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Organizations & affiliations:  American Society for Microbiology 

Microbial Ecology, Plant-Microbe Interactions,Biodegradation of Xenobiotic Compounds

American Society of Agronomy 
Soil Science Society of America 
Research interests: Microbial Ecology, Bioremediation, Microbial Diversity 
Office: 220 Nash Hall 
Telephone: 541-737-4441 
FAX: 541-737-0496 
Mailing address: Department of Microbiology 
220 Nash Hall 
Oregon State University 
Corvallis, OR 97331-3804 
Courses taught: MB 302, General Microbiology 
MB 448/548, Microbial Ecology 
MB 666, Current Topics in Environmental Microbiology 
Degrees: Ph.D., University of Dundee, Scotland 



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.



S.S. Starkenberg, L. Sayavedra-Soto, W.E. Hickey, M. Klotz, P.J. Bottomley, and D.J. Arp. 2006. In press. The genome sequence of the nitrite-oxidizing bacterium, Nitrobacter winogradskyi. Applied Environmental Microbiology

Doughty, D.M., L.A. Sayavedra-Soto, D.J. Arp, and P.J. Bottomley. 2005. Dichloroethenes as substrates and inducers of butane monooxygenase in Pseudomonas butanovora. Applied Environmental Microbiology 71: 6054-6059.

Sayavedro-Soto, L.A., D.M. Doughty, E. Kurth, P.J. Bottomley, and D.J. Arp. 2005. Inducer and inducer –independent induction of butane oxidation in Pseudomonas butanovora. FEMS Microbiology Letters 250: 111-116.

P.J. Bottomley, A.E. Taylor, S.A. Boyle, S.K. McMahon, J.J. Rich, K. Cromack, Jr, and D.D. Myrold. 2004. Responses of nitrification and ammonia oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Microbial Ecology 48: 500-508.

Yeager, C.M., P.J. Bottomley and D.J. Arp. 2004. Trichloroethylene degradation by toluene-oxidizing bacteria grown on non-aromatic substrates. Biodegradation 15: 19-28.

Cliff, J.B., P.J. Bottomley, R. Haggerty, and D.D. Myrold (2002) Modeling the effect of mass transfer limitations on 15 N isotope dilution experiments in soil aggregates. Soil Sci. Soc. Am. J. 66: 1868-1877.

Cliff, J.B., D. Gaspar, D.D. Myrold, and P.J. Bottomley (2002) Exploration of inorganic C and N assimilation by soil microbes with Time-of-flight Secondary Ion Mass Spectrometry. Appl. Environ. Microbiol . 68: 4067-4073.

Yarwood, R.R., M.L. Rockhold, M.R. Niemet, J.S. Selker, and P.J. Bottomley (2002) Non-invasive quantitative measurement of bacterial growth in porous media under unsaturated -flow conditions. Appl. Environ. Microbiol. 68: 3597-3605.

Duddleston, K. N., D. J. Arp, and P. J. Bottomley (2002) Biodegradation of monohalogenated alkanes by soil ammonia-oxidizing bacteria. Appl. Microbiol. Biotechnol . 59: 535-539.

Duddleston, K. N., P. J. Bottomley, A.J. Porter, and D. J. Arp (2000) New insights into methyl bromide cooxidation by Nitrosomonas europaea . obtained by experimenting with moderately low cell density suspensions. Appl. Environ. Microbiol. 66: 2726-2731.

Yeager, C.M. P.J. Bottomley, and D.J. Arp (2001) The requirement of DNA repair mechanisms for the survival of Burkholderia cepacia G4 upon degradation of trichloroethylene. Appl. Environ. Microbiol. 67: 5384-5391.






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