Publications

Our most recent publications...

Further details...

Further details...

  • Salgado O, Guajardo-Leiva S, Moya-Beltrán A, Barbosa C, Ridley CM, Tamayo J, Quatrini R, Mojica FJM, Diez B. Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities. Front. Microbiol.13: 1069452.  doi:  10.3389/fmicb.2022.1069452
  • Quatrini R, Watkin ELJ, Johnson DB. Biomolecular and Cultivation Tools. BIOMINING TECHNOLOGIES: Extracting and Recovering Metals from Ores and Wastes. Springer-Verlag. Chapter 6, 111-131. Eds David Barrie Johnson, Christopher George Bryan, Michael Schlömann and Francisco Figueroa Roberto. Springer, Switzerland. ISBN: 978-3-031-05381-8. doi: 10.1007/978-3-031-05382-5_6
  • Moya-Beltrán A, Makarova KS, Acuña LG, Wolf YI, Covarrubias PC, Shmakov SA, Silva C, Tolstoy I, Johnson DB, Koonin EV, Quatrini R. Evolution of Type IV CRISPR-Cas systems: insights from CRISPR loci in Integrative Conjugative Elements of Acidithiobacillia. CRISPR J. 4:656-672. doi: 10.1089/crispr.2021.0051
  • Degli Esposti M, Moya-Beltran A, Quatrini R, Hedersted L. Respiratory Heme A-containing oxidases originated in the ancestors of iron-oxidizing bacteria. Front. Microbiol., 12: 664216. doi: 10.3389/fmicb.2021.664216
  • Moya-Beltrán A, Beard S, Rojas-Villalobos C, Issotta F, Gallardo Y, Ulloa R, Giaveno A, Degli Esposti M, Johnson DB, Quatrini R. Genomic evolution of the class Acidithiobacillia: deep branching Proteobacteria living in extreme acidic conditions. ISME J. 15:3221-3238.  doi: 10.1038/s41396-021-00995-x
  • Beard S, Ossandón FJ, Rawlings DE, Quatrini R. The Flexible Genome of Acidophilic Prokaryotes. Curr. Issues Mol. Biol., 40: 231-266. doi: 10.21775/cimb.040.231
  • Norris PR, Falagán C, Moya-Beltrán A, Castro M, Quatrini R, Johnson DB*. Acidithiobacillus ferrianus sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph. Extremophiles, 24: 329-337. doi: 10.1007/s00792-020-01157-1.
  • Johnson D B, Quatrini R*. Acidophile Microbiology in Space and Time. Curr. Issues Mol. Biol., 39: 63-76. doi:10.21775/cimb.039.06.
  • Degli Esposti M*, Garcia-Meza V, Ceniceros Gomez A, Moya-Beltran A, Quatrini R, Hedersted L. Heme A-containing oxidases evolved in the ancestors of iron oxidizing bacteria. bioRxiv, 2020.03.01.968255. (preprint) doi: 10.1101/2020.03.01.968255
  • Gonzalez D, Huber K, Tindall B, Hedrich S, Rojas-Villalobos C, Quatrini R, Dinamarca MA, Ibacache-Quiroga C, Schwarz A, Canales C, Nancucheo 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.
  • Saavedra F, Gurard-Levin ZA, 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., 13:6. doi:10.1186/s13072-020-00331-1.
  • Quatrini R*, Johnson DB. Acidithiobacillus ferrooxidans. Trends Microbiol., 27: 282. doi:10.1016/j.tim.2018.11.009.
  • 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.
  • 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.
  • 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.

  • Flores-Rios 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. Biotechnol. J., 17: 746. doi:10.1016/j.csbj.2019.06.010.

  • Quatrini R, Johnson DB. 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.
  • Covarrubias PC, Moya-Beltrán A, Atavales J, Moya-Flores F, Tapia PS, Acuña LG, Spinelli S, Quatrini R*. Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex. Res Microbiol., 169: 628-637. doi:10.1016/j.resmic.2018.07.005.
  • Issotta F, Moya-Beltrán A, Mena C, Covarrubias PC, 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., 169: 608-617. doi:10.1016/j.resmic.2018.08.001.
  • Nuñez H, Moya-Beltrán A, Covarrubias PC, Issotta F, Cardenas JP, Gonzalez M, Atavales J, Acuña LG, Johnson DB, 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
  • Castro-Severyn J, Remonsellez F, Salinas C, Valenzuela SL, Fortt J, Aguilar P, Pardo-Esté C, Aguayo D, Dorador C, Quatrini R, Molina F, Castro-Nallar E*, Saavedra CP*. 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
  • Valdebenito-Maturana B, Reyes-Suarez JA, Henríquez J, Holmes DS, 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.
  • Castillo A, Tello M, Ringwald K, Acuña LG, 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.
  • Quatrini R, Escudero LV, Moya-Beltrán A, Galleguillos PA, Issotta F, Acosta M, Cárdenas JP, Nuñez H, Salinas K, Holmes DS, Demergasso C*. Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile. Stand. Genom. Sci., 12: 84. 2017.doi: 10.1186/s40793-017-0305-8
  • Castro M, Moya-Beltrán A, Covarrubias PC, Gonzalez M, Cardenas JP, Issotta F,  Nuñez H, Acuña LG, Encina G, Holmes DS, Johnson DB, Quatrini R*. Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366). Stand. Genom. Sci., 12: 77. doi: 10.1186/s40793-017-0282-y.
  • Issotta F, Bobadilla-Fazzini R, Moya-Beltrán A, Covarrubias P, Quatrini R*, Martinez P*. Genetic basis of metal resistance in Acidiphilium sp. DSM 27270 (Yenapatur). Solid State Phenom., 262: 358-363. doi:10.4028/www.scientific.net/SSP.262.358
  • Issotta F, Covarrubias PC, Moya-Beltrán A , Bellenberg S, Thyssen C, Wolfgang S, Nuñez H, Mena C, Holmes DS, Quatrini R*, Vera M*. 16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family. Solid State Phenom., 262: 339-343. doi:10.4028/www.scientific.net/SSP.262.339
  • Ulloa R, Moya-Beltrán A, Issotta F, Nuñez H, Covarrubias PC, Donati ER, Quatrini R*, Giaveno A*. Metagenome-derived draft genome sequence of Acidithiobacillus ferroxidans RV1 from an abandoned gold tailing in Neuquén, Argentina.  Solid State Phenom., 262: 439-442. doi:10.4028/www.scientific.net/SSP.262.439
  • Flores-Ríos R, Moya-Beltrán A, Covarrubias PC, Acuña LG, Orellana O, Quatrini R*. Type IV secretion systems diversity in the Acidithiobacillus genus.  Solid State Phenom., 262: 429-433. doi:10.4028/www.scientific.net/SSP.262.429
  • Covarrubias P, Muñoz R , Bobadilla-Fazzini R, Martinez P* and Quatrini R*. Are there viruses in industrial bioleaching econiches? Solid State Phenom., 262: 521-525. doi:10.4028/www.scientific.net/SSP.262.521
  • Cárdenas JP, Quatrini Rand Holmes DS. Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment. Front. Microbiol. 7:1822. doi: 10.3389/fmicb.2016.01822
  • Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res. Microbiol.,  167: 529-38. doi: 10.1016/j.resmic.2016.06.007.
  • Nuñez H, Covarrubias PC, Moya-Beltrán A, Issotta F, Atavales J, Acuña LG,  Johnson DB, Quatrini R*. Detection, identification and typing of Acidithiobacillus species and strains: a review. Res. Microbiol., 167: 555-67. doi:  10.1016/j.resmic.2016.05.006.
  • Issotta F, Galleguillos P, Moya-Beltrán A, Davis-Belmar CS, Rautenbach G, Covarrubias PC, Acosta-Grinok M, Ossandon FJ, Contador Y, Holmes DS, Marín-Eliantonio S, Quatrini R, Demergasso C. 2016. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand. Genom. Sci., 11:19. doi 10.1186/s40793-016-0142-1.
  • Ossandon FJ, Cárdenas JP, Corbett M, Quatrini R, Holmes DS, Watkin E*. Draft genome sequence of the iron-oxidizing, acidophilic and halotolerant ‘Thiobacillus prosperus’ type strain DSM 5130. Genome Announc., 2(5):e01042-14. doi:10.1128/genomeA.01042-14.
  • 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(14)00116-8. doi: 10.1016/j.resmic.2014.07.014.
  • González C, Yanquepe M, Cardenas JP, Valdes J, Quatrini R, Holmes DS, Dopson M. Genetic variability of psychrotolerant Acidithiobacillus ferrivorans revealed  by (meta)genomic analysis. Res. Microbiol., S0923-2508(14)00135-1. doi: 10.1016/j.resmic.2014.08.005.
  • 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(4): e00834-14. doi:  10.1128/genomeA.00834-14.
  •  Arenas-Salinas M, Ortega-Salazar S, Gonzales-Nilo F, Pohl E, Holmes DS, Quatrini R*. AFAL: a web service for profiling amino acids surrounding ligands in proteins. J. Comput. Aided Mol. Des., 28: 1069-1076. doi: 10.1007/s10822-014-9783-6.
  • Molina-Quiroz RC, Loyola DE, Muñoz-Villagrán CM,Quatrini R, Vásquez CC, Pérez-Donoso JM. DNA, Cell Wall and General Oxidative Damage Underlie the Tellurite/Cefotaxime Synergistic Effect in Escherichia coli. PLoS One. 8(11):e79499. doi:10.1371/journal.pone.0079499
  • 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(11):e78237. doi:10.1371/journal.pone.0078237
  • Bustamante P, Covarrubias P,  Levicán G,  Katz A, Tapia P, Bonnefoy V, Holmes DS, Quatrini R*, Orellana O*. ICEAfe1, an actively excising integrative-conjugative element from the biomining bacterium Acidithiobacillus ferrooxidans. J. Mol. Microbiol. Biotech., 22: 399-407. doi: 10.1159/00034666
  • Salazar CN, Acosta M, Galleguillos PA, Shmaryahu A, Quatrini R, Holmes DS, Demergasso CS*. Analysis of Gene Expression in Response to Copper Stress in Acidithiobacillus ferrooxidansStrain D2, Isolated from a Copper Bioleaching Operation. Adv. Mat. Res.,  825: 157-161. doi:10.4028/www.scientific.net/AMR.825.157
  • Galleguillos PA, Music V, Acosta M, Salazar CN, Quatrini R, Shmaryahu A, Holmes DS, Velásquez A, Espoz C, Pinilla C, Demergasso CS. Temporal Dynamics of Genes Involved in Metabolic Pathways of C and N of Leptospirillum ferriphilum, in the Industrial Bioleaching Process of Escondida Mine, Chile. Adv. Mat. Res., 825: 162-165. doi:10.4028/www.scientific.net/AMR.825.162
  • 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. J. Virol., 86:12452-12453. doi:10.1128/JVI.02261-12
  • Norambuena J, Flores R, Cárdenas JP, Quatrini R, Chávez R, Levicán G*. Thiol/Disulfide System Plays a Crucial Role in Redox Protection in the Acidophilic Iron-Oxidizing Bacterium Leptospirillum ferriphilum. PLoS One, 7(9):e44576. doi:10.1371/journal.pone.0044576
  • Cárdenas JP, Covarrubias P, Shmaryahu A, Demergasso C, Levicán G, Holmes DS, Quatrini R. Comparative genomics of the oxidative stress response in bioleaching microorganisms.   Hydrometallurgy, 127–128: 62–167. doi:10.1016/j.hydromet.2012.07.014
  •  Valdés J, Ossandon F,  Quatrini R, Dopson M, Holmes DS. Draft genome sequence of the extreme acidipohillic biomining proteobacterium Acidithiobacillus thiooxidansATCC 19377 provides insights into the evolution of the Acidithiobacillusgenus. J. Bacteriol., 193: 7003-7004. doi:10.1128/JB.06281-11

  • Cárdenas JP, Valdés J, Quatrini R, Duarte F, Holmes DS. Lessons from the Genomes of Extremely Acidophilic Bacteria and Archaea with Special Emphasis on Bioleaching Microorganisms. Appl. Microbiol. Biotechnol., 88: 605-620. doi 10.1007/s00253-010-2795-9

  • Valdés J, Cárdenas JP, Quatrini R, Esparza M, Osorio H, Duarte F, Lefimil C, Sepulveda R, Jedlicki E, Holmes DS. Comparative genomics begins to unravel the ecophysiology of bioleaching. Hydrometallurgy,104: 471-476. doi: 10.1016/j.hydromet.2010.03.028

  • Quatrini R, Appia-Ayme C, Denis Y, Jedlicki E, Holmes DS, Bonnefoy V. Extending the Models for Iron and Sulfur Oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans. BMC Genomics, 10:394. doi:10.1186/1471-2164-10-394
  • Valdes J, Quatrini R, Hallberg K, Dopson M, Valenzuela PD, Holmes DS. Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldusATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus.  J. Bacteriol., 191: 5877-5878. doi:10.1128/JB.00843-09
  • Nieto PA, Covarrubias PC, Jedlicki E, Holmes DS, Quatrini R*. Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans. BMC Mol. Biol., 10: 63. doi: 10.1186/1471-2199-10-63.
  • Holmes DS, Cárdenas JP, Valdés J, Quatrini R, Esparza M, Osorio H, Duarte F, Lefimil C and Jedlicki E. Comparative genomics begins to unravel the ecophysiology of bioleaching. Adv. Mat. Res., 71-73: 143-150. doi:10.4028/www.scientific.net/AMR.71-73.143
  • Levicán G, Katz A, Valdés J, Quatrini R, Holmes DS and Orellana O. 2009. A 300 kpb genome segment, including a complete set of tRNA genes, is dispensable for Acidithiobacillus ferrooxidans. Adv. Mat. Res., 71-73: 187-190. doi:10.4028/www.scientific.net/AMR.71-73.187
  • Lefimil C, Osorio H, Quatrini R, Holmes DS and Jedlicki E. 2009. Regulation of expression of the PetI operon involved in iron oxidation in the biomining bacterium Acidithiobacillus ferrooxidans. Adv. Mat. Res., 71-73: 199-202. doi:10.4028/www.scientific.net/AMR.71-73.199
  • Cárdenas JP, Martínez V, Covarrubias P, Holmes DS, Quatrini R. 2009. Predicted CO/CO2 fixation in Ferroplasma spp. via a novel chimaeric pathway. Adv. Mat. Res., 71-73:219-222. doi:10.4028/www.scientific.net/AMR.71-73.219
  • Osorio H, Martínez V, NietoPA, Holmes DS, Quatrini R. Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiol. 8: 203. doi:10.1186/1471-2180-8-203
  • Valdés J, Pedroso I, Quatrini R, Tettelin H, Eisen JA & Holmes DS. Acidithiobacillus ferrooxidans Metabolism: From Genome Sequence to Industrial Applications. BMC Genomics, 9: 597. doi:10.1186/1471-2164-9-597
  • Osorio H, Martínez V, Veloso FA, Pedroso I, Valdés J, Jedlicki E, Holmes DS, Quatrini R*. Iron Homeostasis Strategies in acidophilic iron oxidizers: studies in Acidithiobacillus and Leptospirillum. Hydrometallurgy, 94:175-179. doi:10.1016/j.hydromet.2008.05.038
  • Valdés J, Pedroso I, Quatrini R, Holmes DS. Comparative Genome Analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: insights into their Metabolism and Ecophysiology. Hydrometallurgy, 94: 180-184. doi:10.1016/j.hydromet.2008.05.039
  • Quatrini R, Lefimil C, Veloso F, Pedroso I, Holmes DS & Jedlicki E. Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res. 35: 2153-2166. doi:10.1093/nar/gkm068
  • Quatrini R, Martínez V, Osorio H, Veloso FA, Pedroso I, Valdés J, Jedlicki E and Holmes DS. 2007. Iron Homeostasis Strategies in Acidophilic Iron Oxidizers:  Comparative Genome Analysis. Adv. Mat. Res., 20-21: 531-534. doi:10.4028/www.scientific.net/AMR.20-21.531
  • Valdés J, Pedroso I, Quatrini R, Hallberg K, Valenzuela PDT, Holmes DS. Insights into the Metabolism and Ecophysiology of Three Acidithiobacilli Species by Comparative Genome Analysis. Adv. Mat. Res., 20-21: 439-442. doi:10.4028/www.scientific.net/AMR.20-21.439
  • Quatrini R, Appia-Ayme C, Denis Y, Ratouchniak J, Veloso F, Valdes J, Lefimil C, Silver S, Roberto, F, Orellana O, Denizot F, Jedlicki E, Holmes DS, Bonnefoy V. Insights into the Iron and Sulfur Energetic Metabolism of Acidthiobacillus ferrooxidans by Microarray Transcriptome Profiling, Hydrometallurgy, 83: 263-272. doi:10.1016/j.hydromet.2006.03.030
  • Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto F, Veloso F, Valdes J, Cárdenas JP, Esparza M, Orellana O, Jedlicki E, Bonnefoy V, Holmes DS. Microarray and Bioinformatic Analyses Suggest Models for Carbon Metabolism in the Autotroph Acidithiobacillus ferrooxidans, Hydrometallurgy, 83: 273-280. doi:10.1016/j.hydromet.2006.03.029
  • Quatrini R, Lefimil C, Holmes DS, Jedlicki E. The Ferric Iron Uptake Regulator (Fur) from the Extreme  Acidophile Acidithiobacillus   ferrooxidans, Microbiology, 151: 2005-2015. doi: 10.1099/mic.0.27581-0
  • Quatrini R, Jedlicki E, Holmes DS. Genomic Insights into the Iron Uptake Mechanisms of the Biomining Microorganism Acidithiobacillus   ferrooxidans, J. Ind. Microbiol. Biotechnol., 32: 606-614. doi: 10.1007/s10295-005-0233-2
Toggle Content

 

  • Barreto M, Quatrini R, Bueno S, Arraigada C, Valdés J, Silver S, et al. Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence. Hydrometallurgy 71: 97–105. doi: 10.1016/S0304-386X(03)00145-2
Toggle Content
  • Quatrini R, Albino A, Barg M. Variación morfológica y dieta en dos poblaciones de Liolaemus elongatus Koslowsky, 1896 (Iguania: Tropiduridae) del noroeste patagónico. Revista Chilena de Historia Natural, 74(3), 639-651. doi: 10.4067/S0716-078X2001000300010