Prophage induction stimulates ribosomal RNA operon recombination and facilitates genome mobility

Bacterial genomes contain multiple ribosomal RNA (rRNA) operons that by homologous recombination facilitate genome rearrangements. Here, we show that a Staphylococcus aureus temperate bacteriophage stimulates homologous recombination between the rRNA operons flanking the prophage and promotes a novel route of horizontal gene transfer we term rrn-linked lateral transduction. By polymerase chain reaction, sequencing of phage-packaged bacterial DNA, and phage transduction assays, we show that upon induction of the prophage, large circles of DNA formed by rRNA operon recombination are packaged and transduced by the phage via the mechanism of lateral transduction. This phenomenon is likely to be widely occurring, with prophage-linked rRNA operon recombination also shown here in Salmonella. Our results challenge the concepts of mobile and core genomes and establish rrn-linked lateral transduction as a new form of gene transfer involving rRNA operons.