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

Graphical abstract ABSTRACT This study aimed to isolate a novel antimony-mineralizing bacterium and elucidate its molecular response mechanisms during Sb(III) biomineralization via integrated multi-omics. The isolate Serratia marcescens (MIC > 250 mM) achieved 96.18% Sb(III) removal under Box-Behnken-optimized conditions (27.7 ℃, pH 4.67, 205.6 rpm). Timeseries Raman and SEM-EDS revealed a nonclassical crystallization pathway proceeding through an amorphous precursor to crystalline Sb2O3 (confirmed by XRD/XPS) within 36 h. Integrated transcriptomic and proteomic profiling showed that Sb(III) stress significantly upregulated TCA cycle enzymes (mqo, mdh, fumC), fatty acid βoxidation (FadL/D/E/A), siderophore/iron uptake (entB/C/E, fepB/A), Fe-S cluster assembly (sufABCS), molybdenum cofactor biosynthesis (moaABCDE), and glutathionemediated antioxidant systems (katCEG, gshAB), while concurrently downregulating flagellar assembly (flgBCDEFGKL) and chemotaxis (cheR) to conserve proton motive force for ArsB-driven Sb(III) efflux. S. marcescens orchestrates a coordinated metabolic reprogramming that enhances energy generation, metal sequestration, and oxidative defence while suppressing motility, effectively transforming toxic aqueous Sb(III) into valuable crystalline Sb2O3. These findings provide a mechanistic blueprint for engineering microbialbased bioremediation and resource recovery from antimonypolluted environments.