Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: A case for the genetic coherence of rhizobial lineages

In prokaryotes, lateral gene transfer across chromosomal lineages may be me diated by plasmids, phages, transposable elements, and other accessory DNA elements. However, the importance of such transfer and the evolutionary for ces that may restrict gene exchange remain largely unexplored in native set tings. In this study, tests of phylogenetic congruence are employed to expl ore the range of horizontal transfer of symbiotic (sym) loci among distinct chromosomal lineages of native rhizobia, the nitrogen-fixing symbiont of l egumes. Rhizobial strains isolated from nodules of several host plant gener a were sequenced at three loci: symbiotic nodulation genes (nodB and nodC), the chromosomal housekeeping locus glutamine synthetase II (GSII), and a p ortion of the 16S rRNA gene. Molecular phylogenetic analysis shows that eac h locus generally subdivides strains into the same major groups, which corr espond to the genera Rhizobium, Sinorhizobium, and Mesorhizobium. This broa d phylogenetic congruence indicates a lack of lateral transfer across major chromosomal subdivisions, and it contrasts with previous studies of agricu ltural populations showing broad transfer of sym loci across divergent chro mosomal lineages. A general correspondence of the three rhizobial genera wi th major legume groups suggests that host plant associations may be importa nt in the differentiation of rhizobial nod and chromosomal loci and may res trict lateral transfer among strains. The second major result is a signific ant incongruence of nod and GSII phylogenies within rhizobial subdivisions, which strongly suggests horizontal transfer of nod genes among congenerics . This combined evidence for lateral gene transfer within, but not between, genetic subdivisions supports the view that rhizobial genera are "reproduc tively isolated" and diverge independently. Differences across rhizobial ge nera in the specificity of host associations imply that the evolutionary dy namics of the symbiosis vary considerably across lineages in native setting s.