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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Acidithiobacillus spp. are key players in metal mobilization and sulfur cycling in acidic environments, with important applications in biomining and bioleaching operations. But the evolutionary organization of the iron and sulfur oxidation systems of these organisms is not well understood. In this study, a comparative genomic analysis of 31 Acidithiobacillus genomes (95,180 predicted proteins) was performed to investigate the distribution, conservation, and genomic organization of genes involved in ferrous iron oxidation, reduced sulfur compound oxidation, respiratory electron transfer, and sulfur trafficking. This study identified key metabolic components including cyc2, rus, cyc1, petA-F, coxA-D, soxA-D, sqr, tetH, doxA, doxD, hdrA-C, tusA, and dsrE-like genes using genome annotation, conserved-domain identification, orthology inference, and gene-neighborhood analyses. The results indicate that energy metabolism in Acidithiobacillus is organized into discrete functional modules rather than as a single universally conserved pathway. The cox terminal oxidase complex and the cyc2\/rus\/cyc1 iron-entry modules were identified in 21 genomes (67.7%) and 19 genomes (61.3%), respectively. Sulfur associated systems displayed greater variation in gene content, Sox genes were found in 10 genomes (32.3%), SQR\/TetH\/Dox components in 12 genomes (38.7%), and the Hdr\/Tus\/DsrE sulfur-transfer system in 22 genomes (71.0%). Phylogenomic analysis revealed iron-enriched, sulfur-enriched and mixed metabolic profiles, in line with differential retention, loss and reorganization of redox modules. These results show that metabolic potential cannot be accurately predicted from single marker genes alone, but must integrate orthology, genomic context and phylogenomic relationships. This comparative genomic framework may facilitate the identification of candidate strains for biomining applications and provide insights into the potential ecological functions of Acidithiobacillus species in acidic environments.<\/jats:p>","DOI":"10.3390\/ijms27156728","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T08:52:01Z","timestamp":1785228721000},"page":"6728","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Genomic Analysis Reveals Distribution, Organization, and Evolution of Ferrous and Sulfur Oxidation Genes in the Genus Acidithiobacillus"],"prefix":"10.3390","volume":"27","author":[{"given":"Zulaikha","family":"Abid","sequence":"first","affiliation":[{"name":"School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China"},{"name":"Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4539-8708","authenticated-orcid":false,"given":"Yuandong","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China"},{"name":"Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Vald\u00e9s, J., Pedroso, I., Quatrini, R., Dodson, R.J., Tettelin, H., Blake, R., Eisen, J.A., and Holmes, D.S. 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