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Harnessing the potential of the microbiome can provide cleaner and greener solutions to various environmental challenges. Globally, microbiome research is a continuously evolving field, with researchers aiming to explore the structural and functional characteristics of the microbiomes in various environmental compartments. Still, there are various system-level knowledge gaps in microbiome research. Therefore, unravelling the complex and dynamic microbial crosstalk in the soil system and the multitrophic interactions will certainly provide new impetus for harnessing the real potential of the soil microbiome for multipurpose environmental benefits.