Although microorganisms are known to dominate Earth’s biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome—tripartite and monopartite—with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

No abstract

Chickpea is an important legume that serves as a vital source of nutrition in many regions of Ethiopia and sustain cropping system productivity due to its ability to fix atmospheric nitrogen. Legumes such as chickpea possess seeds with high protein content therefore, require high supply of nitrogen. To realize this requirement, the crop embraces nodule on its root where bacteria of the genus Mesorhizobium live with a specific function of converting the atmospheric nitrogen into plant available form called biological nitrogen fixation. However, the potential of the crop to accomplished the current demand of nitrogen for poor soils is limited by its association with symbiotic nitrogen fixing bacteria, poor understanding of the relationship between strain diversity and symbiotic performance. Therefore, the present review will be used as a baseline to understand Ethiopian chickpea Mesorhizobium genetic resources for better symbiotic nitrogen fixation in chickpea. Moreover, it allows to supporting research efforts to select efficient rhizobial inoculants in nutrient management for increasing the production and productivity of chickpea as well as maintaining soil health and to solve the future problems.