Multi-omics analysis of Stenotrophomonas maltophilia S-11 reveals its potential for Pb bioremediation in contaminated soil.

Lead (Pb²⁺) contamination in soil poses a significant environmental threat, but bioremediation using plant growth-promoting bacteria offers a sustainable solution. We evaluated the Pb²⁺ detoxification potential of Stenotrophomonas maltophilia strain S-11, isolated from the buckwheat rhizosphere. The strain exhibited high Pb²⁺ tolerance, with a minimum inhibitory concentration of 18 mM, along with a Pb²⁺ removal efficiency of 78.4 % (Q) and a biosorption capacity (q) of 383.5 mg g⁻¹ in aqueous media. Genomic analysis identified key genes involved in Pb²⁺ resistance, including those associated with oxidative stress responses and metal ion binding. Transcriptomic analysis revealed upregulation of metal-binding proteins, extracellular polymeric substances (EPS), NADH oxidoreductase, and membrane transporters under Pb²⁺ stress, indicating a dual detoxification and sequestration strategy. In a pot experiment, inoculation with strain S-11 increased buckwheat biomass and reduced Pb²⁺ accumulation in roots and shoots compared to the uninoculated control. Additionally, strain S-11 successfully colonized the rhizosphere microbial community and decreased bioavailable Pb²⁺ in contaminated soil. The findings demonstrate that Stenotrophomonas sp. S-11 is a promising candidate for sustainable Pb²⁺ remediation, providing genomic, enzymatic, and structural insights into heavy metal stress mitigation and soil reclamation. The strain employs a coordinated resistance strategy involving biosorption, active metal accumulation, electron transport chain (ETC) remodeling, metal sequestration, and upregulation of key metabolic pathways to maintain energy and nutrient homeostasis under Pb²⁺ stress. This multifaceted approach enhances its survival under Pb²⁺ contamination and strengthens its potential as an effective bioinoculant for bioremediation in heavy metal-contaminated environments.