Microbial Ecophysiology


Copper mining is a pillar of the Chilean economy. However, this industry heavily pollutes the environment. Therefore bioleaching, a method that uses microbes to catalyze metal recovery is becoming a cleaner alternative for metal recovery. The procedure still remains quite empirical, hampering copper exploitation in heap reactors. The lack of in situ control of the processes is largely due to our limited understanding of the biology, ecology and dynamics of the consortia of extreme acidphiles acting as catalysts. For this reason our group uses cutting edge technologies and a powerful combination of computational and functional genomics as well as basic biochemistry and molecular biology tools to advance the understanding of the dynamics and the interactions between all players (bacteria, archaea, virus) present in the bioleaching and extreme acidic econiches. Through our research we aim to uncover critical metabolic control points that may affect mineral recovery and contribute to the general knowledge of extremophiles.


Research Head: Raquel Quatrini

Postdoctoral Fellows: Harold Nuñez • Lillian Acuña • Matias Castro

Doctoral students: Juan Pablo Cardenas • Rodrigo Flores • Paulo Covarrubias • Ana Moya • Francisco Issotta

Undergraduate students: María Ignacia von Unger • Víctor Alegria • Fernanda Sazo

Research asistants: Oscar Salgado • Joaquín Atavales

Technician: Mónica González


National Collaborations:
• Dr. Francisco Remonselléz (Universidad Católica del Norte, Antofagasta)
• Dr. Mario Vera (Universidad Católica, Santiago)
• Dr. Nicolás Guiliani (Universidad de Chile, Santiago)
• Rodrigo Muñoz (Los Bronces-Anglo American, Santiago)
• Dr. Juan Rivadeneira (Universidad Adolfo Ibañez, Santiago)

International Collaborations:
• Dr. D. Barrie Johnson (Bangor University, Bangor, North Wales, UK)
• Dr. Jiri Kucera (Masaryk University, Brno, Czech Republic)
• Dr. Pablo Ramírez (Universidad de San Marcos, Lima, Perú)
• Dr. Douglas Rawllings (Stellenbosch University, Stellenbosch, South Africa)
• Dr. Alejandra Giaveno (Universidad Nacional del Comahue, Neuquén, Argentina)


  • Nuñez H., Covarrubias P. C., Moya-Beltrán A., Issotta F., Atavales J., Acuña L. G., Johnson D. B., Quatrini R. Detection, identification and typing of Acidithiobacillus species and strains: a review. Res. Microbiol. In press. (2016) doi:10.1016/j.resmic.2016.05 | | ABSTRACT
  • Issotta F., Galleguillos P., Moya-Beltrán A., Davis-Belmar C. S., Rautenbach G., Covarrubias P. C., Acosta-Grinok M., Ossandon F. J., Contador Y., Holmes D. S., Marín-Eliantonio S., Quatrini R., Demergasso C. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand. Genomic Sci. 11:19 (2016) doi 10.1186/s40793-016-0142-1 | | ABSTRACT
  • Nuñez H, Loyola D, Cárdenas JP, Holmes DS, Johnson DB, Quatrini R. Multi Locus Sequence Typing scheme for Acidithiobacillus caldus strain evaluation and differentiation. Res. Microbiol. S0923-2508, 116-118 (2014) doi: 10.1016/j.resmic.2014.07.014. | | ABSTRACT
  • González C., Yanquepe M., Cardenas J. P., Valdes J., Quatrini R., Holmes D. S., Dopson M. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed by (meta)genomic analysis. Res. Microbiol. S0923-2508, 726-734 (2014) doi: 10.1016/j.resmic.2014.08.005 | | ABSTRACT
  • Moya-Beltrán A, Cárdenas JP, Covarrubias PC, Issotta F, Ossandon FJ, Grail BM, Holmes DS, Quatrini R, Johnson DB. Draft Genome Sequence of the Nominated Type Strain of "Ferrovum myxofaciens," an Acidophilic, Iron-Oxidizing Betaproteobacterium. Genome Announc. 2, e00834-14 (2014) doi: 10.1128/genomeA.00834-14. | | ABSTRACT
  • Acuña LG, Cárdenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nuñez H, Riadi G, Shmaryahu A, Valdés J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R. Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus. PLoS One. 8, e78237 (2013) doi: 10.1371/journal.pone. 0078237. | | ABSTRACT
  • Bustamante P, Covarrubias P, Levicán G, Katz A, Tapia P, Bonnefoy V, Holmes DS, Quatrini R, Orellana O. 2013. ICEAfe1, an actively excising integrative-conjugative element from the biomining bacterium Acidithiobacillus ferrooxidans. Mol. Microbiol. Biotech. 22, 399-407 (2013) doi: 10.1159/000346669 | | ABSTRACT
  • Tapia P, Flores FM, Covarrubias PC, Acuña LG, Holmes DS, Quatrini R. Complete Genome Sequence of Temperate Bacteriophage AcaML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756. Virol. 86, 12452-12453 (2012) doi: 10.1128/JVI.02261-12. | | ABSTRACT
  • Quatrini R., Appia-Ayme C., Denis Y., Jedlicki E., Holmes D. S., Bonnefoy V. Extending the models for iron and sulfur oxidation in the extreme acidophils. Acidithiobacillus ferrooxidans. BMC Genomics, 10:394 (2009) doi: 10.1186/1471-2164-10-394. | | ABSTRACT
  • Quatrini R., Lefimil C., Veloso F. A., Pedroso I., Holmes D. S., Jedlicki E. Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res. 35 (7): 2153–2166 (2007) doi: 10.1093/nar/gkm068 | PDF | ABSTRACT


  • Acidophiles: life in extremely acidic environments. Eds Raquel Quatrini and D. Barrie Johnson. UK: Caister Academic Press. 2016. ISBN 978-1-910190-33-3. | | ABSTRACT
  • Johnson DB, Quatrini R. Acidophile Microbiology in Space and Time. UK: Caister Academic Press. Chapter 1, 3-16. Eds Raquel Quatrini and D. Barrie Johnson. 2016. | | ABSTRACT
  • Cárdenas JP, Quatrini R, Holmes DS. Progress in Acidophile Genomics. UK: Caister Academic Press. Chapter 11, 179-197. Eds Raquel Quatrini and D. Barrie Johnson, 2016. | | ABSTRACT
  • Quatrini R, Ossandon FJ, Rawlings DE. The Flexible Genome of Acidophilic Prokaryotes. UK: Caister Academic Press. Chapter 12, 199-220. Eds Raquel Quatrini and D. Barrie Johnson, 2016. | | ABSTRACT