Root specialized metabolites shape plant-beneficial bacterial communities to mitigate hydrocarbon stress

Abstract

Plant roots secrete various compounds to attract beneficial microbes from soil, enhancing resilience to environmental stresses. The mechanisms by which perennial grasses accumulate specific plant-beneficial bacteria under organic pollution remain unclear. We conducted a pot experiment using ryegrass grown in diesel-contaminated soils (0–15 g/kg) to analyze rhizosphere bacterial community and root exudate, using 16S rRNA gene amplicon sequencing and untargeted metabolomics. A significant increase in the relative abundance of rhizosphere plant-beneficial bacteria was observed along the contamination gradient (r² = 0.64, p < 0.01), with bacterial taxa possessing dual capabilities in hydrocarbon degradation and nitrogen fixation, such as Nocardioides, becoming more dominant. We identified 22 core metabolites (defined as consistently differential metabolites that showed significant increase across all contamination treatments) including organoheterocyclic compounds, benzenoids, and phenylpropanoids. These core metabolites significantly predicted the dissimilarity of plant-beneficial bacterial communities (Mantel test, r² = 0.17, p < 0.001). Additionally, we verified the chemotactic response of two plant-beneficial bacterial strains, Rhodopseudomonas sp. and Pseudomonas sp., towards eugenol (a benzenoid), 7-acetoxy-4-methylcoumarin (a phenylpropanoid), and benzil (a benzenoid). Among these, eugenol is a promising compound that selectively induces beneficial microbes, helping ryegrass cope with hydrocarbon stress. These findings advance beyond prior observations of general exudate changes by identifying conserved metabolic responses across contamination levels, and demonstrating their role in microbial recruitment via chemoattraction. Our study provided valuable insights into the potential application of rhizosphere engineering for phytoremediation of hydrocarbon-contaminated soils, as well as the development of microbial-based strategies to enhance crop resilience under environmental stresses.