Microbial Ecophysiology

PROFILE

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.

LAB MEMBERS

Research Head: Raquel Quatrini

Doctoral Students: Ana Moya-Beltrán • Francisco Issotta Contardo • Dilanaz Arisan • Sebastián Pacheco Acosta • Fernando Díaz Gonzalez

Undergraduate Students: Abraham Zapata Araya

Research Assistants: Yasna Gallardo Briceño • Hector Carrasco Gallardo • Camila Rojas Valdebenito • Danitza Silva Garcia

Post-doctoral Fellows: Simón Beard Bórquez

COLLABORATIONS

National Collaborations:
• Dr. Matías Castro (Universidad San Sebastían, Concepción)
• Dr. Beatriz Diéz (Pontifícia Universidad Católica de Chile, Santiago)
• Dr. Alejandra Loyola (Fundación Ciencia & Vida, Santiago)
• Dr. Iván Ñancucheo (Universidad San Sebastían, Concepción)
• Dr. Francisco Remonselléz (Universidad Católica del Norte, Antofagasta)
• Dr. Mario Vera (Pontifícia Universidad Católica de Chile, Santiago)

International Collaborations:
• Dr. Mauro Degli Esposti (Centro de Ciencias Genómicas, Cuernavaca, Morelos, Mexico)
• Dr. Alejandra Giaveno (Universidad Nacional del Comahue, Neuquén, Argentina)
• Dr. D. Barrie Johnson (Bangor University, Bangor, North Wales, UK)
• Dr. Eugene Koonin (NCBI, National Institutes of Health; Bethesda, USA)
• Dr. Jiri Kucera (Masaryk University, Brno, Czech Republic)
• Dr. Daniel Paredes Sabja (A&E Texas University, Texas, USA)
• Dr. Pedro Temporetti (Universidad Nacional del Comahue, Bariloche, Argentina)

FORMER LAB MEMBERS

Matías Castro Gonzales (former Post-doc 2018-2019/2015-2016)
Research Professor at Universidad San Sebastián, Concepción, Chile

Rodrigo Flores Ríos (former Post-doc 2018-2019; former PhD student, graduated 2018)
Research Associate at the Laboratorio de Biología Molecular Bacteriana, Facultad de Medicina, Universidad de Chile, Santiago, Chile

Lillian Acuña Olivares (former Post-doc 2014-2017; former PhD student, graduated 2013)
Postdoctoral Researcher at the Laboratorio de Genética y Patogénesis Bacteriana, Universidad Andrés Bello, Santiago, Chile

Francisco Ossandón (former Post-doc 2013-2015)
Data Science Manager at Biome Makers Inc., West Sacramento, California, USA

Harold Nuñez Burgos (former Post-doc 2012-2016)
General DTC Manager at Psomagen Inc., Rockville, USA

Paulo Covarrubias Pizarro (former PhD student, graduated 2019)
Professional at the Subdepartamento de Genética Molecular, Instituto de Salud Pública, Santiago, Chile

Juan Pablo Cárdenas Astudillo (former PhD student, graduated 2015)
Profesor Asistente, Investigador del Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile

Mauricio Arenas Salinas (former PhD student, graduated 2014)
Associate Professor and Researcher at the Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile

Stefano Bueno Rossoni (former Master student, graduated 2020)
Cesar Valenzuela Alegría (former Master student, graduated 2020)
Karina Cordero Fernández (former Master student, graduated 2020)
Victor Alegría Mera (former Master student, graduated 2017)
Cristian Silva Fernández (former Master student, graduated 2011)
Cristopher Oporto Alarcón (former Master student, graduated 2009)
Ivette Olave Orellana (former Undergraduate student, graduated 2019)
Yazna Tapia Cisternas (former Undergraduate student, graduated 2018)
Rodolfo Gómez Salinas (former Undergraduate student, graduated 2018)
María Ignacia von Unger (former Undergraduate student, graduated 2016)
María Isabel Yanquepe (former Undergraduate student, graduated 2014)
Francisco Luciano Issotta Contardo (former Undergraduate student, graduated 2014)
Ana Rosa Moya Beltrán (former Undergraduate student, graduated 2014)
Alfredo Monsalve Bustos (former Undergraduate student, graduated 2013)
Pablo Tapia Salinas (former Undergraduate student, graduated 2012)
Juan José Haristoy Lagos (former Undergraduate student, graduated 2012)
David Loyola (former Undergraduate student, graduated 2011
Pamela Nieto Pacheco (former Undergraduate student, graduated 2009)

SELECTED PUBLICATIONS

  • Beard S., Ossandón F.J., Rawlings D.E., Quatrini R. The Flexible Genome of Acidophilic Prokaryotes. Curr. Issues Mol. Biol. 40: 231-266. DOI:10.21775/cimb.040.231 (2020) | PDF | ABSTRACT
  • González D., Huber K., Tindall B., Hedrich S., Rojas-Villalobos C., Quatrini R., Dinamarca M.A., Ibacache-Quiroga C., Schwarz A., Canales C., Ñancucheo I. Acidiferrimicrobium australe gen. nov., sp. nov., an acidophilic and obligately heterotrophic, member of the Actinobacteria that catalyses dissimilatory oxido-reduction of iron isolated from metal-rich acidic water in Chile. Int. J. Syst. Evol. Micr. 70: 3348-3354. DOI: 10.1099/ijsem.0.004179 (2020) | PDF | ABSTRACT
  • Johnson D.B., Quatrini R. Acidophile Microbiology in Space and Time. Curr. Issues Mol. Biol. 39: 63-76. DOI:10.21775/cimb.039.063 (2020) | PDF | ABSTRACT
  • Degli Esposti M., Garcia-Meza V., Ceniceros Gomez A., Moya-Beltrán A., Quatrini R., Hedersted L. Heme A-containing oxidases evolved in the ancestors of iron oxidizing bacteria. bioRxiv 2020.03.01.968255. DOI:10.1101/2020.03.01.968255 (preprint, 2020) | PDF | ABSTRACT
  • Saavedra F., Gurard-Levin Z.A., Rojas-Villalobos C., Vassias I., Quatrini R., Almouzni G., Loyola A. JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability. Epigenetics Chromatin. 13(1): 6. DOI:10.1186/s13072-020-00331-1 (2020) | PDF | ABSTRACT
  • Norris P.R., Falagán C., Moya-Beltrán A., Castro M., Quatrini R., Johnson D.B. Acidithiobacillus ferrianus sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph. Extremophiles 24(2): 329-337. DOI:10.1007/s00792-020-01157-1 (2020) | PDF | ABSTRACT
  • Falagán C., Moya-Beltrán A., Castro M., Quatrini R., Johnson D.B. Acidithiobacillus sulfuriphilus sp. nov.: an extremely acidophilic sulfur-oxidizing chemolithotroph isolated from a neutral pH environment. Int. J. Syst. Evol. Micr. 69: 2907-2913. doi:10.1099/ijsem.0.003576 (2019) | PDF | ABSTRACT
  • Flores-Ríos, R., Quatrini, R., Loyola, A. Endogenous and foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, interactions and effects on Mobile Genetic Elements and host's biology. Comput. Struct. Biotec. 17: 746–756. DOI:10.1016/j.csbj.2019.06.010 (2019) | PDF | ABSTRACT
  • Moya-Beltrán A., Rojas-Villalobos C., Díaz M., Guiliani N., Quatrini R., Castro M. Nucleotide second messenger-based signaling in extreme acidophiles of the Acidithiobacillus species complex: partition between the core and variable gene complements. Front. Microbiol. 10: 381. DOI:10.3389/fmicb.2019.00381 (2019) | PDF | ABSTRACT
  • Flores-Ríos R., Moya-Beltrán A., Pareja-Barrueto C., Arenas-Salinas M., Valenzuela S., Orellana O., Quatrini R. The Type IV Secretion System of ICEAfe1: formation of a conjugative pilus in Acidithiobacillus ferrooxidans. Front. Microbiol. 10: 30. DOI: 10.3389/fmicb.2019.00030 (2019) | PDF | ABSTRACT
  • Ulloa R., Moya-Beltrán A., Rojas-Villalobos C., Nuñez H., Chiacchiarini P., Donati E., Giaveno A., Quatrini R. Domestication of local microbial consortia for efficient recovery of gold through top-down selection in airlift bioreactors. Front. Microbiol. 10: 60. DOI: 10.3389/fmicb.2019.0006 (2019) | PDF | ABSTRACT
  • Quatrini R., Johnson D.B. Acidithiobacillus ferrooxidans. Trends Microbiol. 27: 282. DOI:10.1016/j.tim.2018.11.009 (2019) | PDF | ABSTRACT
  • Quatrini R., Johnson D.B. Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH. Curr. Opin. Microbiol. 43: 139-147. DOI: 10.1016/j.mib.2018.01.011 (2018) | PDF | ABSTRACT
  • Covarrubias P.C., Moya-Beltrán A., Atavales J., Moya-Flores F., Tapia P.S., Acuña L.G., Spinelli S., Quatrini R. Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex. Res. Microbiol. S0923-2508 (18): 30119-0. DOI: 10.1016/j.resmic.2018.07.005. (2018) | PDF | ABSTRACT
  • Issotta F., Moya-Beltrán A., Mena C., Covarrubias P.C., Thyssen C., Bellenberg S., Sand W., Quatrini R., Vera M. Insights into the biology of acidophilic members of the Acidiferrobacteraceae family derived from comparative genomic analyses. Res. Microbiol. S0923-2508(18): 30121-9. DOI: 10.1016/j.resmic.2018.08.001. (2018) | PDF | ABSTRACT
  • Nuñez H., Moya-Beltrán A., Covarrubias P.C., Issotta F., Cardenas J.P., Gonzalez M., Atavales J., Acuña L.G., Johnson D.B., Quatrini R. Molecular systematics of the genus Acidithiobacillus: insights into the phylogenetic structure and diversification of the taxon. Front. Microbiol. 8: 30. DOI: 10.3389/fmicb.2017.00030 (2017) | PDF | ABSTRACT
  • Castro-Severyn J., Remonsellez F., Salinas C., Valenzuela S.L., Fortt J., Aguilar P., Pardo-Esté C., Aguayo D., Dorador C., Quatrini R., Molina F., Castro-Nallar E., Saavedra C.P. Comparative genomics analysis of a new Exiguobacterium strain from Salar de Huasco reveals a repertoire of stress-related genes and arsenic resistance. Front. Microbiol. 8: 456. DOI: 10.3389/fmicb.2017.00456 (2017) | PDF | ABSTRACT
  • Valdebenito-Maturana B., Reyes-Suarez J.A., Henríquez J., Holmes D.S., Quatrini R., Pohl E., Arenas-Salinas M. Mutantelec: an in silico mutation simulation platform for comparative electrostatic potential profiling of proteins. J. Comput. Chem. 38: 467–474. DOI: 10.1002/jcc.24712. (2017) | PDF | ABSTRACT
  • Castillo A., Tello M., Ringwald K., Acuña L.G., Quatrini R., Orellana O. A DNA segment encoding the anticodon stem/loop of tRNA determines the specific recombination of integrative-conjugative elements in Acidithiobacillus species. RNA Biol. 20: 1-8. DOI: 10.1080/15476286.2017.1408765 (2017) | PDF | ABSTRACT
  • Quatrini R., Escudero L.V., Moya-Beltrán A., Galleguillos P.A., Issotta F., Acosta M., Cárdenas J.P., Nuñez H., Salinas K., Holmes D.S., Demergasso C. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Stand Genomic Sci. 12: 84. DOI: 10.1186/s40793-017-0305-8 (2017) | PDF | ABSTRACT
  • Castro M., Moya-Beltrán A., Covarrubias P.C., Gonzalez M., Cardenas J.P., Issotta F., Nuñez H., Acuña L.G., Encina G., Holmes D.S., Johnson D.B., Quatrini R. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Stand Genomic Sci. 12: 77. DOI: 10.1186/s40793-017-0282-y (2017) | PDF | ABSTRACT
  • 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

BOOKS & BOOK CHAPTERS

  • 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