High-efficiency antimony biomineralization by Serratia nematodiphila: process optimization and integrated genomic-transcriptomic-proteomic analysis

This study aims to elucidate the transcriptional, protein expression and mineral crystallization response mechanisms of the Serratia nematodiphila strain during the process of converting Sb³⁺ into Sb₂O₃ through integrating multi-omics methods and various mineral analysis techniques. The isolate Serratia nematodiphila (MIC > 250 mM) achieved 96.18% Sb³⁺ removal under Box-Behnken-optimized conditions (27.7 ℃, pH 4.67, 205.6 rpm). Time-resolved SEM-EDS, Raman, XRD, and XPS revealed a non-classical mineralization pathway from an amorphous precursor to crystalline Sb₂O₃ within 36 h. Integrated genomic-transcriptomic-proteomic analyses resolved a coordinated physiological response: (1) energy metabolic remodeling via upregulated TCA cycle and fatty acid β-oxidation and suppressed anaerobic respiration, may help sustain NAD(P)H and proton motive force that could support ArsB-mediated efflux; (2) Fe-S cluster repair and metal sequestration through Suf assembly, iron/siderophore uptake, and molybdenum cofactor biosynthesis; (3) multi-level antioxidant defense via glutathione, catalase/peroxidase, and SoxR/OxyR systems; and (4) motility suppression, conserving energy and protons while enhanced capsule/EPS functions promote Sb adsorption and mineral nucleation. Together, these processes may promote the hydrolysis and precipitation of aqueous Sb³⁺ species, leading to the formation of crystalline Sb₂O₃. Serratia nematodiphila orchestrates a coordinated metabolic reprogramming that enhances energy generation, metal sequestration, and oxidative defense while suppressing motility, effectively transforming toxic aqueous Sb³⁺ into valuable crystalline Sb₂O₃. These findings provide a mechanistic blueprint for engineering microbial-based bioremediation and resource recovery from antimony-polluted environments.