title: Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications.
abstract: BACKGROUND
  Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.
  
  
  RESULTS
  The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.
  
  
  CONCLUSIONS
  Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
authors.affiliation: Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago, Chile. jorge.valdes@gmail.com
authors.forename: Jorge
authors.initials: J
authors.lastname: Valdés
authors.forename: Inti
authors.initials: I
authors.lastname: Pedroso
authors.forename: Raquel
authors.initials: R
authors.lastname: Quatrini
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Dodson
authors.forename: Herve
authors.initials: H
authors.lastname: Tettelin
authors.forename: Robert
authors.initials: R
authors.lastname: Blake
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: David S
authors.initials: DS
authors.lastname: Holmes
mesh_terms: D042763:Acidithiobacillus / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D007218:Industrial Microbiology; D008969:Molecular Sequence Data; D005810:Multigene Family