Journal of Soils and Sediments

, Volume 13, Issue 8, pp 1439–1449 | Cite as

pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing

  • Hang-Wei Hu
  • Li-Mei Zhang
  • Yu Dai
  • Hong-Jie Di
  • Ji-Zheng He



Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are ubiquitous and important for nitrogen transformations in terrestrial ecosystems. However, the distribution patterns of these microorganisms as affected by the terrestrial environments across a large geographical scale are not well understood. This study was designed to gain insights into the ecological characteristics of AOA and AOB in 65 soils, collected from a wide range of soil and ecosystem types.

Materials and methods

Barcoded pyrosequencing in combination with quantitative PCR was employed to characterize the relative abundance, diversity, and community composition of archaeal 16S rRNA gene, and AOA and AOB amoA genes in 65 soil samples.

Results and discussion

The operational taxonomic unit richness and Shannon diversity of Thaumarchaeota, AOA, and AOB were highly variable among different soils, but their variations were best explained by soil pH. Soil pH was strongly correlated with the overall community composition of ammonia oxidizers, as measured by the pairwise Bray–Curtis dissimilarity across all sites. These findings were further corroborated by the evident pH-dependent distribution patterns of four thaumarchaeal groups (I.1a-associated, I.1b, I.1c, and I.1c-associated) and four AOB clusters (2, 3a.1, 10, and 12). The ratios of AOA to AOB amoA gene copy numbers significantly decreased with increasing pH, suggesting a competitive advantage of AOA over AOB in acidic soils.


These results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils.


454 Pyrosequencing Ammonia oxidizers Nitrogen cycling Soil pH Spatial distribution Thaumarchaeota 



This work was financially supported by the National Natural Science Foundation of China (41230857, 41171217, 41020114001, and 41025004). We are grateful to Profs. Linghao Li and Daizhang Wang, Dr. Wenyan Han for access to the field trial stations, and Drs. Yong Zheng, Huaiying Yao, Mei Yin, Qichun Zhang, Zili Yi, and Xianjun Liu for assistance in soil sampling.

Supplementary material

11368_2013_726_MOESM1_ESM.doc (165 kb)
ESM 1(DOC 165 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Hang-Wei Hu
    • 1
    • 2
  • Li-Mei Zhang
    • 1
  • Yu Dai
    • 1
    • 2
  • Hong-Jie Di
    • 3
  • Ji-Zheng He
    • 1
  1. 1.State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijingChina
  2. 2.Graduate SchoolChinese Academy of SciencesBeijingChina
  3. 3.Centre for Soil and Environmental ResearchLincoln UniversityChristchurchNew Zealand

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