Proteomic Insights into the Adaptation of <i>Acidithiobacillus ferridurans</i> to Municipal Solid Waste Incineration Residues for Enhanced Bioleaching Efficiency

<i>Acidithiobacillus</i> spp. have traditionally been utilized to extract metals from mineral ores through bioleaching. This process has recently expanded to include artificial ores, such as those derived from municipal solid waste incineration (MSWI) residues. Previous studies have indicated that microbial adaptation enhances bioleaching efficiency, prompting this study to identify proteins involved in the adaptation of <i>A. ferridurans</i> to MSWI residues. We employed data-independent acquisition-parallel accumulation serial fragmentation to determine the proteomic response of <i>A. ferridurans</i> DSM 583 to three distinct materials: bottom ash (BA), kettle ash (KA), and filter ash (FA), which represent typical MSWI residues. Our findings indicate that, irrespective of the residue type, a suite of membrane transporters, porins, efflux pumps, and specific electron and cation transfer proteins was notably upregulated. The upregulation of certain proteins involved in anaerobic pathways suggested the development of a spontaneous microaerobic environment, which minimally impacted the bioleaching efficiency. Additionally, the adaptation was most efficient at half the target FA concentration, marked by a significant increase in the detoxification and efflux systems required by microorganisms to tolerate high heavy metal concentrations. Given that metal recovery peaked at lower FA concentrations for most metals of interest, further adaptation at the level of protein expression may not be warranted for improved bioleaching outcomes.