Baker, Gillian; Cowan, Donald A.(Portland Press, 2004)
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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.