Professor - Soil Microbiology

Mailing Address:

Department of Crop and Soil Science
3017 Agricultural and Life Science Building
Oregon State University
Corvallis, OR 97331

Office: Nash 348
Phone: 541-737-1844
Fax: 541-737-5725
E-Mail:

Department Website: Department of Crop and Soil Science
Vita: Short - Long

Current Work Focus: Research on various aspects of soil microbial ecology and microbial physiology including: carbon and nitrogen cycling in soils; population ecology of soil bacteria and soil fungi; transformation of xenobiotic chemicals in soils and groundwater; physiology and ecology of nitrification; genomics of nitrifying bacteria; physiology of hydrocarbon oxidizing bacteria.

Graduate Students:

• DeCrappeo, Nicole

Home Pages:

• Community of Science Database
• Department of Microbiology
• Center for Gene Research
• Western Region Hazardous Substance Research Center

Research Projects:

• Microbial Observatory at HJ Andrews LTER.
• Niche differentiation of nitrification in soils. Global transcriptional response  in nutrient removal processes.
• Hydrocarbon oxidizing metabolism in bacteria.
• Interactions between plant invasions and changes in soil microbial community functions.

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Publications:

Journal Articles

Dubbels, B.L., Sayavedra-Soto, L., Bottomley, P.J., and D.J. Arp. 2009. Thauera butanivorans sp. nov., a C₂-C₉ alkane oxidizing bacterium previously known as ‘Pseudomonas butanovora'. Int. J. Syst. Evolut. Microbiol. 59: 1576-1578.

Chaer, G., D.D. Myrold, and P.J. Bottomley. 2009. Development and validation of a soil quality index based on the equilibria between soil organic matter and biochemical properties in an undisturbed forest ecosystem. Soil Biol. Biochem. 41: 822-830.

Gvakharia, B., Bottomley, P.J., Sayavedra-Soto, L., and D.J. Arp. 2009. Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform. Appl. Microbiol. Biotechnol. 82: 1179-1185.

Chaer, G., Fernando, M., and P.J. Bottomley. 2009.  Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils.  Microbial Ecol. 58: 414-424.

Chaer, G., Fernandez, M., D.D. Myrold, and P.J. Bottomley. 2009.  Shifts in microbial community composition and physiological profiles across a gradient of induced soil degradation.  Soil Sci. Soc. Am. J. 73:1337-1344

Cooley, R.B., B.L. Dubbels, L. Sayavedra-Soto, P.J. Bottomley, and D.J. Arp. 2009. Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans formerly ‘Pseudomonas butanovora'. Microbiology 155: 2086-2096.

Cooley, R.B., P.J. Bottomley, and D.J. Arp. 2009. Growth of a non-methanotroph on natural gas: ignoring the obvious to focus on the obscure.  Environ. Microbiol Reports 1: 408-413.

Boyle, S.A., P.J. Bottomley and D.D. Myrold. 2008. Bacterial and fungal contributions to soil nitrogen cycling under Douglas fir and Red alder at two sites in Oregon.  Soil Biol. Biochem. 40:443-451.

Kurth, E., Doughty, D.M., Bottomley, P.J., Arp, D.J., and Sayavedra-Soto, L. 2008. Involvement of BmoR and BmoG in n-alkane metabolism in Pseudomonas butanovora.  Microbiology. 154:139-147.

Kageyama, S., Posavatz, N.R., Waterstripe, K.E., Jones, S.J., Bottomley, P.J., Cromack, K., and D.D. Myrold. 2008. Fungal and bacterial communities across meadow/forest ecotones in the western Cascades of Oregon. Can. J. For. Res. 38, 1-8.

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: 2933-2938.

Starkenburg, S.S., et al. and P.J. Bottomley. 2008.  The complete genome sequence of Nitrobacter hamburgensis X14 and a comparative genomic analysis of species within the genus Nitrobacter.  Appl. Environ. Microbiol. 74: 2852-2863.

Boyle-Yarwood, 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. 10: 2956-2965.

Norton, J. Bottomley, P.J., Klotz, M., Stein, L., and D.J. Arp. 2008. The genome sequence of the soil-borne ammonium oxidizing bacterium, Nitrosospira multiformis. Appl. Environ. Microbiol. 74: 3559-3572.

Starkenburg, S., D.J. Arp, and P.J. Bottomley. 2008. D-lactate metabolism and the obligate requirement for CO₂ during growth on nitrite by the facultative lithoautotroph, Nitrobacter hamburgensis.  Microbiology. 154: 2473-2481.

Starkenburg, S.S., D.J. Arp and P.J. Bottomley. 2008. Expression of a putative nitrite reductase and the reversible inhibition of nitrite-dependent respiration by nitric oxide in Nitrobacter winogradskyi Nb-255. Environ. Microbiol. 10: 3036-3042.