Environmental Biotechnology

Applied Microbiology and Biotechnology

, Volume 86, Issue 2, pp 781-790

First online:

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments

  • Meng LiAffiliated withDivision of Microbiology, School of Biological Sciences, The University of Hong Kong
  • , Yiguo HongAffiliated withKey Laboratory of Tropical Marine Environment Dynamics (LED), South China Sea Institute of Oceanography, Chinese Academy of Sciences
  • , Martin Gunter KlotzAffiliated withDepartments of Biology, Microbiology and Immunology, University of Louisville
  • , Ji-Dong GuAffiliated withDivision of Microbiology, School of Biological Sciences, The University of Hong KongSwire Institute of Marine Science, The University of Hong Kong Email author 

Rent the article at a discount

Rent now

* Final gross prices may vary according to local VAT.

Get Access


Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus “Scalindua” group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis. The optimized primer set for the 16S rRNA gene and the newly designed primer set for the hzo gene were successfully applied to identify anammox bacteria from marine sediments of aquaculture zone, coastal wetland, and deep ocean where the three ecosystems form a gradient of anthropogenic impact. Results indicated a broad distribution of anammox bacteria with high niche-specific community structure within each marine ecosystem.


Anammox bacteria Primer sets 16S RNA gene hzo gene Marine sediments