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A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples

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Abstract

Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.

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Acknowledgments

This research project was supported in part by a Ph.D. studentship from The University of Hong Kong (PH), Hong Kong GRC GRF grant no. HKU_701913 (J-DG), Leaderman & Associates in Taipei (JGL and YTH), and Environmental and Conservation Fund grant no. 15/2011 (J-DG). Ms. Jessie Lai and Ms. Kelly Lau were thanked for their laboratory assistance.

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Authors and Affiliations

  1. Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People’s Republic of China

    Ping Han & Ji-Dong Gu

  2. Department of Bioenvironmental Engineering and Research Center for Analysis and Identification, Chung Yuan Christian University, Jhong-Li City, 32023, Taiwan

    Yu-Tzu Huang

  3. Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City, 30010, Taiwan

    Jih-Gaw Lin

  4. The Swire Institute of Marine Science, The University of Hong Kong, Shek O, Cape d’Aguilar, Hong Kong SAR, Hong Kong, People’s Republic of China

    Ji-Dong Gu

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  1. Ping Han
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Correspondence to Ji-Dong Gu.

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Han, P., Huang, YT., Lin, JG. et al. A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples. Appl Microbiol Biotechnol 97, 10521–10529 (2013). https://doi.org/10.1007/s00253-013-5305-z

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