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Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments

Applied Microbiology and Biotechnology volume 102, pages 9363–9377 (2018)Cite this article

Abstract

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4–5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process.

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Acknowledgements

We thank anonymous reviewers for constructive comments on the early version of the manuscript.

Funding

This work was funded by the Chinese National Key Programs for Fundamental Research and Development (2016YFA0600904) and the National Natural Science Foundations of China (41725002, 41671463, 41761144062, and 41730646). It was also supported by the Fundamental Research Funds for the Central Universities.

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  1. Chendi Yu, Lijun Hou, and Yanling Zheng contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China

    Chendi Yu, Lijun Hou, Juan Gao, Cheng Liu & Yongkai Chang

  2. Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China

    Yanling Zheng, Min Liu, Guoyu Yin & Ping Han

  3. School of Geographic Sciences, East China Normal University, Shanghai, 200241, China

    Yanling Zheng, Min Liu, Guoyu Yin & Ping Han

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  1. Chendi Yu
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Yu, C., Hou, L., Zheng, Y. et al. Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Appl Microbiol Biotechnol 102, 9363–9377 (2018). https://doi.org/10.1007/s00253-018-9274-0

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Keywords

  • Nitrogen
  • Nitrification
  • Ammonia oxidizer
  • Metagenome
  • Metatranscriptome
  • Diversity
  • Sediment