Horizontal Gene Transfer and Homologous Recombination Drive the Evolution of the Nitrogen-Fixing Symbionts of Medicago Species

Abstract

Using nitrogen-fixing Sinorhizobium species that interact with Medicago plants as a model system, we aimed at clarifying how sex has shaped the diversity of bacteria associated with the genus Medicago on the interspecific and intraspecific scales. To gain insights into the diversification of these symbionts, we inferred a topology that includes the different specificity groups which interact with Medicago species, based on sequences of the nodulation gene cluster. Furthermore, 126 bacterial isolates were obtained from two soil samples, using Medicago truncatula and Medicago laciniata as host plants, to study the differentiation between populations of Sinorhizobium medicae, Sinorhizobium meliloti bv. meliloti, and S. meliloti bv. medicaginis. The former two can be associated with M. truncatula (among other species of Medicago), whereas the last organism is the specific symbiont of M. laciniata. These bacteria were characterized using a multilocus sequence analysis of four loci, located on the chromosome and on the two megaplasmids of S. meliloti. The phylogenetic results reveal that several interspecific horizontal gene transfers occurred during the diversification of Medicago symbionts. Within S. meliloti, the analyses show that nod genes specific to different host plants have spread to different genetic backgrounds through homologous recombination, preventing further divergence of the different ecotypes. Thus, specialization to different host plant species does not prevent the occurrence of gene flow among host-specific biovars of S. meliloti, whereas reproductive isolation between S. meliloti bv. meliloti and S. medicae is maintained even though these bacteria can cooccur in sympatry on the same individual host plants.

Stress Tolerance and Symbiotic and Phylogenic Features of Root Nodule Bacteria Associated with Medicago Species in Different Bioclimatic Regions of Tunisia

“…In the case of rhizobia, Minamisawa et al (22) suggested the potential horizontal transfer of nod genes among bradyrhizobia and other bacterial populations in soil environments. Similarly, Bailly et al (2) suggested that during the evolution of Medicago symbionts, horizontal transfer of nod genes might have occurred either to the common ancestor of the two Ensifer species or to one Ensifer species followed by the other. Additionally, Suominen et al (34), when describing the structure of the common nodulation genes of Rhizobium galegae, reported that lateral nod gene transfer might have occurred from fast growing rhizobia to agrobacteria.…”

Rhizobial communities in symbiosis with legumes: genetic diversity, competition and interactions with host plants

“…Rhizobial genetic plasticity underlies the adaptation of numerous bacterial species to thriving with legumes -a group of plants susceptible to bacterial molecular signals [13], but the detailed role of the different processes participating in this plasticity during evolution of symbioses is still controversial. Some authors emphasize the role of lateral genetic transfer in rhizobial evolution [39,40,[100][101][102][103], whereas others suggest the lateral transfer of nodulation genes occurred in minority of cases [104,105]. Moreover, frequent genetic transfer and recombination events were evidenced within species (between sublineages) in different models [11,36,42,43,49,101].…”

“…Moreover, some of them are selftransmissible or can be transferred to other bacterial cells in the presence of other plasmids [35,36]. The frequency of plasmid transfer between rhizobial strains and the role of this genetic exchange in rhizobial evolution remains controversial [37][38][39][40]. However, the pool of plasmid replicons present in rhizobial cells is regarded as a (mostly) accessory genetic component which is evolving more rapidly than the chromosome [33], due to frequent changes (such as gene duplication, mutation or deletion) within particular replicons [41] or rearrangements between different replicons [42,43].…”

Rhizobial plasmids — replication, structure and biological role

“…Plasmid evolution is further affected by frequent movement of extrachromosomal replicons among the strains. In fact, some of these elements may be transferred to other bacterial cells by itself or in the presence of other mobilizing plasmids [73,92,110,111]. Cervantes et al [123] showed that Sfr plasmids might originate through the transfer of a symbiotic-conjugative-plasmid from the Rhe to a Sfr strain and at least two further recombination events among the Rhe plasmids and the Sfr genome.…”

“…The comparative analyses of genomic features and a single-nucleotide polymorphism pattern on different replicons of Sinorhizobium spp. genomes clearly demonstrated that DNA recombination among closely related bacteria was a major event in the diversification of these genomes, especially in pSymA, resulting in its mosaic structure [71][72][73].…”