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A myriad of microorganisms colonizes the plant habitats and influences the flora and fauna along with the soil microenvironments. These microbes dwell in three major compartments such as spermosphere, rhizosphere, and phyllosphere. Plant rhizodeposits are the root exudates that determine the nature of root-colonizing microbes. Plant microbiome is also influenced by multiple biotic and abiotic factors. The functions of ecosystems are closely modulated by the plant and soil microbiome and their signal-mediated complex communications. These interactions facilitate the biogeochemical cycles of nutrients and minerals. Furthermore, these interactions regulate nutrient uptake of plants, growth promotion, and lead to the increase of resistance and suppression of plant pests and pathogens, reduction of soil pollutants, and soil health. Thus, understanding the biodiversity, dynamics, and interactions of a …