Omics on Bioleaching: Current and Future Impacts

Overview

Journal Appl Microbiol Biotechnol

Specialties Biomedical Engineering
Biotechnology
Microbiology

Date 2015 Aug 18

PMID 26278538

Citations 7

Authors

Patricio Martinez

Mario Vera

Roberto A Bobadilla-Fazzini

Affiliations

Soon will be listed here.

Abstract

Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.

Citing Articles

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Progress in bioleaching: fundamentals and mechanisms of microbial metal sulfide oxidation - part A.

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References

Guo L, Brugger K, Liu C, Shah S, Zheng H, Zhu Y . Genome analyses of Icelandic strains of Sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. J Bacteriol. 2011; 193(7):1672-80. PMC: 3067641. DOI: 10.1128/JB.01487-10. View

You X, Liu C, Wang S, Jiang C, Shah S, Prangishvili D . Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles. Extremophiles. 2011; 15(4):487-97. PMC: 3119797. DOI: 10.1007/s00792-011-0379-y. View

Denef V, VerBerkmoes N, Shah M, Abraham P, Lefsrud M, Hettich R . Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol. 2008; 11(2):313-25. DOI: 10.1111/j.1462-2920.2008.01769.x. View

Bobadilla Fazzini R, Levican G, Parada P . Acidithiobacillus thiooxidans secretome containing a newly described lipoprotein Licanantase enhances chalcopyrite bioleaching rate. Appl Microbiol Biotechnol. 2010; 89(3):771-80. PMC: 3023857. DOI: 10.1007/s00253-010-3063-8. View

Martinez P, Galvez S, Ohtsuka N, Budinich M, Cortes M, Serpell C . Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay. Metabolomics. 2013; 9(1):247-257. PMC: 3548112. DOI: 10.1007/s11306-012-0443-3. View

Friedman S, Oshima T . Polyamines of sulfur-dependent archaebacteria and their role in protein synthesis. J Biochem. 1989; 105(6):1030-3. DOI: 10.1093/oxfordjournals.jbchem.a122761. View

Guo X, Yin H, Liang Y, Hu Q, Zhou X, Xiao Y . Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PLoS One. 2014; 9(6):e99417. PMC: 4062416. DOI: 10.1371/journal.pone.0099417. View

Remonsellez F, Galleguillos F, Moreno-Paz M, Parro V, Acosta M, Demergasso C . Dynamic of active microorganisms inhabiting a bioleaching industrial heap of low-grade copper sulfide ore monitored by real-time PCR and oligonucleotide prokaryotic acidophile microarray. Microb Biotechnol. 2011; 2(6):613-24. PMC: 3815317. DOI: 10.1111/j.1751-7915.2009.00112.x. View

Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D . Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. Proc Natl Acad Sci U S A. 2000; 97(7):3509-14. PMC: 16270. DOI: 10.1073/pnas.97.7.3509. View

10.

Chi A, Valenzuela L, Beard S, Mackey A, Shabanowitz J, Hunt D . Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis. Mol Cell Proteomics. 2007; 6(12):2239-51. PMC: 4631397. DOI: 10.1074/mcp.M700042-MCP200. View

11.

Vera M, Schippers A, Sand W . Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation--part A. Appl Microbiol Biotechnol. 2013; 97(17):7529-41. DOI: 10.1007/s00253-013-4954-2. View

12.

Wilmes P, Bowen B, Thomas B, Mueller R, Denef V, VerBerkmoes N . Metabolome-proteome differentiation coupled to microbial divergence. mBio. 2010; 1(5). PMC: 2962434. DOI: 10.1128/mBio.00246-10. View

13.

Johnson D, Rolfe S, Hallberg K, Iversen E . Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ Microbiol. 2001; 3(10):630-7. DOI: 10.1046/j.1462-2920.2001.00234.x. View

14.

Justice N, Norman A, Brown C, Singh A, Thomas B, Banfield J . Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics. 2014; 15:1107. PMC: 4378227. DOI: 10.1186/1471-2164-15-1107. View

15.

Almarcegui R, Navarro C, Paradela A, Albar J, von Bernath D, Jerez C . New copper resistance determinants in the extremophile acidithiobacillus ferrooxidans: a quantitative proteomic analysis. J Proteome Res. 2014; 13(2):946-60. DOI: 10.1021/pr4009833. View

16.

Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A . Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science. 2007; 316(5824):593-7. DOI: 10.1126/science.1132067. View

17.

Okibe N, Gericke M, Hallberg K, Johnson D . Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred-tank bioleaching operation. Appl Environ Microbiol. 2003; 69(4):1936-43. PMC: 154788. DOI: 10.1128/AEM.69.4.1936-1943.2003. View

18.

Lo I, Denef V, VerBerkmoes N, Shah M, Goltsman D, DiBartolo G . Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature. 2007; 446(7135):537-41. DOI: 10.1038/nature05624. View

19.

Amouric A, Brochier-Armanet C, Johnson D, Bonnefoy V, Hallberg K . Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways. Microbiology (Reading). 2010; 157(Pt 1):111-122. DOI: 10.1099/mic.0.044537-0. View

20.

Travisany D, Cortes M, Latorre M, Di Genova A, Budinich M, Bobadilla-Fazzini R . A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment. Res Microbiol. 2014; 165(9):743-52. DOI: 10.1016/j.resmic.2014.08.004. View