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Peter Bottomley
Professor, Microbiology
Professor, Crop and Soil Science
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RESEARCH:
Research is directed generally at various aspects of the activities of microorganisms and their population dynamics in soil ecosystems. Specifically, we are interested in how N cycling processes such as mineralization and immobilization of nitrogen can occur simultaneously in soils, and the role that soil microsites play in permitting key N cycle processes to remain spatially and temporally coupled. This research is being conducted in the laboratory and in forest and agroecosystems throughout Oregon. A second research area is focused upon certain aspects of bioremediation. In this arena we ask basic questions about the physiological characteristics of bacteria that influence their ability to sustain biodegradation of halogenated aliphatic hydrocarbon pollutants via cooxidative processes.
To achieve our experimental goals we take a variety of approaches that span the disciplines of microbiology, molecular biology, and the physical sciences. Radioactive and stable isotopes of carbon and nitrogen are used to monitor processes in soil, and molecular biological and biochemical techniques are used to examine the composition of microbial communities in soil compartments. Our studies on biodegradation involve a combination of approaches which require interactions among microbiologists, molecular biologists, and nonbiological scientists.
We have shown that the activities of indigenous microbial communities in different sizes of soil aggregates (compartments) recovered from different ecosystems are not identical. We believe these compartments are sufficiently different to influence the relative rates of immobilizing and mineralizing activities. We have obtained evidence that the sustainability of bioremediation by cometabolism in soils and other porous media is influenced by the physical and mineralogical properties of the latter because they control water availability, water flow properties, and differentially affect the bioavailabilities of natural substrates and pollutants (cosubstrates). At a basic microbiological level we have obtained evidence that during biodegradation, extensive DNA damage occurs, and that the bacteria must repair this damage if biodegradation is to be sustained. We have shown that the characteristics of microbial growth in porous media in response to substrate are influenced profoundly by the flow rate of water and the substrate concentration, and that microbial growth modifies water flow paths in a complex manner.
The goals of modern day agriculture and industrial technology are to increase or to sustain our quality of life, while at the same time maintaining the quality of the environment. A major component of our research is centered around the element nitrogen.
Understanding how soil ecosystems efficiently utilize their N inputs is crucial if human life as we know it is to be sustained on earth. Learning how to optimize the inputs of nitrogen into agricultural soils and how to use this fixed nitrogen wisely are important goals for improving the sustainability of agriculture.
Furthermore, the success of modern day agriculture and industrial technology depends upon the use of many different chemicals. As society becomes increasingly aware and skeptical of these chemicals it is important to carry out research to determine the validity of society's concerns. While much research has shown that many chemicals are easily degraded by soil microorganisms, nevertheless, situations occur where chemicals escape from the surface soil environment undegraded, and where biodegradation occurs in an unpredictable fashion. The interactions which occur between the dynamic physical properties of porous media and microorganisms must be understood more completely if we are to develop better models to predict the fate and transport of pollutants, and better technologies for remediating polluted environments.