1998 RESEARCH PROJECTS Program Element 5 Assessment PROJECT: Artificial Neural Networks: An Innovative Tool for the Assessment of Microbial Communities PRINCIPAL INVESTIGATOR: Craig C. Brandt PROGRAM ELEMENT 5 Assessment OBJECTIVE: The overall goal of this research is to provide an improved understanding and predictive capability of the relationship between microbial membrane lipids and associated environmental factors for the assessment of the subsurface microbial community. Our objectives are to (1) develop new data analysis techniques that can help in predicting microbial community structure from membrane lipid profiles, (2) extend these techniques to the classification of metal-reducing microorganisms, and (3) predict metabolic processes of metal reduction based on lipid membrane and associated environmental data. The proposed work addresses two critical needs of the Natural and Accelerated Bioremediation Research (NABIR) program. First it fulfills the need for interpretation of complex data sets within the Assessment research element of NABIR. Second it focuses on assessing metal bioremediation that is an emphasis area within NABIR. APPROACH: Our approach involves (a) using artificial neural networks (ANNs) to predict microbial functional groups from membrane lipids and (b) determining membrane lipid compositions for selected metal and humic reducers to provide additional data for training of the ANNs, and (c) extending the scope of the ANNs to predict microbial metabolic processes. The tools, data, and scientific insights resulting from this research ill contribute to the goals of the NABIR Program by providing better means for assessing the structure and diversity of subsurface microbial communities, thus improving bioremediation efforts for metals and radionuclides. PROJECT: Rapid Gene Probe for Microorganisms Monitoring by Novel MS Approaches PRINCIPAL INVESTIGATOR: Chung-Hsuan Chen PROGRAM ELEMENT 5 Assessment OBJECTIVE: This work is to develop an innovative and better assessment technology for bioremediation processes. Our approach is to have new gene probe methods based on the coupling of hybridization, polymerase chain reaction (PCR) and mass spectrometry DNA analysis. We will also develop two novel approaches for mass spectrometry DNA analysis. One is to use laser-induced acoustic desorption (LIAD) to improve mass resolution for analysis or sequencing long oligonucleotides. The other is to develop direct sequencing of short DNA by matrix-assisted laser desorption/ionization/fragmentation (MALDIF) without the need of DNA ladders preparation. With MALDIF, sequencing time may be reduced to below one minute per sample. We expect the proposed technology will help to do faster and more reliable identification and characterization of microbial genes that are related to bioremediation of radionuclides and organic contaminants. APPROACH: With this approach, the hybridization process does not require either radioactive or fluorescent chemical tagging. We expect the approach to be faster and more reliable than other methods presently available. Since laser desorption mass spectrometry can be used for much faster DNA analysis and sequencing, the proposed technology also has the potential to achieve quick identification of the function of genes that are related to the capability of bioremediation of heavy metal and organic wastes. Our specific objectives are 1) to develop LIAD and MALDIF for the analysis of DNA probes for hybridization, 2) to demonstrate the capability of quantitative measurements of selected DNA segments, 3) to develop innovative matrix-assisted laser MALDIF for direct sequencing long DNA segments, and 4) to adapt the technology for in-situ field use. PROJECT: An In Situ Tracer Method for Establishing the Presence and Predicting the Activity of Heavy Metal-Reducing Microbes in the Subsurface PRINCIPAL INVESTIGATOR: Kirk Hatfield PROGRAM ELEMENT 5 Assessment OBJECTIVE: The objective of the proposed research is to develop an in situ tracer method for detecting the presence and quantifying the activity of microbial communities associated with reduction of heavy metals in the subsurface. A mathematical model describing aqueous tracer and dissolved metal transport will be developed based on the laboratory studies using microcosms. APPROACH: The study will consist of laboratory experimentation, theoretical development and mathematical modeling, with the ultimate goal of developing a tool which can be used to determine the potential for microbe-catalyzed heavy metal reduction in the subsurface. The team will use batch and one-dimensional flow through microcosms to study the chemistry, biochemistry, and microbial ecology of a representative consortium from a DOE site. The transport, partitioning behavior, microbial utilization of tracer chemicals, and the reduction of representative heavy metal will be studied under dynamic groundwater flow conditions in lab scale three dimensional microcosms. [Back to Award Recipients Page]