Pioneer phytoremediation of highly acidic mineral soil: O-glycoside components of rhizosphere exudates inhibit Acidithiobacillus ferrooxidans

Acid mine drainage (AMD) remains a critical environmental challenge worldwide, primarily driven by acidophilic microorganisms such as Acidithiobacillus ferrooxidans. Traditional remediation methods, including lime neutralization and topsoil covering, often have limited effectiveness. A 180-day incubation trial using highly acidic mineral soil and a subsequent 90-day plant cultivation experiment was conducted to investigate the inhibitory mechanisms of key root-secreted compounds against A. ferrooxidans. The results demonstrated that the compost–biogas slurry amendment significantly elevated soil pH, nutrient availability, and enzymatic activities in the highly acidic mineral soil. The introduction of Hylotelephium erythrostictum (Miq.) H. Ohba further improved soil physicochemical properties, leading to a marked reduction in acid-producing bacteria, particularly members of A. ferrooxidans, while concurrently promoting beneficial microbial communities. Moreover, the amendment enhanced the release of rhizosphere exudates, notably O-glycosides and terpenoids. Among them, arbutin—an O-glycoside compound—was identified through pure culture assays and microscopic observations as a potent inhibitor of A. ferrooxidans. Arbutin suppressed bacterial growth and Fe²⁺ oxidation activity and disrupted cellular integrity. Molecular dynamics simulations revealed that arbutin binds to critical membrane-associated proteins of A. ferrooxidans (Cyc2B, Cyc2, and Omp40), resulting in significant reductions in α-helical content and destabilization of hydrophobic domains, thereby impairing catalytic functionality. These findings highlight O-glycosides as key antimicrobial constituents within the polyphenolic exudates of Hylotelephium erythrostictum (Miq.) H. Ohba. Overall, the combined use of compost–biogas slurry amendment and pioneer plant cultivation present an effective and sustainable strategy for the remediation of highly acidic mine soils, offering valuable insights for future ecological management of AMD-affected sites.