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

  • SOILS, SEC 5 • SOIL AND LANDSCAPE ECOLOGY • RESEARCH ARTICLE
  • Published:
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Abstract

Purpose

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.

Conclusions

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China

    Hang-Wei Hu, Li-Mei Zhang, Yu Dai & Ji-Zheng He

  2. Graduate School, Chinese Academy of Sciences, Beijing, 100049, China

    Hang-Wei Hu & Yu Dai

  3. Centre for Soil and Environmental Research, Lincoln University, P.O. Box 84, Lincoln 7647, Christchurch, New Zealand

    Hong-Jie Di

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  1. Hang-Wei Hu
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  2. Li-Mei Zhang
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  5. Ji-Zheng He
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Correspondence to Ji-Zheng He.

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Responsible editor: Yanfen Wang

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Hu, HW., Zhang, LM., Dai, Y. et al. pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing. J Soils Sediments 13, 1439–1449 (2013). https://doi.org/10.1007/s11368-013-0726-y

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