Niche differentiation of nitrification in soils

This is a collaborative project among Drs. Peter Bottomley, David Myrold, and Anne Taylor that has been supported by two grants from the USDA NIFA/AFRI Soil Processes program.

Nitrification is the microbial process that converts ammonium (NH4+) to nitrate (NO3-). In soils, nitrification regulates the transformation of organic N and fertilizer N into plant useable NO3-, and influences the magnitude of N loss by leaching, run off, and microbial production of nitrogen oxides. There has been considerable debate about how the composition of the active nitrifier community is influenced by environmental factors, and what influences the magnitude of the nitrifier sink for NH4+ relative to other NH4+ consuming processes. This issue has become more complex with the discovery of ammonia oxidizing archaea (AOA). Recent work of our own and others has developed methods that show both AOA and ammonia oxidizing bacteria (AOB) contribute to nitrification in soil, and we have shown that the relative contributions differ seasonally.

Graduate students: Andrew Giguere, Xinda Lu, Stephanie Yarwood
Undergraduate students: Tom Wanzek, Sandra Dooley, Brina Tennigkeit

Publications

The project has produced the following publications:

Taylor, A.E., Vajrala, N., Giguere, A.T., Gitelman, A.I., 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. 79:6544-6551. (doi: 10.1128/AEM.01928-13)

Taylor, A.E., Vajrala, N., Giguere, A.T., Gitelman, A.I.,. 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. 79:6544-6551. (doi: 10.1128/AEM.01928-13) 

Bottomley, P.J., D.D. Myrold, and Taylor, A.E. 2012. A consideration of the relative contributions of different microbial subpopulations to the soil N cycle. Front. Microbiol. 3:373. (doi:10.3389/fmicb.2012.00373)

Taylor, A.E., L.H. Zeglin, T.A. Wanzek, D.D. Myrold, and P.J. Bottomley. 2012. Dynamics of ammonia oxidizing archaea and bacteria populations and contributions to soil nitrification potentials. ISME J. (doi:10.1038/ismej.2012.51)

Zeglin, L.H., A.E. Taylor, D.D. Myrold, and P.J. Bottomley. 2011. Bacterial and archaeal amoA gene distribution covaries with soil nitrification properties across a range of land uses. Environ. Microbiol. Rep. 3:717-726.

Taylor, A.E., L.H. Zeglin, S. Dooley, D.D. Myrold, and P.J. Bottomley. 2010. Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils. Appl. Environ. Microbiol. 76:7691-7698.

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.