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Applied Microbiology and Biotechnology

, Volume 88, Issue 3, pp 605–620 | Cite as

Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms

  • Juan Pablo Cárdenas
  • Jorge Valdés
  • Raquel Quatrini
  • Francisco Duarte
  • David S. HolmesEmail author
Mini-Review

Abstract

This mini-review describes the current status of recent genome sequencing projects of extremely acidophilic microorganisms and highlights the most current scientific advances emerging from their analysis. There are now at least 56 draft or completely sequenced genomes of acidophiles including 30 bacteria and 26 archaea. There are also complete sequences for 38 plasmids, 29 viruses, and additional DNA sequence information of acidic environments is available from eight metagenomic projects. A special focus is provided on the genomics of acidophiles from industrial bioleaching operations. It is shown how this initial information provides a rich intellectual resource for microbiologists that has potential to open innovative and efficient research avenues. Examples presented illustrate the use of genomic information to construct preliminary models of metabolism of individual microorganisms. Most importantly, access to multiple genomes allows the prediction of metabolic and genetic interactions between members of the bioleaching microbial community (ecophysiology) and the investigation of major evolutionary trends that shape genome architecture and evolution. Despite these promising beginnings, a major conclusion is that the genome projects help focus attention on the tremendous effort still required to understand the biological principles that support life in extremely acidic environments, including those that might allow engineers to take appropriate action designed to improve the efficiency and rate of bioleaching and to protect the environment.

Keywords

Acidophiles Genomics Bioinformatics Metabolic reconstruction Ecophysiology 

Notes

Acknowledgments

The authors thank Fondecyt 1090451 and 1100887, UNAB DI-15-06-I, Conicyt Basal CCTE PFB16, Innova 08CM01-03, and Conicyt postgraduate studies grant 2010.

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Juan Pablo Cárdenas
    • 1
    • 2
  • Jorge Valdés
    • 1
    • 2
    • 3
  • Raquel Quatrini
    • 1
  • Francisco Duarte
    • 1
    • 2
  • David S. Holmes
    • 1
    • 2
    Email author
  1. 1.Center for Bioinformatics and Genome BiologyFundación Ciencia para la VidaSantiagoChile
  2. 2.Depto. de Ciencias Biológicas, Facultad de Ciencias BiológicasUniversidad Andrés BelloSantiagoChile
  3. 3.Computational Genomics Laboratory, Center for Bioinformatics and Molecular SimulationsUniversidad de TalcaSantiagoChile

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