Multi-omics reveals the response and adaptation of Acidithiobacillus ferrooxidans BY-3 under arsenic stress

Acidithiobacillus ferrooxidans ( A. ferrooxidans ) exhibits strong arsenic resistance and plays a pivotal role in biometallurgy and sulfur cycling in ecosystems. In this study, integrated transcriptomic, proteomic, and metabolomic analyses were employed to elucidate the molecular response mechanisms of Acidithiobacillus ferrooxidans BY-3 ( At. f BY-3) under arsenic stress. The study also evaluated its capacity for heavy metal bioleaching and provided new insights into bioremediation applications. Transcriptomic profiling revealed that the number of differentially expressed genes increased in an arsenic dose-dependent manner. Under arsenic stress, At. f BY-3 displayed global downregulation of genes involved in secondary metabolism and chemotaxis, thereby reducing unnecessary energy expenditure and reallocating metabolic resources toward arsenic resistance. Proteomic analysis identified 337 significantly differentially abundant proteins, which were primarily enriched in c-di-GMP signal transduction, sulfur cycling, redox homeostasis, and transmembrane transport. Metabolomic analysis detected 53 differential metabolites that were mainly associated with ABC transport systems, sulfur metabolism, and stress signaling pathways. Multi-omics integration demonstrated that At. f BY-3 maintained energy homeostasis through coordinated carbon and sulfur metabolism, enhanced arsenic efflux via activation of ABC transporters, and optimized membrane structure and signaling systems for improved stress perception. Sulfur cycling emerged as the central adaptive strategy for arsenic resistance. Furthermore, bioleaching assays confirmed the robust arsenic bioleaching capability of At. f BY-3, which was further enhanced following domestication. Overall, this work clarifies the molecular mechanisms underlying arsenic resistance in A. ferrooxidans , providing a theoretical foundation for optimizing biohydrometallurgy processes and heavy metal bioremediation strategies.