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

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Abstract
Using nitrogen-fixingSinorhizobiumspecies that interact withMedicagoplants as a model system, we aimed at clarifying how sex has shaped the diversity of bacteria associated with the genusMedicagoon 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 withMedicagospecies, based on sequences of the nodulation gene cluster. Furthermore, 126 bacterial isolates were obtained from two soil samples, usingMedicago truncatulaandMedicago laciniataas host plants, to study the differentiation between populations ofSinorhizobium medicae,Sinorhizobium melilotibv. meliloti, andS. melilotibv. medicaginis. The former two can be associated withM. truncatula(among other species ofMedicago), whereas the last organism is the specific symbiont ofM. laciniata. These bacteria were characterized using a multilocus sequence analysis of four loci, located on the chromosome and on the two megaplasmids ofS. meliloti.The phylogenetic results reveal that several interspecific horizontal gene transfers occurred during the diversification ofMedicagosymbionts. WithinS. meliloti, the analyses show thatnodgenes 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 ofS. meliloti, whereas reproductive isolation betweenS. melilotibv. meliloti andS. medicaeis maintained even though these bacteria can cooccur in sympatry on the same individual host plants.