Plasmids related to the symbiotic nitrogen fixation are not only cooperated functionally but alsomay have evolved over a time span in family rhizobiaceae

Abstract

Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using aphylogenomics approach. Intriguingly, althoughthegenetic expansion thatoccurredin chromosomal regionswas themainreason for thehigh proportionof low-frequencyflexible gene families inthe pan-genome, genegain events associatedwith accessory plasmids introducedmore genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfermay be impeded by, such as, the host's physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped themachieve nitrogen fixation. These findings provide newinsights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.