Applied Microbiology and Biotechnology

, Volume 97, Issue 18, pp 8351–8363 | Cite as

Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments

  • Yanling Zheng
  • Lijun Hou
  • Min Liu
  • Min Lu
  • Hui Zhao
  • Guoyu Yin
  • Junliang Zhou
Environmental biotechnology


Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 104–6.47 × 105 copies g−1 sediment) was always greater than that of AOA amoA gene (7.98 × 103–3.51 × 105 copies g−1 sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03–5.39 pmol N copy−1 day−1) compared with winter (0.16–0.38 pmol N copy−1 day−1), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons.


Nitrification Ammonia-oxidizing bacteria (AOB) Ammonia-oxidizing archaea (AOA) amoA gene Intertidal sediment Yangtze estuary 



This work was funded by the National Natural Science Foundations (Nos. 41130525, 40721004, 41021064, and 41071135) and the State Key Laboratory of Estuarine and Coastal Research (No. 2010RCDW07). It was also supported by the Fundamental Research Funds for the Central Universities and the Marine Scientific Research Project for Public Interest (No. 200905007). We thank Drs. Xiaoli Zhang, Jun Gong and Bing Xie for sharing their analytical expertise on measurements of ammonia-oxidizers. Professor Wayne S. Gardner and the anonymous reviewers are thanked for their constructive comments on a preliminary draft of the manuscript.

Supplementary material

253_2012_4512_MOESM1_ESM.pdf (127 kb)
ESM 1 (PDF 127 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yanling Zheng
    • 1
  • Lijun Hou
    • 1
  • Min Liu
    • 2
  • Min Lu
    • 2
  • Hui Zhao
    • 3
  • Guoyu Yin
    • 1
  • Junliang Zhou
    • 1
  1. 1.State Key Laboratory of Estuarine and Coastal ResearchEast China Normal UniversityShanghaiChina
  2. 2.College of Resource and Environmental ScienceEast China Normal UniversityShanghaiChina
  3. 3.Research CenterShanghai Botanical GardenShanghaiChina

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