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.

Recent shift in trends of agricultural practices from application of synthetic fertilizers and pesticides to organic farming has brought into focus the use of microorganisms that carryout analogous function. Trichoderma spp. is one of the most popular genera of fungi commercially available as a plant growth promoting fungus (PGPF) and biological control agent. Exploitation of the diverse nature of secondary metabolites produced by different species of Trichoderma augments their extensive utility in agriculture and related industries. As a result, Trichoderma has achieved significant success as a powerful biocontrol agent at global level. The endorsement of Trichoderma spp. by scientific community is based on the understanding of its mechanisms of action against a large set of fungal, bacterial and in certain cases viral infections. However, it is still an agnostic view that there could be any single major mode of operation, although it is argued that all mechanisms operate simultaneously in a synchronized fashion. The central idea behind this review article is to emphasize the potentiality of applications of target specific secondary metabolites of Trichoderma for controlling phytopathogens as a substitute of commercially available whole organism formulations. With the aim to this point, we have compiled an inclusive list of secondary metabolites produced by different species of Trichoderma and their applications in diverse areas with the major emphasis on agriculture. Outlining the importance and diverse activities of secondary metabolites of Trichoderma besides its relevance to agriculture would generate greater understanding of their other important and beneficial applications apart from target specific biopesticides.

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