Profiling Soil–Plant–Microbial Communities: DNA and Multi-Omics Techniques

Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.