Genome Plasticity Depends on Positions both Inside and Outside of the Symbiosis Island of Bradyrhizobium diazoefficiens

Insertion sequences (ISs) are major drivers of genomic plasticity in rhizobia, frequently promoting local recombination events. To quantitatively compare the stability of genomic regions inside and outside of the symbiosis island, we engineered Bradyrhizobium diazoefficiens USDA122 mutants carrying a sacB/aadA counter-selectable cassette at four distinct loci—three on symbiosis island A (SymA) and one in the core genome. During 5 days of saprophytic growth, cassette deletion occurred at frequencies of up to 1.77×10–3 within SymA, whereas the deletion rate in core genomic regions was markedly lower (3.29×10–6). Within SymA, cassettes inserted adjacent to the nif and rhc clusters, where IS copies with the same orientation were enriched, were lost more frequently than those placed in other SymA regions, indicating marked intra-island variability in genomic stability. Similar yet overall lower deletion frequencies were observed in B. diazoefficiens USDA110. These results demonstrate that SymA contains genomic loci with greater susceptibility to IS-mediated rearrangements and also that such recombination events may contribute to the diversification of Bradyrhizobium symbiosis islands. Based on our comparative IS mapping in B. japonicum and B. ottawaense, we discuss the potential for the IS-mediated deletion of genome regions harboring nod genes.