College of Agricultural Sciences

M. L. Rockhold, Yarwood, R. R., Niemet, M. R., Bottomley, P. J., Brockman, F. J., and Selker, J., “Visualization and modeling of the colonization dynamics of a bioluminescent bacterium in variably saturated, translucent quartz sand”, Advances in water resources, vol. 30, pp. 1593–1607, 2007.

A. E. Taylor, Vajrala, N., Giguere, A. T., Gitelman, A. I., Arp, D. J., Myrold, D. D., Sayavedra-Soto, L. A., and Bottomley, P. J., “Use of Aliphatic n-Alkynes To Discriminate Soil Nitrification Activities of Ammonia-Oxidizing Thaumarchaea and Bacteria”, Applied and Environmental Microbiology, vol. 79, no. 21, pp. 6544 - 6551, 2013.

H. B. Runes, Jenkins, J. J., Moore, J. A., Bottomley, P. J., and Wilson, B. D., “Treatment of atrazine in nursery irrigation runoff by a constructed wetland.”, Water Res, vol. 37, no. 3, pp. 539-50, 2003.

B. L. Mellbye, Giguere, A., Chaplen, F., Bottomley, P. J., and Sayavedra-Soto, L. A., “Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea.”, Appl Environ Microbiol, vol. 82, no. 11, pp. 3310-8, 2016.

G. M. Chaer, Myrold, D. D., and Bottomley, P. J., “A soil quality index based on the equilibrium between soil organic matter and biochemical properties of undisturbed coniferous forest soils of the Pacific Northwest”, Soil Biology and Biochemistry, vol. 41, no. 4, pp. 822 - 830, 2009.

S. A. Yarwood, Bottomley, P. J., and Myrold, D. D., “Soil Microbial Communities Associated with Douglas-fir and Red Alder Stands at High- and Low-Productivity Forest Sites in Oregon, USA”, Microbial Ecology, vol. 60, no. 3Database issue, pp. 606 - 617, 2010.

G. M. Chaer, Fernandes, M. F., Myrold, D. D., and Bottomley, P. J., “Shifts in Microbial Community Composition and Physiological Profiles across a Gradient of Induced Soil Degradation”, Soil Science Society of America Journal, vol. 73, no. 4, p. 1327, 2009.

P. J. Bottomley, Yarwood, R. R., Kageyama, S. A., Waterstripe, K. E., Williams, M. A., Cromack, K., and Myrold, D. D., “Responses of soil bacterial and fungal communities to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon”, Plant and Soil, vol. 28, no. 1-2, pp. 35 - 45, 2006.

S. BOYLE, RICH, J., Bottomley, P. J., CROMACKJR, K., and Myrold, D. D., “Reciprocal transfer effects on denitrifying community composition and activity at forest and meadow sites in the Cascade Mountains of Oregon”, Soil Biology and Biochemistry, vol. 38, no. 5, pp. 870 - 878, 2006.

R. R. Yarwood, Rockhold, M. L., Niemet, M. R., Selker, J., and Bottomley, P. J., “Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions”, Applied and environmental microbiology, vol. 68, pp. 3597–3605, 2002.

D. D. Myrold and Bottomley, P. J., “Nitrogen mineralization and immobilization”, in Nitrogen in Agricultural Soils, Madison, WI: American Society of Agronomy, 2008, pp. 157-172.

J. B. Cliff, Bottomley, P. J., Gaspar, D. J., and Myrold, D. D., “Nitrogen mineralization and assimilation at millimeter scales”, Soil Biology and Biochemistry, vol. 39, no. 3, pp. 823 - 826, 2007.

D. D. Myrold, Pett-Ridge, J., and Bottomley, P. J., “Nitrogen Mineralization and Assimilation at Millimeter Scales”, in Methods in Enzymolog, vol. 496, 2011.

L. A. Sayavedra-Soto, Ferrell, R., Dobie, M., Mellbye, B., Chaplen, F., Buchanan, A., Chang, J. H., Bottomley, P. J., and Arp, D. J., “Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations.”, FEMS Microbiol Lett, vol. 362, no. 3, pp. 1-7, 2015.

A. T. Giguere, Taylor, A. E., Myrold, D. D., and Bottomley, P. J., “Nitrification Responses of Soil Ammonia-Oxidizing Archaea and Bacteria to Ammonium Concentrations”, Soil Science Society of America Journal, vol. 79, no. 5, p. 1366, 2015.

S. L. Uesugi, Yarwood, R. R., Selker, J., and Bottomley, P. J., “A model that uses the induction phase of lux gene-dependent bioluminescence in Pseudomonas fluorescens HK44 to quantify cell density in translucent porous media”, Journal of microbiological methods, vol. 47, pp. 315–322, 2001.

F. W. R. Chaplen, Pérez, J., Bottomley, P. J., Buchanan, A., Murthy, G. S., Chang, J. H., and Sayavedra-Soto, L. A., “Model integration for elucidating the coupled environmental dynamics of the nitrifying bacteria Nitrosomonas europaea and Nitrobacter winogradskyi”, in ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014.

D. D. Myrold, Bottomley, P. J., Högberg, M. N., Högberg, P., and Sulzman, E. W., “Linking microbial communities to activity in soil with molecular and stable isotope techniques”, in Linking Management to Global Climate Challenges: The Proceedings of the International Symposium on Forest Soils and Ecosystem Health, Griffith University, Brisbane, Australia, 2007.

J. Pérez, Buchanan, A., Mellbye, B., Ferrell, R., Chang, J. H., Chaplen, F., Bottomley, P. J., Arp, D. J., and Sayavedra-Soto, L. A., “Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture”, Archives of Microbiology, vol. 19, no. 1, pp. 79 - 89, 2015.

J. Pérez, Buchanan, A., Mellbye, B., Ferrell, R., Chang, J. H., Chaplen, F., Bottomley, P. J., Arp, D. J., and Sayavedra-Soto, L. A., “Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture”, Archives of Microbiology, vol. 19, no. 1, pp. 79 - 89, 2015.

J. Pérez, Buchanan, A., Mellbye, B., Ferrell, R., Chang, J. H., Chaplen, F., Bottomley, P. J., Arp, D. J., and Sayavedra-Soto, L. A., “Interactions of Nitrosomonas europaea and Nitrobacter winogradskyi grown in co-culture.”, Arch Microbiol, vol. 197, no. 1, pp. 79-89, 2015.

A. E. Taylor, Taylor, K., Tennigkeit, B., Palatinszky, M., Stieglmeier, M., Myrold, D. D., Schleper, C., Wagner, M., and Bottomley, P. J., “Inhibitory Effects of C2 to C10 1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species”, Applied and Environmental Microbiology, vol. 81, no. 6, pp. 1942 - 1948, 2015.

R. R. Yarwood, Rockhold, M. L., Niemet, M. R., Selker, J., and Bottomley, P. J., “Impact of microbial growth on water flow and solute transport in unsaturated porous media”, Water resources research, vol. 42, 2006.

M. L. Rockhold, Yarwood, R. R., Niemet, M. R., Bottomley, P. J., and Selker, J., “Experimental observations and numerical modeling of coupled microbial and transport processes in variably saturated sand”, Vadose Zone Journal, vol. 4, pp. 407–417, 2005.

A. E. Taylor, Zeglin, L. H., Dooley, S., Myrold, D. D., and Bottomley, P. J., “Evidence for Different Contributions of Archaea and Bacteria to the Ammonia-Oxidizing Potential of Diverse Oregon Soils”, Applied and Environmental Microbiology, vol. 76, no. 23, pp. 7691 - 7698, 2010.