Soil Microbiome Engineering for Sustainable Agriculture: Technological, Ecological, and Sociosystem-based Perspectives

The stability of global agroecosystems is increasingly threatened by climate change and unsustainable agricultural practices, including intensive tillage, monoculture, and excessive agrochemical use. Soil microbiome engineering, which involves the targeted manipulation of microbial communities using advanced biofertilizers, synthetic consortia (SynComs), and genetic tools, represents a critical frontier for developing climate-resilient agriculture. This comprehensive review synthesizes knowledge from 2020 to 2025, focusing on the technological advancements, ecological validation challenges, and crucial socio-economic dimensions of soil microbiome engineering. We identify three major, interconnected gaps hindering field-scale impact: (1) the reliance on short-term, single-stress inoculation studies, which fails to capture multi-year ecological stability; (2) the absence of standardized application protocols and harmonized regulatory frameworks necessary for reproducible success and streamlined commercialization; and (3) the underdeveloped analysis of socio-economic barriers, including farmer adoption behavior and equitable access in resource-scarce regions. We argue that future success requires a holistic, interdisciplinary approach that bridges biotechnology, ecology, and social science. This synthesis proposes a three-scale research–policy–practice framework for equitable scaling, positioning the soil as an engineered living system essential for achieving global food security and climate adaptation goals (SDGs 2 and 13).