Applied Microbiology and Biotechnology

, Volume 86, Issue 2, pp 781–790

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

  • Meng Li
  • Yiguo Hong
  • Martin Gunter Klotz
  • Ji-Dong Gu
Environmental Biotechnology

Abstract

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.

Keywords

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

Supplementary material

253_2009_2361_MOESM1_ESM.doc (148 kb)
Supplementary materials(DOC 151 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Meng Li
    • 1
  • Yiguo Hong
    • 2
  • Martin Gunter Klotz
    • 3
  • Ji-Dong Gu
    • 1
    • 4
  1. 1.Division of Microbiology, School of Biological SciencesThe University of Hong KongHong KongPeople’s Republic of China
  2. 2.Key Laboratory of Tropical Marine Environment Dynamics (LED), South China Sea Institute of OceanographyChinese Academy of SciencesGuangzhouPeople’s Republic of China
  3. 3.Departments of Biology, Microbiology and ImmunologyUniversity of LouisvilleLouisvilleUSA
  4. 4.Swire Institute of Marine ScienceThe University of Hong KongHong KongPeople’s Republic of China

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