Peter Bottomley

Soil Microbial Ecology, Nitrogen metabolism and cycling, Biodegradation of Xenobiotic Compounds

Research Interests:  Microbial Ecology,

Bioremediation, Microbial Diversity

Office:  348 Nash Hall

Courses taught:  MB 302, General Microbiology; MB 448/548, Microbial Ecology

Degrees:  Ph.D., University of Dundee, Scotland

Research

Research is directed generally at various aspects of the physiology and ecoloy of microorganisms associated with nitrogen cycling in soil ecosystems.  Specifically, we are interested in how N cycling processes such as mineralization and immobiliation 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 regulation of enzymes and pathways in bacteria that influence their ability to sustain biodegradation of halogenated aliphatic hydrocarbon pollutants via cooxidative processes. 

A third area of research is focused upon the genomes of nitrifying bacteria which has resulted in targeted research directed at understanding their properties and roles in N processing in soils and waste water systems. 

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 environmental engineers.

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.  At the other extreme, excesses of nitrogen need to be removed expediently from waste, and much more information is required about the functioning of bacteria in waste water treatment to improve upon the efficiency of the process.

The success of modern day agriculture and industrial technology depends upon the use of many different chemicals.  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 microbial iodegradation occurs in an unpredictable fashion.  The mechanisms of biodegradation by icroorganisms 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.

Selected Publications

Pub Med

Doughty, D.M., Kurth, E.G., Sayavedra-Soto, L., D.J. Arp, and P.J. Bottomley. 2008. Evidence for the involvement of copper ions and redox in regulation of butane monooxygenase in Pseudomonas butanovora.  J. Bacteriol. 190: doi:10.1128/JB.01409-07.

Starkenburg, S.S., et al. 2008.  The complete genome sequence of Nitrobacter hamburgensis X14 and a comparative genomic analysis of species within the genus Nitrobacter.  Appl. Environ. Microbiol. 74: doi:10.1128/AEM.02311-07

Boyle, S.A., P.J. Bottomley and D.D. Myrold. 2008.  Community composition of ammonia oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon.  Environ. Microbiol. doi: 10.1111/j.1462-2920.2008.01600.x

Norton, J. Bottomley, P.J., Klotz, M., Stein, L., and D.J. Arp. 2008. The genome sequence of the soil-borne ammonia-oxidizing bacterium, Nitrosospira multiformis. Appl. Environ. Microbiol. 74: doi:10.1128/AEM.02722-07

Myrold, D.D., and  P.J. Bottomley. 2008.  Mineralization and immobilization of nitrogen in soils. Chapter 5, pp 153-167.  In: Nitrogen in Agricultural Soils, Monograph. American Society of Agronomy, Madison, WI

Cliff, J.B., P.J. Bottomley, D. J. Gaspar, and D.D. Myrold. 2007.  Nitrogen Mineralization and Assimilation at millimeter scales.  Soil Biology and Biochemistry. 39: 823-826.

Taylor, A.E., Semprini, L, and P.J. Bottomley. 2007. Use of fluoroethene as a surrogate to evaluate oxidative biodegradation of vinyl chloride.  Environ. Sci. Techn. 41: 6378-6383.

Halsey, K.H., D.M. Doughty, P.J. Bottomley, and D.J. Arp. 2007. Evidence for modified mechanisms of chloroethene oxidation in P. butanovora mutants containing single aminoacid substitutions in the hydroxylase α subunit of butane monooxygenase.  J. Bacteriol.189: 5068-5074.

Gvakharia, B., Sayavedra-Soto, L.A., P.J. Bottomley, and D.J. Arp. 2007. Global transcriptional response of Nitrosomonas  europaea to chloroform and chloromethane.  Appl. Environ. Microbiol. 73: 3440-3445.

S.S. Starkenburg, L. Sayavedra-Soto, M. Klotz, P.J. Bottomley, D.J. Arp, and W.e. Hickey, 2006.  The genome sequence of the nitrite-oxidizing bacterium, Nitrobacter winogradskyi.  Appl. Environ. Microbiol.. 72, 2050-2063.

Doughty, D.M., L. Sayavedra-Soto, P.J. Bottomley and D.J. Arp.  2006. Product repression of butane monooxygenase expression in 'Pseudomonas butanovora'. J. Bacteriol. 188:2586-2592.

Halsey, K.H., Sayavedra-soto, L.A., Bottomley, P.J., and D.J. Arp. 2006. Site directed amino acid substitutions in the hydroxylase a subunit of butane monooxygenase from P. butanovora; implications for substrates knocking at the gate. J. Bacteriol. 188, 4962-4969.

Arp, D.J., and P.J. Bottomley. 2006.  Nitrifiers: more than 100 years from isolation to genome sequences.  Microbe 1, 229-234.

Taylor, A.E., and P.J. Bottomley.  2006. comparative kinetics of ammonia oxidation and growth of Nitrosospira AV and Nitrosomonas europaea in different Oregon soils.  Soil Biol. & Biochem. 38, 828-836.

Yarwood, R.R., M.L. Rockhold, M.R. Niemet, J.S. Selker, and P.J. Bottomley. 2006.  Impact of microbial growth on water flow and solute transport in unsaturated porous media.  Water Resources.  Res. 42,W10405, doi:10.1029/2005WR004550.

P.J. Bottomley, D.D. Myrold, K. Cromack Jr, M.A. Williams, R. Yarwood, K. Waterstripe and s. Kageyawa. 2006.  Effects on soil bacterial and fungal microbial communities of receprocally transplanting soil from meadows and forests in the Cascade Mountains of Oregon.  Plant and Soil. 289, 35-45.

Doughty, D.M., L.A. Sayavedra-Soto, D.J. Arp, and P.J. Bottomley. 2005. Dichlorethenes 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.