Nitrification is recognized as a key process in the terrestrial nitrogen cycle.  Until five years ago, the first step in nitrification was thought to be dominated by a phylogenetically restricted group of autotrophic, ammonia-oxidizing bacteria (AOB); however, the discovery of ammonia-oxidizing archaea (AOA) has spurred the exploration of various habitats for the presence of these two groups. Examination of soil habitats has often found AOA abundance to equal or even exceed that of AOB, suggesting that AOA contribute significantly to nitrification in soils. Our objective was to explore the connection between the abundance and composition of AOB and AOA communities to their activity. To do this, we selected soils located at three positions along a catena in western Oregon: upland ultisols forested with either Douglas-fir or red alder, improved and unimproved pasture on mid-elevation mollisols, and fallow and intensively cropped mollisols in the floodplain of the Willamette River. We sampled surface soil from each of these six locations and characterized them for soil physical and chemical properties. We used the amoA functional gene to measure AOA and AOB abundance by quantitative PCR and assessed community composition by T-RFLP supported with cloning and sequencing. Potential nitrification was determined using a shaken slurry assay modified in various ways in attempts to differentiate AOA and AOB activities.

Results/Conclusions

We found that both abundances and composition of AOA and AOB communities varied across the catena. Pasture soils had higher relative abundances of AOA vs. AOB compared to the forest or agricultural soils. T-RFLP fingerprints of the amoA gene showed distinct soil AOA and AOB communities among the different sites, each of which was characterized by taxonomically unique phylotypes of AOA and AOB. Nitrification potential was high and variable (2.7 to 34.0 mg N g^-1 d^-1) but uncorrelated to AOA or AOB composition or abundance. The response of nitrification potentials to incubation temperature and inhibitors did vary among sites, however. This variation was related to the relative abundance of AOA and AOB, suggesting that it may be possible to partition the potential contribution of each of these groups of ammonia-oxidizers to nitrification in soils.