Group-specific polymerase chain reaction amplification of SSU rRNA-encoding gene fragments from 12 microbial taxa

Starting from an alignment of all known representatives in GenBank, we designed group specific primers targeting SSU rRNA-encoding sequences of 12 microbial taxa known to contain insect pathogens and symbionts. We tested the specificity of these primers using representative species of all 12 groups as control templates. Polymerase chain reaction amplification conditions were modified until only group-specific templates yielded a positive signal. The presented primer pairs thus allow for the amplification of SSU rRNA-encoding sequences representing specific microbial groups directly from the environment (a social insect host in our study). We discuss possible applications of the identified molecular tools.