Assessment of molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in different environmental samples using PCR primers based on 16S rRNA and functional genes

Research output: Contribution to journalResearch articleContributedpeer-review


  • Ping Han - , The University of Hong Kong (Author)
  • Uli Klümper - , Laboratory of Environmental Microbiology and Toxicology, The University of Hong Kong, University of Duisburg-Essen (Author)
  • Alex Wong - , The University of Hong Kong (Author)
  • Meng Li - , Shenzhen University (Author)
  • Jih Gaw Lin - , National Yang Ming Chiao Tung University (Author)
  • Zhexue Quan - , Fudan University (Author)
  • Martin Denecke - , University of Duisburg-Essen (Author)
  • Ji Dong Gu - , The University of Hong Kong, City University of Hong Kong (Author)


Eleven published PCR primer sets for detecting genes encoding 16S ribosomal RNA (rRNA), hydrazine oxidoreductase (HZO), cytochrome cd1-containing nitrite reductase (NirS), and hydrazine synthase subunit A (HzsA) of anaerobic ammonium-oxidizing (anammox) bacteria were assessed for the diversity and abundance of anammox bacteria in samples of three environments: wastewater treatment plant (WWTP), wetland of Mai Po Nature Reserve (MP), and the South China Sea (SCS). Consistent phylogenetic results of three biomarkers (16S rRNA, hzo, and hzsA) of anammox bacteria were obtained from all samples. WWTP had the lowest diversity with Candidatus Kuenenia dominating while the SCS was dominated by Candidatus Scalindua. MP showed the highest diversity of anammox bacteria including C. Scalindua, C. Kuenenia, and Candidatus Brocadia. Comparing different primer sets, no significant differences in specificity for 16S rRNA gene could be distinguished. Primer set CL1 showed relatively high efficiency in detecting the anammox bacterium hzo gene from all samples, while CL2 showed greater selectivity for WWTP samples. The recently reported primer sets of the hzsA gene resulted in high efficiencies in detecting anammox bacteria while nirS primer sets were more selective for specific samples. Results collectively indicate that the distribution of anammox bacteria is niche-specific within different ecosystems and primer specificity may cause biases on the diversity detected.


Original languageEnglish
Pages (from-to)7689-7702
Number of pages14
JournalApplied Microbiology and Biotechnology
Issue number20
Publication statusPublished - 1 Oct 2017
Externally publishedYes

External IDs

PubMed 28932888
ORCID /0000-0002-4169-6548/work/142247362



  • 16S rRNA, Anammox bacteria, Diversity, hzo, hzsA, Molecular detection, nirS, Nitrogen cycle

Library keywords