevant bacteria and verify that it can rapidly identify the genes expressed in the biodegradation of a model organic compound.
  • Develop an internal "standard addition" control method to quantify the efficiency of the cDNA subtraction method so that it can be applied to uncharacterized bacteria.
  • Assess the capability of the cDNA subtraction tool to determine the pollutant degradation pathways in a relatively uncharacterized bacterial species.
  • Use the gene sequence information obtained in the steps above to quantify gene expression patterns in microbial cultures degrading BTEX mixtures. It is our intent to verify that the cDNA subtraction tool and focused gene expression studies can be used to efficiently determine regulation patterns in key biodegradation pathways.
  • Examine the utility of the cDNA subtraction tool and focused gene expression studies to assess the biodegradation potential of the mixed microbial cultures typically found in biological treatment systems.

    Expected Results:

    The proposed project period is three years and the total GCHSRC funding requested is as follows: $49,811 (Year 1), $49,555 (Year 2) and $49,917 (Year 3). The final product of this research effort will be a cDNA subtraction tool which has been developed specifically for delineating biodegradation pathways utilized in environmental treatment applications. Rather than having to sequence the whole genome of a particular microbial species (a multiyear effort), the cDNA subtraction method allows one to delineate those genes expressed only during the biodegradation of a particular pollutant. Since this effort is much more focused, it allows one to identify the environmentally relevant genes in a matter of days or weeks. This information lays the foundation for efficient development of molecular probes to monitor gene expression in ex situ or in situ biological treatment systems. The ultimate cost savings provided by the cDNA subtraction method coupled with focused gene expression will likely be site and treatment system specific. However, if one considers the hundreds of thousands (to multimillions) of dollars that are often spent to investigate and remediate a single hazardous waste site, successful deployment of this molecular tool has the potential to provide significant cost savings.

    Publications and Presentations:

    Publications have been submitted on this subproject: View all 4 publications for this subprojectView all 472 publications for this center

    Supplemental Keywords:

    INTERNATIONAL COOPERATION, TREATMENT/CONTROL, Scientific Discipline, Waste, RFA, Remediation, Technology, Hazardous Waste, Environmental Chemistry, Hazardous, Treatment Technologies, microbial degradation, biotechnology, cDNA subtraction tool, bioremediation, hazardous waste treatment, organic contaminants

    Progress and Final Reports:
    2004 Progress Report


    Main Center Abstract and Reports:
    CR831276    Gulf Coast HSRC (Lamar)

    Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
    R822721C529 Environmentally Acceptable Endpoints: Risk Based Remediation Using Bioremediation
    R822721C552 Degradative Solidification/Stabilization Technology for Chlorinated Hydrocarbons
    R822721C569 Treatment and Product Recovery: Supercritical Water Oxidation of Nylon Monomer Manufacturing Waste
    R822721C620 Colloidal Fouling of Membranes: Implications in the Treatment of Textile Dye Wastes and Water Reuse
    R822721C626 Catalytic Hydroprocessing of Chlorinated Organics
    R822721C627 The Interaction of Microbial Activity and Zero Valent Iron Permeable Barrier Technology
    R822721C630 Microbial Cometabolism of Recalcitrant Chemicals in Contaminated Air Streams
    R822721C633 Catalyst Lifetime Studies for Chlorocarbon Steam Reforming
    R822721C635 Electrokinetic/Surfactant-Enhanced Remediation of Hydrophobic Pollutants in Low Permeability Subsurface Environments
    R822721C636 Transformation Reactions of Nitroaromatic and Nitrogen Heterocyclic Compounds on Granular Activated Carbon (GAC) Surfaces: Enhancement of GAC Adsorption in Natural and Engineered Environmental Systems
    R822721C640 Environmentally Friendly Organic Synthesis in Supercritical Fluids
    R822721C645 Development and Evaluation of an Integrated Model to Facilitate Risk-Based Corrective Action at Superfund Sites
    R822721C651 Adjustable Biopolymer Chelators for Cadmium, Lead and Mercury
    R822721C653 New Electrochemically Smart Catalysts for Hazardous Waste Management and Development of Capillary Electrophoresis for Analysis of their Products
    R822721C655 Soil Sampling in South Alabama Oil Fields
    R822721C659 Subsurface Contamination Site Characterization via a Computer-Aided Visual Tool
    R822721C661 New Insoluble supports for Protein Immobilization for Use in Metalloprotein Affinity Metal Chromatography
    R822721C663 Soil Remediation with Ultra-High-Efficiency Hydrocyclones
    R822721C669 Solid Acid Catalyzed Alkylation in Supercritical Fluids
    R822721C679 Regeneration/Reactivation of Carbon Adsorbents by Radio Frequency (RF) Induction Heating
    R822721C687 Improved Halogen Resistance of Catalytic Oxidation
    R822721C696 Phytoremediation and Bioremediation of Land Contaminated By PAHs, PCBs, and TNT
    R822721C697 Fundamental and Kinetic Investigation of Sorbent Technology for Optimum Mercury Emission Control
    R822721C700 Effects of Natural and Cyclic Variations on Contaminant Fate and Transport
    R822721C703 Enhancement of DNAPL Dissolution Rates by Dechlorinating Anaerobes
    R826694C620 Colloidal Fouling of Membranes: Implications in the Treatment of Textile Dye Wastes and Water Reuse
    R826694C625 Enhanced Treatment of DNAPLs Contaminated Soils and Groundwater Using Biosurfactants: In-Situ Bioremediation
    R826694C626 Catalytic Hydroprocessing of Chlorinated Wastes
    R826694C627 The Interaction of Microbial Activity and Zero Valent Iron Permeable Barrier Technology
    R826694C629 Biofiltration of BTEX in Petroleum-Contaminated Soil Remediation Off-Gas
    R826694C630 Microbial Cometabolism of Recalcitrant Chemicals in Contaminated Air Streams
    R826694C633 Catalyst Lifetime Studies for Chlorocarbon Steam Reforming
    R826694C635 Electrokinetic/Surfactant-Enhanced Remediation of Hydrophobic Pollutants in Low Permeability Subsurface Environments
    R826694C636 Transformation Reactions of Nitroaromatic and Nitrogen Heterocyclic Compounds on Granular Activated Carbon (GAC) Surfaces: Enhancement of GAC Adsorption in Natural and Engineered Environmental Systems
    R826694C640 Environmentally Friendly Organic Synthesis in Supercritical Fluids
    R826694C645 Development and Evaluation of an Integrated Model to Facilitate Risk-Based Corrective Action at Superfund Sites
    R826694C651 Adjustable Biopolymer Chelators for Cadmium, Lead, and Mercury Remeidation
    R826694C659 Subsurface Contamination Site characterization Via a Computer-Aided Visual Tool
    R826694C661 New Insoluble supports for Protein Immobilization for Use in Metalloprotein Affinity Metal Chromatography
    R826694C669 Solid Acid Catalyzed Alkylation in Supercritical Reaction Media
    R826694C679 Regeneration and Reactivation of Carbon Adsorbents by Radio Frequency Induction Heating
    R826694C696 Phytoremediation and Bioremediation of Land Contaminated By PAHs, PCBs, and TNT
    R826694C697 Fundamental and Kinetic Investigation of Sorbent Technology for Optimum Mercury Emission Control
    R826694C700 Effects of Natural Cyclic Variations on Contaminated Fate and Transport
    R826694C703 Enhancement of DNAPL Dissolution Rates by Dechlorinating Anaerobes
    R826694C705 A Pilot Plant for Producing Mixed Ketones from Waste Biomass
    R826694C722 The Effects of an Oily-Phase on VOC Emissions from Industrial Wastewater
    R826694C724 Mercury Removal from Stack Gas by Aqueous Scrubbing
    R826694C725 Transport, Fate and Risk Implications of Environmentally Acceptable Endpoint Decisions
    R826694C731 Development and Application of a Real-Time Optical Sensor for Atmospheric Formaldehyde
    R826694C734 An Advanced System for Pollution Prevention in Chemical Complexes
    R828598C001 Field Study Abstract: A Model of Ambient Air Pollution in Southeast Texas Using Artificial Neural Network Technology
    R828598C002 Hollow Fiber Membrane Bioreactors for Treating Water and Air Streams Contaminated with Chlorinated Solvents
    R828598C003 Fugitive Emissions of Hazardous Air Pollutants from On-Site Industrial Sewers
    R828598C004 Biofiltration Technology Development
    R828598C005 A Risk-Based Decision Analysis Approach for Aquifers Contaminated with DNAPLs
    R828598C006 In-Situ Remediation for Contaminated Soils Using Prefabricated Vertical Drains
    R828598C007 Membrane Technology Selection System for the Metal Finishing Industry
    R828598C008 Sequential Environments for Enhanced Bioremediation of Chlorinated Aliphatic Hydrocarbons
    R828598C009 Waste Minimization in the Magnetic Tape Industry: Waterborne Coating Formulations for Magnetic Tape Manufacture
    R828598C010 Soil Remediation by Agglomeration with Petroleum Coke
    R828598C011 Recovery of Dilute Phosphoric Acid in Waste Streams Using Waste Gas Ammonia: The Regenerative MAP/DAP Process
    R828598C012 Stochastic Risk Assessment for Bioremediation
    R828598C013 Selective Removal of Heavy Metals from Wastewater by Chelation in Supercritical Fluids
    R828598C014 Optimization of Treatment Technologies for Detoxification of PCB Contaminated Soils
    R828598C015 Wastewater Remediation by Catalytic Wet Oxidation
    R828598C016 Permanence of Metals Containment in Solidified and Stabilized Wastes
    R828598C017 Combustion Enhancement by Radial Jet Reattachment - Low Generation of Hazardous Gases and High Thermal Efficiency
    R828598C018 A Process To Convert Industrial Biosludge and Paper Fines to Mixed Alcohol Fuels
    R828598C019 Homogeneous Catalysis in Supercritical Carbon Dioxide
    R828598C020 Ultrasonic Enhancement of the Removal of Heavy Metals
    R828598C021 The Binding Chemistry and Leaching Mechanisms of Advanced Solidification/Stabilization Systems for Hazardous Waste Management
    R828598C022 Development of an Air-Stripping and UV/H2O2 Oxidation Integrated Process To Treat a Chloro-Hydrocarbon-Contaminated Ground Water
    R828598C023 A Comparative Study of Siting Opposition in Two Counties
    R828598C024 Sonochemical Treatment of Hazardous Organic Compounds II: Process Optimization and Pathway Studies
    R828598C025 Laser Diagnostics of the Combustion Process within a Rotary Kiln Incinerator
    R828598C026 Use of Inorganic Ion Exchangers for Hazardous Waste Remediation
    R828598C027 Kaolinite Sorbent for the Removal of Heavy Metals from Incinerated Lubricating Oils
    R828598C028 Destruction of Chlorinated Hydrocarbons in Process Streams Using Catalytic Steam Reforming
    R828598C029 Integrated Process Treatment Train (Bioremediation {Aerobic/Anaerobic} and Immobilization) for Texas Soils Contaminated with Combined Hazardous Wastes
    R828598C030 Photo-Oxidation by H2O2/VisUV of Off-Gas Atmospheric Emissions from Industrial and Environmental Remediation Sources
    R828598C031 Concentrated Halide Extraction and Recovery of Lead from Soil
    R828598C032 Biodegradable Surfactant for Underground Chlorinated Solvent Remediation
    R828598C033 A Software Guidance System for Choosing Analytical Subsurface Fate and Transport Models Including a Library of Computer Solutions for the Analytical Models
    R828598C034 Hydrodynamic Modeling of Leachate Recirculating Landfill
    R828598C035 Measurement of Oxygen Transfer Rate in Soil Matrices
    R828598C036 Sorbent Technology for Multipollutant Control During Fluidized Bed Incineration
    R828598C037 Pollution Prevention by Process Modification Using On-Line Optimization
    R828598C038 Pollution Prevention by Process Modification
    R828598C039 Water Solubility and Henry's Law Constant
    R828598C040 Transferring Technical Information on Hazardous Substance Research by Publishing on the World Wide Web
    R828598C041 Stress Protein Responses to Multiple Metal Exposure in Grass Shrimp
    R828598C042 Life-Cycle Environmental Costing for Managing Pollution Prevention in the Chemical and Petroleum Refining Industries: A Cross-Border Approach
    R828598C687 Improved Halogen Resistance of Catalytic Oxidation Through Efficient Catalyst Testing
    R828598C696 Phytoremediation and Bioremediation of Land Contaminated By PAHs, PCBs, and TNT
    R828598C697 Fundamental and Kinetic Investigation of Sorbent Technology for Optimum Mercury Emission Control
    R828598C700 Effects of Natural Cyclic Variations on Contaminated Fate and Transport
    R828598C703 Enhancement of DNAPL Dissolution Rates by Dechlorinating Anaerobes
    R828598C705 A Pilot Plant for Producing Mixed Ketones from Waste Biomass
    R828598C722 The Effects of an Oily-Phase on VOC Emissions from Industrial Wastewater
    R828598C724 Mercury Removal from Stack Gas by Aqueous Scrubbing
    R828598C725 Transport, Fate and Risk Implications of Environmentally Acceptable Endpoint Decisions
    R828598C731 Development and Application of a Real Time Optical Sensor for Atmospheric Formaldehyde
    R828598C734 An Advanced System for Pollution Prevention in Chemical Complexes
    R828598C743 Field Demonstration of Ultrasound Enhancement of Permeable Treatment Walls
    R828598C744 Optical Fibers Coated With Titania Membrane/UV-Generating Crystal in a Distributed-Light Photoreactor for VOC Oxidation
    R828598C749 Characterization and Modeling of Indoor Particulate Contaminants In a Heavily Industrialized Community
    R828598C753 Adsolubilization and Photocatalysis in a Semiconducting Monolithic Reactor for Wastewater Treatment
    R828598C754 Remote Detection of Gas Emissions in Industrial Processes
    R828598C759 Searching for Optimum Composition of Phosphogypsum: Fly ash: Cement Composites for Oyster Culch Materials
    R828598C761 Development of a Phytologically-Based Biosorptive Water Treatment Process
    R828598C766 Chlorinated Solvent Impact and Remediation Strategies for the Dry Cleaning Industry
    R828598C769 Soil/Sediment Remediation by Hot Water Extraction Combined with In-Situ Wet Oxidation
    R828598C771 Fluoracrylate Polymer Supported Ligands as Catalysts for Environmentally Benign Synthesis in Supercritical Fluids
    R828598C774 The Feasibility of Electrophoretic Repair of Impoundment Leaks
    R828598C777 Surfactant Enhanced Photo-oxidation of Wastewaters
    R828598C778 Stationary Power Generation Via Solid Oxide Fuel Cells: A Response to Pollution and Global Warming
    R828598C786 Photocatalytic Recovery of Sulfur and Hydrogen From Hydrogen Sulfide
    R828598C787 Biosurfactant Produced from Used Vegetable Oil for removal of Metals From Wastewaters and Soils
    R828598C789 Genetic Engineering of Enzymatic Cyanide Clearance
    R828598C791 Characterizing the Intrinsic Remediation of MTBE at Field Sites
    R828598C799 Simultaneous Water Conservation/Recycling/Reuse and Waste Reduction in Semiconductor Manufacturing
    R828598C801 Building Defined Mixed Cultures To Biodegrade Diverse Mixtures Of Chlorinated Solvents
    R828598C802 Engineering of Nanocrystal Based Catalytic Materials for Hydroprocessing of Halogenated Organics
    R828598C807 Commercial Demonstration of Hydrogen Peroxide Injection to Control NOx Emissions from Combustion Sources
    R828598C809 Evaluating Source Grouting and ORC for Remediating MTBE Sites
    R828598C810 Application of Total Cost Assessment To Process Design In the Chemical Industry
    R828598C846 Quantitative Demonstration of Source-Zone Bioremediation in A Field-Scale Experimental Controlled Release System
    R831276C001 DNAPL Source Control by Reductive Dechlorination with Fe(II)
    R831276C002 Arsenic Removal and Stabilization with Synthesized Pyrite
    R831276C003 A Large-Scale Experimental Investigation of the Impact of Ethanol on Groundwater Contamination
    R831276C004 Visible-Light-Responsive Titania Modified with Aerogel/Ferroelectric Optical Materials for VOC Oxidation
    R831276C005 Development of a Microwave-Induced On-Site Regeneration Technology for Advancing the Control of Mercury and VOC Emissions Employing Activated Carbon
    R831276C006 Pollution Prevention through Functionality Tracking and Property Integration
    R831276C007 Compact Nephelometer System for On-Line Monitoring of Particulate Matter Emissions
    R831276C008 Effect of Pitting Corrosion Promoters on the Treatment of Waters Contaminated with a Nitroaromatic Compounds Using Integrated Reductive/Oxidative Processes
    R831276C009 Linear Polymer Chain and Bioengineered Chelators for Metals Remediation
    R831276C010 Treatment of Perchlorate Contaminated Water Using a Combined Biotic/Abiotic Process
    R831276C011 Rapid Determination of Microbial Pathways for Pollutant Degradation
    R831276C012 Simulations of the Emission, Transport, Chemistry and Deposition of Atmospheric Mercury in the Upper Gulf Coast Region
    R831276C013 Reduction of Environmental Impact and Improvement of Intrinsic Security in Unsteady-state
    R831276C014 Integrated Chemical Complex and Cogeneration Analysis System: Greenhouse Gas Management and Pollution Prevention Solutions
    R831276C015 Improved Combustion Catalysts for NOx Emission Reduction
    R831276C016 A Large-Scale Experimental Investigation of the Impact of Ethanol on Groundwater Contamination
    R831276C017 Minimization of Hazardous Ion-Exchange Brine Waste by Biological Treatment of Perchlorate and Nitrate to Allow Brine Recycle
    R831276C018 Integrated Chemical Complex and Cogeneration Analysis System: Greenhouse Gas Management and Pollution Prevention Solutions

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    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.


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