Intragenomic conflict between transformation and prophage explains taxon-specific DNA acquisition.

The activation of many chromosomally integrated mobile genetic elements by RecA-DNA nucleoprotein filaments may represent an adaptation to evading deletion through homologous recombination. Consistent with bacterial transformation facilitating such eliminations of inserted viral DNA, cross-taxa comparisons found isolates' prophage content was negatively associated with homologous recombination rates. Assaying the effect of the composition of the extracellular DNA pool on transformation of a lysogen demonstrated that DNA from conspecific donors drove both prophage activation and deletion, whereas DNA originating from different species triggered only prophage activation. Accordingly, rates of horizontal DNA transfer mechanisms varied across bacterial ecologies, with homologous recombination common relative to prophage accumulation when DNA originated from fewer donor species.