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Applied Soil Ecology
Vol. 85, 2015, Pages: 21–29

High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils

Jing Che, Xue Qiang Zhao, Xue Zhou, Zhong Jun Jia, Ren Fang Shen

State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.


The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH4+ on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO3-manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO3. The ammonia monooxygenase (amoA) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO3 + NH4+ than NH4+ during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO3-enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO3 with or without NH4+ supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

Keywords: Soil pH; Ammonium; amoA; CaCO3; Denaturing gradient gel electrophoresis.

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