Abstract
The microbial solubilization of metals using chemolithoautotrophic microorganisms has successfully been used in industrial processes called biomining to extract metals such as copper, gold, uranium and others. The most studied leaching bacteria are from the genus Acidithiobacillus belonging to the Gram-negative γ-proteobacteria. Acidithiobacillus spp. obtain their energy from the oxidation of ferrous iron, elemental sulfur, or partially oxidized sulfur compounds. Other thermophilic archaeons capable of oxidizing sulfur and iron (II) have also been known for many years, and they are mainly from the genera Sulfolobus, Acidianus, Metallosphaera and Sulfurisphaera. Recently, some mesophilic iron (II)-oxidizing archaeons such as Ferroplasma acidiphilium and F. acidarmanus belonging to the Thermoplasmales have also been isolated and characterized. Recent studies of microorganisms consider them in their consortia, integrating fundamental biological knowledge with metagenomics, metaproteomics, and other data to obtain a global picture of how a microbial community functions. The understanding of microbial growth and activities in oxidizing metal ions will be useful for improving applied microbial biotechnologies such as biomining, bioshrouding, biomonitoring and bioremediation of metals in acidic environments.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Akcil A, Koldas S (2006) Acid mine drainage (AMD): causes, treatment and case studies. J Clean Prod 14:1139–1145
Alvarez S, Jerez CA (2004) Copper ions stimulate polyphosphate degradation and phosphate efflux in Acidithiobacillus ferrooxidans. Appl Environ Microbiol 70:5177–5182
Barnes LJ, Janssen FJ, Sherren J, Versteegh JH, Koch RO, Scheeren PJH (1991) A new process for the microbial removal of sulphate and heavy metal from contaminated waters extracted by a geohydrological control system. Chem Eng Res Des 69A:184–186
Bosio V, Viera M, Donati E (2007) Integrated bacterial process for the treatment of a spent nickel catalyst. J Hazard Mater 154:804–810
Bruscella P, Appia-Ayme C, Levicán G, Ratouchniak J, Jedlicki E, Holmes DS, Bonnefoy V (2007) Differential expression of two bc1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation. Microbiology 153:102–110
Butcher BG, Deane SM, Rawlings DE (2000) The chromosomal arsenic resistance genes of Thiobacillus ferrooxidans have an unusual arrangement and confer increased arsenic and antimony resistance to Escherichia coli. Appl Environ Microbiol 66:1826–1833
Cabrera G, Viera M, Gómez JM, Cantero D, Donati D (2007) Bacterial removal of chromium (VI) and (III) in a continuous system. Biodegradation 18:505–513
Cerruti C, Curutchet G, Donati E (1998) Bio-dissolution of spent nickel–cadmium batteries using Thiobacillus ferrooxidans. J Biotechnol 62:209–219
Chi A, Valenzuela L, Beard S, Mackey AJ, Shabanowitz J, Hunt DF, Jerez CA (2007) Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomic analysis. Mol Cell Proteomics 6:2239–2251
Choi MS, Cho KS, Kim DS, Kim DJ (2004) Microbial recovery of copper from printed circuit boards of waste computer by Acidithiobacillus ferrooxidans. J Environ Sci Health A Tox Subst Environ Eng 39:2973–2982
Collinet MN, Morin D (1990) Characterization of arsenopyrite oxidizing Thiobacillus. Tolerance to arsenite, arsenate, ferrous and ferric iron. Anton van Leeuwenh 57:237–244
Darkwah L, Rowson NA, Hewitt CJ (2005) Laboratory scale bioremediation of acid mine water drainage from a disused tin mine. Biotechnol Lett 17:1251–1257
Das A, Modak JM, Natarajan KA (1998) Surface chemical studies of Thiobacillus ferrooxidans with reference to copper tolerance. Anton van Leeuwenh 73:215–222
Dopson M, Baker-Austin C, Koppineedi PR, Bond PL (2003) Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. Microbiology 149:1959–1970
Dove PM, Rimstidt JD (1985) The solubility and stability of scorodite, FeAsO4• 2H2O. Am Mineralog 70:838–844
Duquesne K, Lebrun S, Casiot C, Bruneel O, Personné JC, Leblanc M, Elbaz-Poulichet F, Morin G, Bonnefoy V (2003) Immobilization of arsenite and ferric iron by Acidithiobacillus ferrooxidans and its relevance to acid mine drainage. Appl Environ Microbiol 69:6165–6173
Ehrlich HL (1964) Bacterial oxidation of arsenopyrite and enargite. Econ Geol 59:1306–1312
Guiliani N, Casanova A, Demergasso C, Jerez CA (2001) Bacterial biosensor for arsenic biomonitoring: applications in Northern Chile. Biol Res 34:R–126
Hallberg KB, Johnson DB (2001) Biodiversity of acidophilic prokaryotes. Adv Appl Microbiol 49:37–84
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Harms H, Wells MC, van der Meer JR (2006) Whole-cell living biosensors — are they ready for environmental application? Appl Microbiol Biotechnol 70:273–280
Jerez CA (2008) The use of genomics, proteomics and other OMIC technologies for the global understanding of biomining microorganisms. Hydrometallurgy 94:162–169
Johnson DB, Hallberg KB (2005) Acid mine drainage remediation options: a review. Sci Total Environ 338:3–14
Johnson DB, Yajie L, Okibe N (2008) “Bioshrouding”: a novel approach for securing reactive mineral tailings. Biotechnol Lett 30:445–449
Kaur P, Rosen BP (1992) Plasmid-encoded resistance to arsenic and antimony. Plasmid 27:29–40
Kelly DP, Shergill JK, Lu W-P, Wood AP (1997) Oxidative metabolism of inorganic sulfur compounds by bacteria. Anton van Leeuwenh 71:95–107
Lloyd JR, Anderson RT, Macaskie LE (2005) Bioremediation of metals and radionuclids. In: Atlas RM, Philp J (eds) Bioremediation. Applied microbial solutions for real-world environmental cleanup. ASM Press, Washington DC, pp 293–317
Lo I, Denef VJ, VerBerkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537–541
Lundgren DG (1980) Ore leaching by bacteria. Annu Rev Microbiol 34:263–283
Mishra D, Kim DJ, Ralph DE, Ahn JG, Rhee YH (2008) Bioleaching of metals from spent lithium ion secondary batteries using Acidithiobacillus ferrooxidans. Waste Manage 28:333–338
Müller FH, Bandeiras TM, Urich T, Teixeira M, Gomes CM, Kletzin A (2004) Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol 53:1147–1160
Norman NC (1998) Chemistry of arsenic, antimony and bismuth. J Natl Cancer Inst 40:453–463.
Olson GJ, Brierley JA, Brierley CL (2003) Bioleaching review, Part B: Progress in bioleaching: applications of microbial processes by the minerals industries. Appl Microbiol Biotechnol 63:249–257
Outten FW, Huffman DL, Hale JA, O’Halloran TV (2001) The independent cue and cus systems confer copper tolerance during aerobic and anaerobic growth in Escherichia coli. J Biol Chem 276:30670–30677
Puig S, Rees EM, Thiele DJ (2002) The ABCDs of periplasmic copper trafficking. Structure 10:1292–1295
Quatrini R, Lefimil C, Veloso FA, Pedroso I, Holmes DS, Jedlicki E (2007) Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res 35:2153–2166
Quatrini R, Appia-Ayme C, Dennis Y, Ratouchniak J, Veloso F, Valdes J, Lefimil C, Silver S, Roberto F, Orellana O, Denizot F, Jedlicki E, Holmes D, Bonnefoy V (2006) Insights into the iron and sulfur energetic metabolism of Acidithiobacillus ferrooxidans by microarray transcriptome profiling. Hydrometallurgy 83:263–272
Ram RJ, VerBerkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake II RC, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915–1920
Ramirez P, Guiliani N, Valenzuela L, Beard S, Jerez CA (2004) Differential protein expression during growth of Acidithiobacillus ferrooxidans on ferrous iron, sulfur compounds, or metal sulfides. Appl Environ Microbiol 70:4491–4498
Rawlings DE (2002) Heavy metal mining using microbes. Annu Rev Microbiol 56:65–91
Rawlings DE (2005) Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microb Cell Fact 4:13
Rawlings DE, Johnson DB (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153:315–324
Remonsellez F, Orell A, Jerez CA (2006) Copper tolerance of the thermoacidophilic archaeon Sulfolobus metallicus: possible role of polyphosphate metabolism. Microbiology 152:59–66
Rohwerder T, Sand W (2003) The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology 149:1699–1709
Rohwerder T, Sand W (2007) Oxidation of inorganic sulfur compounds in acidophilic prokaryotes. Eng Life Sci 7:301–309
Rohwerder T, Gehrke T, Kinzler K, Sand W (2003) Bioleaching review part A: progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation. Appl Microbiol Biotechnol 63:239–248
Ruitenberg R, Buisman CJN (2000) Process for immobilizing arsenic waste. WO/2000/078402
Ruiz LM, Valenzuela S, Castro M, Gonzalez A, Frezza M, Soulère L, Rohwerder T, Queneau Y, Doutheau A, Sand CW, Jerez CA, Guiliani N (2008) AHL communication is a widespread phenomenon in biomining bacteria species and seems to be involved in mineral-adhesion efficiency. Hydrometallurgy 94:133–137.
Schippers A (2007) Microorganisms involved in bioleaching and nucleic acid-based molecular methods for their identification and quantification. In: Donati ER, Sand W (eds) Microbial processing of metal sulfides. Springer, Berlin, pp 3–33
Schippers A, Sand W (1999) Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur. Appl Environ Microbiol 65:319–321
Silver M, Lundgren DG (1968) Sulfur-oxidizing enzyme of Ferrobacillus ferrooxidans (Thiobacillus ferrooxidans). Can J Biochem 46:457–461
Stocker J, Balluch D, Gsell M, Harms H, Feliciano J, Daunert S, Malik KA, van der Meer JR (2003) Development of a set of simple bacterial sensors for quantitative and rapid measurements of arsenite and arsenate in potable water. Environ Sci Technol 37:4743–4750
Streit WR, Schmitz RA (2005) Metagenomics — the key to the uncultured microbes. Curr Opin Microbiol 7:492–498
Sugio T, Katagiri T, Moriyama M, Zhèn YL, Inagaki K, Tano T (1987) Existence of a new type of sulfite oxidase which utilizes ferric ions as an electron acceptor in Thiobacillus ferrooxidans. Appl Environ Microbiol 54:153–157
Suzuki I (1999) Oxidation of inorganic sulfur compounds: chemical and enzymatic reactions. Can J Microbiol 45:97–105
Suzuki I (2001) Microbial leaching of metals from sulfide minerals. Biotechnol Adv 19:119–132
Takeuchi F, Sugio T (2006) Volatilization and recovery of mercury from mercury-polluted soils and wastewaters using mercury-resistant Acidithiobacillus ferrooxidans strains SUG 2-2 and MON-1. Environ Sci 13:305–316
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43
Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA (2006) Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol Adv 24:197–211
Valenzuela L, Chi A, Beard S, Shabanowitz J, Hunt DF, Jerez CA (2007) Differential-expression proteomics for the study of sulfur metabolism in the chemolithoautotrophic Acidithiobacillus ferrooxidans. In: Friedrich C, Dahl C (eds) Microbial sulfur metabolism. Springer, Berlin, pp 77–86
Vera M, Pagliai F, Guiliani N, Jerez CA (2008) The chemolithoautotroph Acidithiobacillus ferrooxidans can survive under phosphate-limiting conditions by the expression of a C-P lyase operon allowing it to grow in phosphonates. Appl Environ Microbiol 74:1829–1835
Watling HR (2006) The bioleaching of sulphide minerals with emphasis on copper sulphides — a review. Hydrometallurgy 84:81–108
White CA, Sharman AK, Gadd GM (1998) An integrated microbial process for the bioremediation of soil contaminated with toxic metals. Nat Biotechnol 16:572–575
Wu J, Rosen BP (1991) The ArsR protein is a trans-acting regulatory protein. Mol Microbiol 5:1331–1336
Xu C, Rosen BP (1997) Dimerization is essential for DNA binding and repression by the ArsR metalloregulatory protein of Escherichia coli. J Biol Chem 272:15734–15738
Yagi K (2007) Applications of whole-cell bacterial sensors in biotechnology and environmental science. Appl Microbiol Biotechnol 73:1251–1258
Yarzabal A, Appia-Ayme C, Ratouchniak J, Bonnefoy V (2004) Regulation of the expression of the Acidithiobacillus ferrooxidans rus operon encoding two cytochromes c, a cytochrome oxidase and rusticyanin. Microbiology 150:2113–2123
Acknowledgements
Part of our work was supported by FONDECYT1030767 and 1070986, FONDEF D99I1026 and ICM P-05-001-F projects.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Jerez, C.A. (2009). Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation. In: Singh, A., Kuhad, R., Ward, O. (eds) Advances in Applied Bioremediation. Soil Biology, vol 17. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89621-0_13
Download citation
DOI: https://doi.org/10.1007/978-3-540-89621-0_13
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-89620-3
Online ISBN: 978-3-540-89621-0
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)