Open Access Highly Accessed Research article

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

Jorge Valdés1, Inti Pedroso1, Raquel Quatrini1, Robert J Dodson2, Herve Tettelin23, Robert Blake6, Jonathan A Eisen245 and David S Holmes1*

Author Affiliations

1 Center for Bioinformatics and Genome Biology, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias de la Salud, Universidad Andres Bello, Santiago Chile

2 J. Craig Venter Institute, Rockville, MD, USA

3 The Institute for Genomic Sciences, University of Maryland, Baltimore, MD, USA

4 University of California Davis Genome Center, Section of Evolution and Ecology, U.C. Davis, Davis, CA, USA

5 University of California Davis Genome Center, Dept of Medical Microbiology and Immunology, U.C. Davis, Davis, CA, USA

6 Division of Basic Pharmaceutical Sciences, Xavier University, New Orleans, LA, USA

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BMC Genomics 2008, 9:597  doi:10.1186/1471-2164-9-597

Published: 11 December 2008



Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-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.


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.


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.