Genomic diversity and distribution of Mesorhizobium nodulating chickpea (Cicer arietinum L.) from low pH soils of Ethiopia.

Chickpea is the third most important grain legume worldwide. This is due in part to its high protein content that results from its ability to acquire bioavailable nitrogen when colonized by diverse, nitrogen fixing Mesorhizobium species. However, the diversity and distribution of mesorhizobia communities may depend on their adaptation to soil conditions. Therefore, this study was initiated in order to isolate and investigate the diversity and taxonomic identities of chickpea-nodulating Mesorhizobium species from low pH soils of Ethiopia. A total of 81 rhizobia strains were isolated from chickpea nodules harvested from low pH soils throughout Ethiopia, and their genomes were sequenced and assembled. Considering a representative set of the best-sequenced 81 genomes, the average sequence depth was 30X, with estimated average genome sizes of approximately 7 Mbp. Annotation of the assembled genome predicted an average of 7,453 protein-coding genes. Concatenation of 400 universal PhyloPhlAn conserved genes present in the genomes of all 81 strains allowed detailed phylogenetic analysis, from which eight well-supported species were identified, including M.opportunistum, M.australicum, Mesorhizobium sp. LSJC280BOO, M.wenxiniae, M.amorphae, M.loti and M.plurifarium, as well as a novel species. Phylogenetic reconstructions based on the symbiosis-related (nodC and nifH) genes were different from the core genes and consistent with horizontal transfer of the symbiotic island. The two major genomic groups, M.plurifarium and M.loti, were widely distributed in almost all the sites. The geographic pattern of genomic diversity indicated there was no relationship between geographic and genetic distance (r = 0.01, p > 0.01). In conclusion, low pH soils in Ethiopia harbored a diverse group of Mesorhizobium species, several of which were not previously known to nodulate chickpea.

Phosphate solubilization and multiple plant growth promoting properties of Mesorhizobium species nodulating chickpea from acidic soils of Ethiopia.

The main purpose of this study was to screen and select strains from seven Mesorhizobium spp. for efficient phosphate solubilizing and other plant growth-promoting traits. Mesorhizobium species were tested for their ability to dissolve inorganic phosphate sources and multiple plant growth-promoting attributes. From a total of 62 Mesorhizobium strains, 47(76%) strains formed clear zones with an average PSI of 1.9-2.7 on Pikovskaya's agar plate. The selected strains also released soluble phosphorus [125-150 P (µgml-1)] from tri-calcium phosphate and low level of phosphorous i.e., 15.4 µg/ml and 14.5 µg/ml from inorganic ferrous and aluminum phosphates, respectively, in a liquid medium after 4 days of incubation. The release of soluble P was significantly (P < 0.01) correlated with a drop in pH of the medium. Moreover, screening for multiple plant growth-promoting attributes showed that 40, 28, 26, 21, and 38% of the strains were capable of producing indole-3-acetic acid, hydrogen cyanide, siderophores, ACC deaminase, and antagonism against Fusarium oxysporum f.sp. ciceris under in vitro conditions. The Mesorhizobium strains were endowed with the presence of ACC deaminase which was rarely reported elsewhere. All taken together, the acidic soils harbor numerous and more diverse phosphate solubilizing and plant growth-promoting Mesorhizobium spp. However, greenhouse and field conditions can be further studied within the context of improving chickpea production in Ethiopia.

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.

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.