Advances in Soil Microbiome Engineering for Sustainable Crop Productivity: A Review

Abstract

Soil microbiome engineering is increasingly recognised as a sustainable approach for improving crop productivity by managing beneficial microbial communities and their functions in agricultural soils. The soil microbiome comprises bacteria, fungi, archae a, viruses and other microorganisms that influence nutrient cycling, organic matter decomposition, soil structure, plant growth and ecosystem stability. This review summarises current understanding of soil microbial diversity, plant-microbe interactions and the major approaches used to manipulate soil microbiomes for agricultural benefit. It considers microbial inoculants, biofertilisers, synthetic microbial communities, host-mediated microbiome selection, soil amendments, habitat engineering and genetic or metabolic engineering of beneficial microorganisms. The review also discusses the contribution of metagenomics, other multi-omics methods, genome editing, synthetic biology, artificial intelligence, machine learning and precision agriculture tools to the characterisation, prediction and management of microbial functions. Evidence presented in the manuscript indicates that microbiome-based strategies can support nutrient acquisition, improve plant growth, suppress pathogens, enhance tolerance to abiotic stress and promote soil health. However, the practical use of these approaches is constrained by microbial community complexity, environmental variability, inconsistent field performance, limited persistence of introduced microorganisms, biosafety issues, regulatory requirements and adoption barriers. The synthesis is limited to the themes addressed in the manuscript and therefore emphasises practical engineering strategies, enabling technologies and implementation constraints rather than presenting a quantitative meta-analysis of crop responses. Future progress will require crop-specific and site-specific microbiome management, resilient microbial consortia, improved formulation and delivery systems, and integration with sustainable and climate-smart agricultural practices. Soil microbiome engineering offers a biologically based pathway to support productive, resilient and resource-efficient farming systems while reducing dependence on external chemical inputs.