FROM SOIL METAGENOMICS TO FUNCTIONAL MULTI OMICS: DECIPHERING PLANT–SOIL–MICROBIOME INTERACTIONS FOR SUSTAINABLE AGRICULTURE – A REVIEW

Abstract

Sustainable agriculture requires a comprehensive understanding of the molecular mechanisms through which soil microorganisms regulate ecosystem functioning and plant productivity. While metagenomics has significantly advanced the characterization of microbial diversity and functional potential, it provides limited insight into the biological activities occurring under dynamic environmental conditions. Functional multi-omics, integrating metagenomics, metatranscriptomics, metaproteomics and metabolomics, overcomes this limitation by linking microbial genetic potential with active biological processes. This integrated systems biology approach provides unprecedented insights into plant-soil-microbiome interactions and their roles in nutrient cycling, disease suppression, abiotic stress tolerance and carbon sequestration. Advances in functional multi-omics have elucidated the molecular mechanisms governing microbial community assembly, rhizosphere communication and ecosystem functioning, enabling the identification of key microbial taxa, functional genes, proteins and metabolites associated with sustainable agricultural processes. These discoveries have accelerated the development of microbiome engineering strategies, microbiome informed crop improvement, synthetic microbial communities and next generation microbial biofertilizers aimed at enhancing nutrient-use efficiency, improving crop resilience and reducing dependence on synthetic agrochemicals. Despite these advances, challenges related to experimental standardization, multi-omics data integration, computational analyses, field scale validation and regulatory frameworks continue to constrain large scale agricultural implementation. Future integration of functional multi omics with artificial intelligence, precision agriculture, remote sensing and predictive ecological modelling is expected to facilitate site-specific microbiome management and climate-smart farming practices. Overall, functional multi-omics provides a transformative framework for bridging microbial diversity with ecosystem function, offering new opportunities to improve soil health, agricultural productivity and environmental sustainability.