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Soil Biology and Biochemistry
Vol. 85, 2015, Pages: 54–62

Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Xinda Lu, Peter J. Bottomley, David D. Myrold

Department of Crop and Soil Science, Oregon State University, USA.


Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH4+ amendment ranged from 0.4 to 3.3 mg N kg-1 soil d-1. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH4+-N kg-1 soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH4+-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH4+-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.

Graphical abstract

Keywords: Nitrification; Ammonia oxidation; Archaea; Bacteria; Forest soil.

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