Despite the successful contributions of existing knowledge about biodegradation and biotransformation mechanisms, there is still much that research can contribute. At present, the understanding of biotransformation and biodegradation pathways and mechanisms in the field is incomplete. Although the degradation of many organics and the biotransformation of some inorganic compounds in laboratory cultures have been well described, it is unclear how this information relates to bioremediation processes under field conditions. In addition, research is needed to understand recently discovered biotransformation processes such as metal biotransformations and biosequestration, coupled aerobic and anaerobic processes, co-metabolism, biotransformations in the presence of alternative electron donors/acceptors, and biotransformations catalyzed by consortia (Ehrlich, 1990; Francis, 1990; Lovley, 1993; Macaskie, 1991).
In both the short and long term, a sound understanding of the fundamental mechanisms of biotransformation and detoxification will lead to improved prediction, control, and assessment of bioremediation performance, facilitate the selection and prioritization of contaminated sites for bioremediation, and result in the transfer of improved bioremediation processes for cleanup of contaminated sites.
Investigations and the expected results will integrate closely with those of the other program elements. Examples of important linkages with the other elements include: identifying rate-limiting enzymatic steps and enzymes as potential targets for the Biomolecular Science and Engineering element; developing the understanding of contaminant transformations required to better assess bioremediation endpoints and performance in the Assessment element; and providing fundamental kinetic data required for the System Integration, Prediction and Optimization element and the Acceleration element.
The Biotransformation and Biodegradation element will focus on four subelements:
Fundamental research on those mechanisms that affect the speciation, bioavailability, mobilization, immobilization, and transport of metals and radionuclides in the environment.
Identify the dominant redox processes catalyzed by microorganisms and other biota that affect metal speciation, toxicity, and mobility in soils, sediments, and waters. Achieving this goal will involve initial characterization of mechanisms for microbially mediated metal redox reactions and estimation of the importance and potential applicability of these redox reactions in the field. Results obtained will help to identify systems for more detailed study in subsequent years.
Identify and initially characterize biomineralogical processes which affect the mobility and toxicity of toxic metals and radionuclides in soils, sediments, and waters. As with the first goal in this subelement, these results will be used to identify important systems and scientific questions for future study.
Identify those biological processes involving complexation and bioaccumulation of toxic metals and radionuclides that either immobilize or mobilize metals and radionuclides in the environment. This area of research encompasses extracellular metal complexation, complexation to cell surfaces, and intracellular processes for bioaccumulation.
Five-Year
Isolate and characterize enzymes or other molecules responsible for oxidation or reduction of metals and radionuclides and their mobilization or immobilization.
Characterize the role of microbial action on the formation and transport of colloids containing toxic metals and radionuclides in the environment. Because of the multiple mechanisms potentially involved in colloid formation and transport, achieving this goal will require collaboration with other subelements within the Biotransformation and Biodegradation element (complexation with extracellular products and with cell surfaces) and with the Biogeochemical Dynamics element.
Ten-year
Be able to apply the knowledge of biologically mediated redox reactions to improve the management of toxic metal and radionuclide contamination in the environment.
Fundamental research in identifying and characterizing the pathways, processes, and molecules responsible for biotransformations of contaminants that are relevant to field conditions.
Conceive and initiate investigations of combinations of biological, chemical, and physical processes to degrade mixtures of recalcitrant contaminants in situ or ex situ in reactors. Identify the scientific challenges to application of these methods in the field.
Identify promising targets for biomolecular engineering. Achieving this goal will involve identifying rate-limiting steps in the biodegradation of contaminants and developing methods for identifying and purifying the enzymes or other molecules catalyzing those steps. This goal will include characterization of the catalytic mechanism involved in order to aid in the rational modification of molecules for enhanced activity.
Identify pathway end products and intermediates produced during biodegradation that can be used to measure or assess activity. The purpose is to discover and develop strategies for better measurement of bioremediation activities in the field.
Five-Year
Develop and test one or more strategies, based on fundamental understanding of biodegradation mechanisms, for enhanced biodegradation of organic contaminants in field experimental centers.
Ten-Year
Utilize the understanding of biodegradation mechanisms to improve bioremediation practices and performance in the field.
Fundamental research on the biologically mediated interactions between toxic metals, radionuclides, and organics.
Identify and characterize mechanisms whereby biota modify the speciation, mobility, and toxicity of toxic metals and radionuclides during biodegradation of organic contaminants or organic matter. These mechanisms include, for example, the biodegradation of organic complexing agents and the modification of soil organic matter.
Identify and characterize radiological and chemical toxicity and mechanisms for mediation of this toxicity to microorganisms catalyzing beneficial biotransformations of contaminants.
Five-Year
Develop sufficient understanding of the interactions between organic biodegradation, metal and radionuclide toxicity, speciation and mobility, and soil and water biota to test new concepts for control of metal toxicity and mobility in field experimental centers.
Ten-Year
Understand the ways that microorganisms, toxic metals, and radionuclides interact with organic contaminants and organic soil matter to guide bioremediation practices at sites where there are mixtures of metals and organics.
Fundamental research in the kinetics of multi-step, multi-component biodegradation and biotransformation pathways.
Initiate studies on the kinetics of coupled biological processes (e.g., cell transport, enzyme transformations of contaminants, cell growth, competition and predation, and feedback inhibition) for the biotransformation of mixtures of contaminants. Although the kinetics of biological processes will be emphasized in this subelement, thermodynamics and reversibility of relevant biotransformations will also be considered. The results of these studies will be used in collaboration with the System Integration element to develop mechanistic models for biodegradation and biotransformation processes at field sites. These studies are directed at identifying (in concert with the Systems Integration, Biogeochemical Dynamics, and Acceleration elements) those processes that have the most value for predicting and improving the performance of bioremediation under field conditions. Therefore, studies of nutrient and substrate limiting conditions, field temperatures, consortia, and other conditions particularly relevant to the field will be emphasized.
Five-Year
Extend investigations of the kinetics of coupled biological processes to field experimental centers and to a more comprehensive collection of contaminants and environmental conditions.
Test the validity, applicability, and ability of the models to predict bioremediation based on the interrelationships of biological, chemical, and physical processes at field experimental centers. Uncertainties of model predictions and sensitivity to accuracies of measured parameters will also be addressed.
Ten-Year
Attain a quantitative and mechanistic understanding of the kinetics and thermodynamics of biodegradation and biotransformation processes to improve bioremediation practices and performance in the field.