Applied Microbiology and Biotechnology

, Volume 102, Issue 21, pp 9363–9377 | Cite as

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

  • Chendi Yu
  • Lijun HouEmail author
  • Yanling Zheng
  • Min LiuEmail author
  • Guoyu Yin
  • Juan Gao
  • Cheng Liu
  • Yongkai Chang
  • Ping Han
Environmental biotechnology


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.


Nitrogen Nitrification Ammonia oxidizer Metagenome Metatranscriptome Diversity Sediment 



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

Funding information

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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals.

Supplementary material

253_2018_9274_MOESM1_ESM.pdf (631 kb)
ESM 1 (PDF 630 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Chendi Yu
    • 1
  • Lijun Hou
    • 1
    Email author
  • Yanling Zheng
    • 2
    • 3
  • Min Liu
    • 2
    • 3
    Email author
  • Guoyu Yin
    • 2
    • 3
  • Juan Gao
    • 1
  • Cheng Liu
    • 1
  • Yongkai Chang
    • 1
  • Ping Han
    • 2
    • 3
  1. 1.State Key Laboratory of Estuarine and Coastal ResearchEast China Normal UniversityShanghaiChina
  2. 2.Key Laboratory of Geographic Information Science (Ministry of Education)East China Normal UniversityShanghaiChina
  3. 3.School of Geographic SciencesEast China Normal UniversityShanghaiChina

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