Dr. Peter Bottomley, Professor
Research Interests: Soil Microbial Ecology, Nitrogen Metabolism and Cycling, Microbial Diversity; Microbial Physiology
Courses Taught: MB 302, General Microbiology; MB 448/548, Microbial Ecology; MB 555 Biology of the Procaryotes
Research is directed generally at various aspects of the physiology and ecology of microorganisms associated with nitrogen and C processing in soil ecosystems. Specifically, we are interested in the microbial ecology, physiology, and community composition associated with N cycling processes to understand how the N cycle remains spatially and temporally coupled. This research is being conducted both in the laboratory and in forest and agroecosystems throughout Oregon. To achieve our experimental goals, we take an interdisciplinary approach that spans the disciplines of microbiology, molecular biology, and the physical soil sciences. Radioactive and stable isotopes of carbon and nitrogen are used to monitor processes in soil, and genomic, molecular, biological and biochemical techniques are used to examine the composition of microbial communities in soil compartments and their relative contributions to activity. We combine the use of pure culture lab-based studies with measurements of microbial activities in situ to gain a better understanding of how the soil environment modifies physiological behavior of microbes and its influence on microbial community composition. Understanding how soil ecosystems efficiently utilize their N inputs and sequester C 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.
Mellbye, B.L., Giguere, A.T., Murthy, G.S., Bottomley, P.J., Sayavedra-Soto, L.A., and Chaplen, F.W.R. 2018. Genome-scale constraint-based modeling of nitrogen oxide fluxes during coculture of Nitrosomonas europaea and Nitrobacter winogradskyi. mSystems Mar. 13; 3(3). PMID 29577088.
Giguere, A.T., Taylor, A.E., Myrold, D.D., Mellbye, B.L. Sayavedra-Soto, L.A., and Bottomley, P.J. 2018. Nitrite-oxidizing activity responds to nitrite accumulation in soil. FEMS Microbiol. Ecol. Mar. 1 94(3). PMID 29360963.
Taylor, A.E., Bottomley, P.J., and Semprini, L. 2018. Contrasting growth properties of Nocardioides JS614 on three different vinyl halides. Appl. Mirobiol. Biotechnol. Jan 3 doi:10.1007/s00253-017-8723-5. PMID 29297101.
Mellbye, B.L., Spieck, E., Bottomley, P.J. and Sayavedra-Soto, L.A. 2017. A survey of putative quorum sensing genes in nitrifying bacteria reveals acyl-homoserine lactone production in ammonia- and nitrite-oxidizing bacteria from the genera Nitrosospira, Nitrobacter, and Nitrospira. Appl. Environ. Microbiol. doi: 10.1128/AEM.01540-17.
Mellbye, B.L., Davis, E.W., Spieck, E., Chang, J.H., Bottomley, P.J. and Sayavedra-Soto, L.A. 2017. Draft genome sequence of nitrobacter vulgaris strain Ab1, a nitrite-oxidizing bacterium. Genome Announc. 4:5(18).
DeCrappeo, N.M., DeLorenze, E., Giguere, A.T., Pyke, D., and Bottomley, P.J. 2017. Contributions of bacteria and fungi to N cycling in soils under sagebrush steppe and cheat grass. Plant and Soil DOI 10.1007/s11104-017-3209x.
Giguere, A.T.,Taylor, A.E., Myrold, D.D. and Bottomley, P.J. 2017. Uncoupling of ammonia oxidation from nitrite oxidation: impacts upon nitrous oxide production in non-cropped Oregon soils. Soil Biol. and Biochem. 104:30-38.
Taylor, A.E., Giguere, A.T., Zoebelein, C.M., Myrold, D.D., and Bottomley, P.J. 2016. Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria. ISME J. Dec 20. doi: 10.1038/ismej
Mellbye, B.L., Giguere, A.T., Bottomley, P.J. and Sayavedra-Soto, L.A. 2016. Quorum quenching of Nitrobacter winogradskyi suggests that quorum sensing regulates fluxes of nitrogen oxide(s) during nitrification. MBio. 7(5); pii e01753-16. doi: 10.1128/mBio.01753-16.
Rice, M.C., Norton, J.M., Valois, F., Bollman, A., Bottomley, P.J., Klotz, M.G., Laanbroek, H.J., Suwa, Y., and et al. 2016. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Stand Genomic Sci. 11:46.
Mellbye, B.L., Giguere, A., Chaplen, F., Bottomley, P.J., Sayavedra-Soto, L.A. 2016. Steady-state growth under inorganic carbon limitation conditions increases energy consumption for maintenance and enhances nitrous oxide productoin in Nitrosomonas europaea. Appl. Environ. Microbiol. 82(11):3310-8.
Giguere, A.T., Taylor, A.E., Myrold, D.D., and Bottomley, P.J. 2015. Nitrification responses of soil ammonia oxidizing Archaea and Bacteria to ammonium concentrations. Soil Sci. Soc. Am. J. 79:1366-1374.
Mellbye, B.L., Bottomley, P.J. and Sayavedra-Soto, L.A. 2015. Nitrite-oxidizing bacterium Nitrobacter winogradskyi produces N-acyl-hmooserine lactone autoinducers. Appl. Environ. Microbiol. 81(17):5917-26.
Taylor, A.E., Taylor, K., Tennigkeit, B., Palatinszky, M. Stieglmeier, M., Myrold, D.O., Schleper, C., Wagner, M. and Bottomley, P.J. 2015. Inhibitory effects of C2-C10 1-alkynes on ammonia oxidation in two Nitrososphaera species. Appl. Environ. Microbiol. 81(6):1942-8.
Pérez J., Buchanan A., Mellbye B., Ferrell R., Chang J.H., Chaplen F., Bottomley P.J., Arp D.J., and Sayavedra-Soto L.A. 2014. Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture. Arch. Microbiol. 197(1):79-89.
Vajrala, N., Bottomley, P.J., Stahl, D.A., Arp, D.J., and Sayavedra-Soto, L.A. 2014. Cycloheximide prevents the de novo polypeptide synthesis required to recover from acetylene inhibition in Nitrosopumilus maritimus. FEMS Microbiol. Ecol. 3:495-502.
Myrold, D., David, M., Prestat, E., Zeglin, L., Bottomley, P., Hettich, R. and Jansson, J. 2014. Integrating omics to understand soil C cycling responses to precipitation variation. Twentieth World Congress of Soil Science. 410.
Myrold, D.D., Bottomley, P.J., Jumpponen, A., Rice, C.W., Zeglin, L.H. and David, M.M. 2014. Unveiling microbial carbon cycling processes in key U.S. soils using "omics". Oregon State University Press, OSU Technical Report, Corvallis, Oregon.
Zeglin, L.H., Bottomley, P.J., Jumpponen, A., Rice, C.W., Arango, M., Lindsley, A., McGowan, A., Mfombep, P. and Myrold, D.D. 2013. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales. Ecology, 94:2334-2345. http://dx.doi.org/10.1890/12-2018.1
Vajrala, N., Martens-Habbena, W., Sayavedra-Soto, L.A., Schauer, A., Bottomley, P.J., Stahl, D.A., and Arp, D.J. 2013. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proc. Natl. Acad. Sci. 110: 1006-1011.
Taylor, A.E., Vajrala, N., Giguere, A.T., Gitelman, A., Arp, D.J., Myrold, D.D., Sayavedra-Soto, L. and Bottomley, P.J. 2013. Use of aliphatic n-alkynes to discriminate soil nitrification activities of ammonia oxidizing Thaumarchaea and bacteria. Appl. Environ. Microbiol. 79(21):6544-6551.
Bottomley, P.J., Taylor, A.E. and Myrold, D.D. 2012. A consideration of the relative contributions of different microbial subpopulations to the soil N cycle. Frontiers in Terr. Micro. Vol 3: 1-7.
Taylor, A.E., Zeglin, L.H., Wanzek, T., Myrold, D.D. and Bottomley, P.J. 2012. Dynamics of ammonia oxidizing archaeal and bacterial populations and contributions to soil nitrification potentials. ISME J., 6: 2024-2032.
Zeglin, L.H., David, M., Bottomley, P., Hettich, R.L., Jansson, J., Jupponen, A. 2012. Microbial response to modified precipitation patterns in tall grass prairie soil: Molecular mechanisms, activity rates, and organic matter dynamics. AGU Fall Meeting Abstracts.
Zeglin, L.H., David, M.M., Lindsley, A., Arango, M., Bottomley, P.J. 2012. Microbial functional response to altered precipitation timing and duration--implications for the soil carbon cycle. Conference: 97th ESA Annual Convention 2012.
Starkenburg, S.R., Spieck, E. and Bottomley, P.J. 2011. Metabolism and genomics of nitrite oxidizing bacteria. Pp. 267-293. IN: Nitrification. (Ward, B.B., Arp, D.J., and Klotz, M., eds.) ASM Press, Washington, D.C.
Sayavedra-Sota, L.A., Gvakharia, B., Bottomley, P.J., Arp, D.J. and Dolan, M. 2010. Nitrification and degradation of halogenated hydrocarbons—a tenuous balance for ammonia oxidizing bacteria. Mini-Review. Appl. Environ. Microbiol. 86: 435-444.
Taylor, A.E., Zeglin, L., Dooley, S., Myrold, D. and Bottomley, P.J. 2010. Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils. Appl. Environ. Microbiol. 76:7691-7698.