Genetic Adaptation of Mesorhizobium Symbionts Associated With Caragana in Northern China Deserts

<i>Caragana</i>, a keystone leguminous species dominating arid semi-fixed deserts in northern China, forms specialized symbiotic nitrogen-fixing partnerships with <i>Mesorhizobium</i>, which are indispensable for sustaining ecosystem function globally. However, the roles of membrane transporters and nucleotide repair genes in conferring survival advantages to desert-dwelling <i>Mesorhizobium</i> across desert environments remained poorly elucidated. Therefore, a total of 68 representative <i>Mesorhizobium</i> strains associated with <i>Caragana</i>, isolated from five geographically distant areas (A to E) in the desert belt of northern China, were investigated to elucidate the pivotal roles of three membrane transporters (<i>cysW</i>, <i>exoY</i>, <i>idhA</i>) and two nucleotide repair genes (<i>mutS</i>, <i>uvrC</i>) in microbial adaptation to environmental stress. Phylogenetic analysis results revealed that strains assigned to the same genospecies primarily clustered by genetic lineage rather than geographic origin, with stronger intralineage sequence cohesion observed relative to interregional divergence. Notably, phylogenetic trees of membrane transporter genes, nucleotide repair genes, and core genes showed high topological congruence, underscoring their concerted evolutionary dynamics and shared selective pressures. Furthermore, consistent nucleotide diversity (<i>π</i>), low <i>πN/πS</i> ratios (<< 1.0) and genetic distance (<i>Dxy</i>) across populations indicated that purifying selection predominated in membrane transporters and nucleotide repair genes. Elevated recombination impact (<i>r/m</i>) and frequency (<i>ρ/θ</i>) revealed that homogenizing gene flow, rather than mutation, was the primary driver of population differentiation enabling rapid adaptation to desert environments.