title: New PCR primers targeting hydrazine synthase and cytochrome c biogenesis proteins in anammox bacteria.
abstract: PCR primers targeting genes encoding the two proteins of anammox bacteria, hydrazine synthase and cytochrome c biogenesis protein, were designed and tested in this study. Three different ecotypes of samples, namely ocean sediments, coastal wetland sediments, and wastewater treatment plant (WWTP) samples, were used to assess the primer efficiency and the community structures of anammox bacteria retrieved by 16S ribosomal RNA (rRNA) and the functional genes. Abundances of hzsB gene of anammox bacteria in South China Sea (SCS) samples were significantly correlated with 16S rRNA gene by qPCR method. And hzsB and hzsC gene primer pair hzsB364f-hzsB640r and hzsC745f-hzsC862r in combination with anammox bacterial 16S rRNA gene primers were recommended for quantifying anammox bacteria. Congruent with 16S rRNA gene-based community study, functional gene hzsB could also delineate the coastal-ocean distributing pattern, and seawater depth was positively associated with the diversity and abundance of anammox bacteria from shallow- to deep-sea. Both hzsC and ccsA genes could differentiate marine samples between deep and shallow groups of the Scalindua sp. clades. As for WWTP samples, non-Scalindua anammox bacteria reflected by hzsB, hzsC, ccsA, and ccsB gene-based libraries showed a similar distribution pattern with that by 16S rRNA gene. NH4+and NH4+/Σ(NO3-+ NO2-) positively correlated with anammox bacteria gene diversity, but organic matter contents correlated negatively with anammox bacteria gene diversity in SCS. Salinity was positively associated with diversity indices of hzsC and ccsB gene-harboring anammox bacteria communities and could potentially differentiate the distribution patterns between shallow- and deep-sea sediment samples. SCS surface sediments harbored considerably diverse community of Scalindua. A new Mai Po clade representing coastal estuary wetland anammox bacteria group based on 16S rRNA gene phylogeny is proposed. Existence of anammox bacteria within wider coverage of genera in Mai Po wetland indicates this unique niche is very complex, and species of anammox bacteria are niche-specific with different physiological properties towards substrates competing and chemical tolerance capability.
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: Zhichao
authors.initials: Z
authors.lastname: Zhou
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: Jing
authors.initials: J
authors.lastname: Chen
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: Han
authors.initials: H
authors.lastname: Meng
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.|Department of Life Sciences, College of Science and General Studies, Alfaisal University, P.O. Box 50927, Riyadh, 11533, Saudi Arabia.
authors.forename: Volodymyr
authors.initials: V
authors.lastname: Dvornyk
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. jdgu@hku.hk.
authors.forename: Ji-Dong
authors.identifier: http://orcid.org/0000-0002-7082-9784
authors.initials: JD
authors.lastname: Gu
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism*; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics*; D044822:Biodiversity; D002681:China; D045304:Cytochromes c / Q000096:biosynthesis* / Q000235:genetics; D017931:DNA Primers; D004269:DNA, Bacterial / Q000235:genetics; D014644:Genetic Variation; D006834:Hydrazines / Q000378:metabolism*; D059013:Microbial Consortia / Q000235:genetics / Q000502:physiology; D010084:Oxidation-Reduction; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA; D053833:Wetlands
chemical_list: D064751:Ammonium Compounds; D017931:DNA Primers; D004269:DNA, Bacterial; D006834:Hydrazines; D012336:RNA, Ribosomal, 16S; D045304:Cytochromes c
keywords: Anammox bacteria; Coastal-ocean pattern; Primer development; ccsA gene, ccsB gene; hzsB gene, hzsC gene