title: A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples.
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.
authors.affiliation: 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.
authors.forename: Ping
authors.initials: P
authors.lastname: Han
authors.forename: Yu-Tzu
authors.initials: YT
authors.lastname: Huang
authors.forename: Jih-Gaw
authors.initials: JG
authors.lastname: Lin
authors.forename: Ji-Dong
authors.initials: JD
authors.lastname: Gu
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D058448:Biota; D002681:China; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics*; D004783:Environmental Microbiology; D056186:Metagenomics / Q000379:methods*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D053833:Wetlands
chemical_list: D064751:Ammonium Compounds; D017931:DNA Primers; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S