title: 16 S rDNA primers and the unbiased assessment of thermophile diversity.
abstract: Our understanding of thermophile diversity is based predominantly on PCR studies of community DNA. "Universal" and domain-specific rRNA gene PCR primers have historically been used for the assessment of microbial diversity without adequate regard to the degree of specificity of primer pairs to different prokaryotic groups. In a reassessment of the published primers commonly used for "universal" and archaeal 16 S rDNA sequence amplification we note that substantial variations in specificity exist. An unconsidered choice of primers may therefore lead to significant bias in determination of microbial community composition. In particular, Archaea-specific primer sequences typically lack specificity for the Korarchaeota and Nanoarchaea and are often biased towards certain clades. New primer pairs specifically designed for "universal" archaeal 16 S rDNA sequence amplification, with homology to all four archaeal groups, have been designed. Here we present the application of these new primers for preparation of 16 S libraries from thermophile communities.
authors.affiliation: Advanced Research Centre for Applied Microbiology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa. gbaker@uwc.ac.za
authors.forename: G C
authors.initials: GC
authors.lastname: Baker
authors.forename: D A
authors.initials: DA
authors.lastname: Cowan
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D019766:Genes, Archaeal; D014644:Genetic Variation; D020745:Genome, Archaeal; D006358:Hot Temperature; D017017:Methanococcus / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D019711:Pyrococcus / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D016944:Sulfolobus / Q000235:genetics; D019712:Thermococcus / Q000235:genetics
chemical_list: D017931:DNA Primers; D004275:DNA, Ribosomal; D009711:Nucleotides; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D004247:DNA