Soil Microbiome and Nutrient Cycling: Implications for Sustainable Agriculture

Soil microbial communities—including bacteria, archaea, fungi, and viruses—play a pivotal role in mediating critical nutrient cycling processes (carbon, nitrogen, and phosphorus transformations) that underpin agricultural productivity and ecosystem resilience. Recent advancements in high-throughput sequencing, multi-omics (metagenomics, metatranscriptomics, metabolomics), exudate chemistry, isotope-tracing, and synthetic microbiome engineering (SynComs, microbial inoculants) have enabled mechanistic insights into how soil microbiomes regulate nutrient fluxes under diverse agroecosystem contexts. This review synthesizes findings from 2019–2025 regarding: (1) microbial community composition and functional potential; (2) microbial mechanisms underlying N, P, and C cycling; (3) the impact of agricultural practices (fertilizer regimes, tillage, crop rotations, cover cropping, organic amendments) on soil microbiomes and nutrient dynamics; (4) emerging technologies and strategies for microbiome-based nutrient management—including SynCom design, host genotypic selection, and precision agriculture tools; and (5) major challenges such as context dependency, reproducibility, scale-up logistics, and socio-economic barriers. We propose research priorities including trait- and interaction-focused approaches, coordinated multi-site field trials, host-microbiome co-selection, digital decision-support integration, and supportive policy mechanisms to realize robust, field-deployable microbiome-based strategies for sustainable agriculture.