Soil microbiomes and crop productivity: A comprehensive review of recent advances

Soil microbiomes, complex assemblages of bacteria, archaea, fungi, protists, and viruses, govern many of the biogeochemical and ecological processes that underpin crop productivity. Over the past decade, rapid advances in high-throughput sequencing, multi-omics, microbial cultivation, and computational modelling have shifted the field from descriptive community profiling toward mechanistic and increasingly predictive understanding. This review synthesizes recent advances (with emphasis on 2023-2025 developments) in (i) how soil microbiomes regulate nutrient availability, plant growth signalling, disease suppression, and stress resilience; (ii) how agricultural management, soil properties, and plant traits shape microbiome assembly and function; (iii) emerging methodological toolkits, including long-read and shotgun metagenomics, metatranscriptomics, metabolomics, stable-isotope approaches, synthetic microbial communities (SynComs), and machine-learning frameworks; and (iv) translational strategies to harness microbiomes for yield gains, such as inoculants, microbial consortia, microbiome-informed soil health practices, and plant-microbiome co-engineering. Evidence increasingly indicates that context dependency—driven by soil type, climate, resident “core” communities, crop genotype, and farm practices—largely explains inconsistent field performance of bioinoculants and highlights the need for diagnostics that predict responsiveness. We propose a way forward centred on causal inference, standardised reporting, trait-based consortia design, and field-scale validation across environments, integrating microbial ecology with agronomy and breeding. By aligning measurement, modelling, and management, soil microbiome science is poised to become a practical lever for sustainable productivity and climate-resilient cropping systems.