Post-Release Changes of the Goat’s Rue Rhizobia (Neorhizobium galegae bv. orientalis) Genomes in the Field: Prospects for Breeding the Symbiotically Effective Strains

Root nodule bacteria (rhizobia) fixing N2 in cooperation with legumes are broadly used for improving production of these plants inoculated with strains selected for high symbiotic activity. These bacteria are characterized by enormous evolutionary plasticity based on genomic rearrangements and horizontal gene transfer. However, this native plasticity is still poorly used for symbiotic improvement of the inoculant strains. In the presented paper, we analyzed genomic structure and symbiotic efficacy in ten clones isolated from nodules formed by the highly effective strain Gr30-13 of goat’s rue rhizobia (Neorhizobium galegae bv. orientalis) on the host plant (Galega orientalis) grown for 1 or 2 years in the soil devoid of aboriginal populations of this rhizobia species. The genome analysis based on nanopore sequencing technology revealed different genomic rearrangements (IS transpositions, tandem duplications) in three clones, which exceed the remaining six clones in symbiotic efficiency. One clone with two tandem duplications in its genome significantly outperformed the initial strain in symbiotic efficiency by more than 35%. We tentatively suggest that the enhanced symbiotic efficiency may be linked to the detected genomic changes; if confirmed, such effects could be described as the “self-improvement” of rhizobia, driven by genomic plasticity and subsequent selection under field conditions. The presented model experiment suggests a new approach for breeding programs using nature-like technology based on the spontaneous genetic variability of symbiotically active rhizobia.