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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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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DOI: https://doi.org/10.1007/s00253-013-5305-z