review · Frontiers in Plant Science
Engineering the rhizosphere microbiome offers an innovative method to boost plant growth, support stress adaptation, and restore soil health without the harmful impacts of conventional agriculture. Advanced sequencing and omics tools, such as metagenomics and metabolomics, have revealed how plants use root exudates containing sugars, amino acids, organic acids, and secondary metabolites to shape beneficial microbial populations. In turn, synthetic microbial communities, known as SynComs, show promising capability in helping crops tolerate abiotic challenges like drought and salinity, as well as biotic threats from pests and pathogens. Combining tailored microbial communities with optimised root exudate dynamics enhances nutrient cycling, suppresses soil-borne diseases, and decreases reliance on synthetic chemical inputs. Harnessing these ecological plant and microbe relationships provides a multi-disciplinary pathway to enhance crop yields sustainably while protecting soil quality and supporting long-term food security goals.
Conventional farming relies heavily on synthetic chemicals, which can harm soil health and surrounding ecosystems. Harnessing natural plant and microbe partnerships within the soil offers an alternative way to cultivate resilient crops. Optimising these microbial systems helps plants withstand climate stresses such as drought, suppresses damaging crop diseases, and supports food production without continued reliance on chemical inputs.
The insights support the development of tailored synthetic microbial inoculants and biologically based crop protection treatments. Potential users include agricultural input manufacturers, biofertiliser formulators, and farming enterprises seeking to lower chemical use and combat soil-borne diseases. Given the focus on synthesising research advancements in omics and synthetic microbial communities, these applications currently sit within the applied research and testing stage.
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The rhizosphere, a biologically active zone where plant roots interface with soil, plays a crucial role in enhancing plant health, resilience, and stress tolerance. As a key component in achieving Sustainable Development Goal 2, the rhizosphere is increasingly recognized for its potential to promote sustainable agricultural productivity. Engineering the rhizosphere microbiome is emerging as an innovative strategy to foster plant growth, improve stress adaptation, and restore soil health while mitigating the detrimental effects of conventional farming practices. This review synthesizes recent advancements in omics technologies, sequencing tools, and synthetic microbial communities (SynComs), which have provided insights into the complex interactions between plants and microbes. We examine the role of root exudates, composed of organic acids, amino acids, sugars, and secondary metabolites, as biochemical cues that shape beneficial microbial communities in the rhizosphere. The review further explores how advanced omics techniques like metagenomics and metabolomics are employed to elucidate the mechanisms by which root exudates influence microbial communities and plant health. Tailored SynComs have shown promising potential in enhancing plant resilience against both abiotic stresses (e.g., drought and salinity) and biotic challenges (e.g., pathogens and pests). Integration of these microbiomes with optimized root exudate profiles has been shown to improve nutrient cycling, suppress diseases, and alleviate environmental stresses, thus contributing to more sustainable agricultural practices. By leveraging multi-disciplinary approaches and optimizing root exudate profiles, ecological engineering of plant-microbiome interactions presents a sustainable pathway for boosting crop productivity. This approach also aids in managing soil-borne diseases, reducing chemical input dependency, and aligning with Sustainable Development Goals aimed at global food security and ecological sustainability. The ongoing research into rhizosphere microbiome engineering offers significant promise for ensuring long-term agricultural productivity while preserving soil and plant health for future generations.
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DOI: 10.3389/fpls.2025.1503730
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