Yutaka Okano, David LeBauer, Tim Cavagnaro, Kate Scow, Louise Jackson

The ecology and activity of ammonia oxidizing bacteria are not well understood because they are difficult to culture, and to study in soil. Conversion of soil NH4+ to NO2- by these bacteria has important implications for emissions of greenhouse trace N gases and accumulation of soil NO3-, which can be readily leached.

The conversion of soil NH4+ to NO3- paralleled the population size of nitrifiers using a Taqman realtime quantitative PCR method for the active subunit of ammonia monooxygenase (AmoA) in laboratory and field experiments.

The Taqman assay is being further developed to study AOB populations in soils from an organic tomato farm. The diversity of AOB in these soils is high, providing a model system to study not only AOB and nitrification rates, but also their relationships with other soil processes. In particular we are focusing on the AOB in the context of the wider soil microbial community (PLFA, mycorrhizae and nematodes). This multidisciplinary approach is yielding direct information about the microbes involved in agronomically important processes.

References

Cavagnaro, T.R., L.E. Jackson, K. Hristova, and K.M. Scow. 2008. Short-term
     population dynamics of ammonia oxidizing bacteria in an agricultural soil.
     Applied Soil Ecology 40:13-18. groups.ucanr.org/jacksonlab/files/64128.pdf

Okano, Y., K.R. Hristova, C.M. Leutenegger, L.E. Jackson, R.F. Denison, B.
     Gebreyesus, D. LeBauer, and K.M. Scow. 2004. Application of real-time PCR to
     study effects of ammonium on population size of ammonia-oxidizing bacteria in
     soil. Applied and Environmental Microbiology 70:1008-1016.
     ucce.ucdavis.edu/files/filelibrary/5472/21422.pdf