PCR primers to amplify 16S rRNA genes from cyanobacteria

TLDR

The study demonstrates using the specific PCR with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities. The authors developed and tested a set of oligonucleotide primers for specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR, and applied this PCR with denaturing gradient gel electrophoresis to assess microbial diversity. PCR products were obtained from all tested cyanobacteria and diatom cultures but not from other bacteria or archaea; the primers selectively retrieved gene segments from cyanobacteria and diatoms in unialgal, nonaxenic cultures and cyanobionts in lichens, enabling direct sequencing and rapid, phylogenetically meaningful identification without pure cultures or cloning.

Abstract

We developed and tested a set of oligonucleotide primers for the specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR. PCR products were recovered from all cultures of cyanobacteria and diatoms that were checked but not from other bacteria and archaea. Gene segments selectively retrieved from cyanobacteria and diatoms in unialgal but nonaxenic cultures and from cyanobionts in lichens could be directly sequenced. In the context of growing sequence databases, this procedure allows rapid and phylogenetically meaningful identification without pure cultures or molecular cloning. We demonstrate the use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities.