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Biological Treatment, Bioremediation, and Natural Attenuation

Biological treatment, bioremediation and natural attenuation has been a rapidly growing area of science over the past decade. The acceptance of natural attenuation as a solution for cleaning up contaminated sites and DOE’s recognition that they will have long-term stewardship issues that they must address at the most contaminated sites has greatly increased the urgency for basic and applied research related to microbial ecology and biogeochemistry. This type of research is truly enabling for natural attenuation since characterization, predictions, and verification monitoring require a strong scientific basis. Natural attenuation is viewed as the best solution for cleaning up many waste sites and will save billions of dollars in cleanup costs. Bioremediation, both in situ and ex situ have also enjoyed strong scientific growth, in part due to the increased use of natural attenuation, since most natural attenuation is due to biodegradation. Bioremediation and Natural Attenuation are also seen as a solution for emerging contaminant problems, e.g. MTBE, endocrine disrupters, landfill stabilization, mixed waste biotreatment, and biological carbon sequestration.The Center for Environmental Biotechnology is a recognized leader in the field of biological treatment, bioremediation, and natural attenuation. The Center includes a world-class bioengineering laboratory and CEB investigators have extensive experience in both water treatment and bioremediation, especially co-metabolic biodegradation and the treatment of inhibitory compounds. In addition to basic research, CEB investigators have been involved in various aspects of more than 60 field demonstrations and deployments, and have 5 patents in this area that are licensed to more than 30 companies. The types of contaminants that CEB investigators have expertise with include chlorinated solvents, petroleum hydrocarbons, polynuclear aromatic hydrocarbons, ketones, MTBE, TNT, inorganic nitrogen (NO3, NH4), tritium, Pu, Np, Cr, and U. The Biotreatment, Bioremediation and Natural Attenuation area has both basic research and field application foci for the CEB. The basic research foci are co-metabolism, biotreatability, biotransformation kinetics, and modeling of biogeochemical processes. The field application foci are co-metabolic techniques, biogeochemical assessment techniques, and modeling of attenuation and environmental fate.

Basic Research Areas

Co-Metabolism. CEB scientists are recognized leaders in the field of co-metabolic pollutant transformation. Research conducted by scientists at CEB has demonstrated that co-metabolism is a dominant process for the degradation of PAHs, chlorinated solvents, and fuel oxygenates. Co-metabolic processes are difficult to study and require novel experimental approaches. One approach under development is the use of genetic probes to identify the presence of metabolic pathways implicated in co-metabolic processes. In this research, physiological responses are being linked to gene probe signatures to develop methods for identifying co-metabolic potential in environmental samples. The second approach uses a kinetic evaluation of partial transformation reactions to compare and characterize bacterial enzyme systems implicated in co-metabolism. Co-metabolic processes are competitive enzyme reactions and can be tested and modeled as such. Both these approaches are yielding unique and valuable advances in our understanding and application of co-metabolic and partial transformations.Biotreatability. CEB does a number of types of treatability tests for contaminants in soil and water, using soil columns, respirometers, bioreactors, and field respiration tests. Real-time direct biogeochemical techniques are being developed to provide the most direct possible methods to measure the rates of biodegradation and the effect stimulants and environmental conditions have on both the functional microbial components and the biogeochemistry of the environment being studied. For example, mixed waste biotreatment includes both the engineering of bioreactors for the treatment of high strength waste streams and understanding how natural attenuation or active bioremediation can be applied to mitigate the impact of the DOE weapons legacy. Past projects have examined how bacterial blooms on solvents may effect the environmental fate of actinides in the subsurface. Current studies are examining the biotreatment of tritiated solvent wastes and the transformation of uranium on bacteria surfaces. Biological processes are increasingly being recognized by DOE as important factors effecting the fate of radionuclides in the environment and are more often being considered as useful tools in the clean-up of mixed wastes and waste sites. Biotransformation Kinetics. CEB is linking engineering and microbiology in an integrated program to examine biotransformation kinetic for pollutant clean-up and microbial product formation. The kinetic program examines microbial response and activity as a function of substrate concentrations and time. The results of kinetic studies are being used in reactor design and operations analysis. Future research will focus on the application of kinetic approaches to predicting microbial population response to pollutant inputs.

Modeling. CEB currently does not have a modeling program, but is developing collaboration with a modeling groups within ESD. Modeling is targeted as an area for increased collaboration in the next three years. In particular, there is an need to link biodegradation kinetic information with subsurface fate and transport of pollutants. Modeling is also needed to further understand the control and operation of co-metabolizing biological reactors.

Field Applications

Co-Metabolic Techniques. Increasingly we are finding that contaminants can be deleterious at extremely low concentrations, eg. endocrine disrupters at parts per trillion concentrations. These concentrations of contaminants are too low to allow the contaminant to be a carbon or energy source for the microflora. Thus, a secondary carbon and energy source is needed to stimulate the microbes that are capable of degrading the contaminants of concern, since the excess enzymes produced will degrade the contaminants co-metabolically or fortuitously. CEB scientists have demonstrated the ability of methane to be injected with air into soil and groundwater contaminated with chlorinated solvents and petroleum compounds and shown how this stimulation of methanotrophs can cleanup sites to non-detect levels of these contaminants. They have also shown how various other gases can be added to supplement nutrient deficiencies in both nitrogen and phosphorus, thus allowing the microbes to achieve higher biomass levels and higher rates of biodegradation of the contaminants. Current studies are focusing on chlorinated solvent contaminants at DOD and DOE sites, MTBE at commercial sites, PAHs at DOD sites and municipal solid water landfills. CEB is also focusing other nutrients and surfactants that might stimulate bioremediation of more recalcitrant and strongly sorbed contaminants.Electrokinetic treatment of soil, ground water and ex-situ treatment systems. This technology being studied in collaboration with EETD is particularly applicable to metal ion contamination, which may be removed without damage to the indigenous microorganisms. The electrokinetic treatment also provides gentle heat to soil, which is also biocompatible, and the current can also supply nutrients and even transport organisms themselves.Biogeochemical Assessment Techniques. Our ability to determine the rates of bioremediation or biodegradation in the field is quite often hampered by the need to collect samples and transport them back to the laboratory for analysis. This obviously introduces bottle effect, collection contamination, and changes the in situ conditions so that the final measurements may not reflect accurately what is going on in that environment. In order to get a truer understanding of conditions as they occur we have been studying techniques that allow direct assessment, eg. helium tracer tests, soil gas measurements, isotopic analysis of contaminants and daughter products, and immediate lipid and nucleic acid extraction from sediment and groundwater. These techniques are being applied at a number of field sites to determine their efficiency over conventional baseline laboratory analyses.

Modeling of Attenuation & Environmental Fate. Using the powerful codes developed for fate and transport by the Yucca Mt. Program (TOUGH & ITOUGH) CEB is applying kinetic information relevant to biodegradation but especially aerobic processes that have received little attention. Using the computing facilities at LBNL (NERSC) and collaborations with the Nuclear Waste Program, we are currently developing contaminant fate and transport codes that will be used to model aerobic injection into municipal solid waste landfills. These models may allow us to better control the composting type processes that are occurring and discover better parameters to monitor and characterize the process.


LBNL (EETD, ALS, CSD, LSD), UC Berkeley, Washington State University, Geokinetics, Earth Tech, North Carolina State, Utah State University, USGS, NSF, Yolo County, INEEL, ORNL, PNNL, SRTC, IconGenetics, Maxygen, Physical Optics Systems, American Home Products, DuPont Agrobusiness, UMBI, VECTOR (Russia)) International Institute for Applied Microbiology (Ukraine); Utah Water Research Laboratory at Utah State University, Sandia National Lab, Department of Genetics at Cambridge University in the Great Britain, Institute of Physics at Georgian Academy of Sciences, Brain Tumor Research Center UCSF, Department of Molecular and Cell Biology UC Davis, Department of Chemical and Biochemical Engineering UC Irvine,; Department of Pathology at Stanford University Medical Center, Department of Physics and School of Medicine at Boston University. EETD/CEB collaborates closely with Geokinetic/EDA in Berkeley for electrochemical/electrokinetic technology. EETD also has several close collaborations with UCB Chemistry, Materials Science and Chemical Engineering Departments with CEB associated investigators.FacilitiesLab Space: 2321 ft2. Office Space: 2553 ft2.EquipmentSterilGARD II 4-foot vertical laminar-flow, biological safety cabinet (Baker)Avanti J-25 high performance centrifuge (Beckman)GS-6R tabletop centrifuge (Beckman)DU 640 UV/VIS scanning spectrophotometer (Beckman)Ultra-low temperature freezer (Revco)Axioskop RLF for DIC, phase contrast, and epifluorescence with microphotography (Carl Zeiss)Stereo microscope with microphotography (Carl Zeiss)Integrated environmental SpeedVac (Savant)MilliQ PF water purification systems (Millipore)GeneAmp PCR system 9600 (Perkin-Elmer)GeneAmp PCR system 9700 (Perkin-Elmer)RoboCycler Gradient Temperature Cycler 96 (Stratagene)Expedite 8909 DNA synthesizer (PerSeptive Biosystems)Vision Workstation BioCAD (PerSeptive Biosystems)Model 377 ABI Prism automated DNA sequencer (Perkin Elmer)TriCarb Liquid Scintillation Counter (Packard Instruments)TopCount microplate counter (Packard Instruments)CHEF DRII pulsed field electrophoresis equipment (Bio-Rad)MIDI identification system (Hewlett Packard)High sensitivity MSD mainframe for the HP 6890 GC (Hewlett Packard)Accelerated solvent extractor, model ASE 200 (DIONEX)BIOLOG microbial identification system (BIOLOG)Innova 4230 environmental shaker (New Brunswick)Innova 4900 Multi Shaker Environmental Chamber (New Brunswick)2 Landtec landfill gas analyzers2 20-liter US Filter fluidized bed bioreactorssoil gas sampling kitrespirometer3 55-gal landfill bioreactorsMark 4 Helium detector5-liter New Brunswick fermentorOther necessary support equipment and installations such as autoclaves, DI-water, refrigerators, freezers for low temperature storage of temperature sensitive materials, balances, ice-maker, shakers, incubators, magnetic stirrer, hotplates, microcentrifuges, computers, different electrophoresis boxes and power supplies, chemical fume hoods are also available.

Note: EETD investigators collaborating with CEB have several labs in the 70 area that can be utilized for CEB purposes plus labs in 62, which contain polymer synthesis and characterization activities for fuel cells, batteries, polymer LEDs and electrochromic windows. The laboratories are well equipped with chemical, thermal, rheological and electrochemical analytical equipment. CEB also possesses up to six electrokinetic lab cell systems and all appropriate power supplies and monitoring equipment. These facilities may also be applied to bioprocessing.

FY2001 Funding






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