Skip to main content

The Use Of Bioinformatics And Genome Biology To Advance Our Understanding Of Bioleaching Microorganisms

  • Chapter

Keywords

  • Extracellular Polymeric Substance
  • Iron Uptake
  • Acidithiobacillus Ferrooxidans
  • Genome Biology
  • Thiobacillus Ferrooxidans

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, access via your institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • DOI: 10.1007/1-4020-5589-7_11
  • Chapter length: 19 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   149.00
Price excludes VAT (USA)
  • ISBN: 978-1-4020-5589-8
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   199.99
Price excludes VAT (USA)
Hardcover Book
USD   249.99
Price excludes VAT (USA)

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • 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. 2006. Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans. Hydrometallurgy 83: 273-280.

    CrossRef  CAS  Google Scholar 

  • Bacelar-Nicolau P, Johnson B. 1999. Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures. Appl Environ Microbiol 65: 585-590.

    PubMed  CAS  Google Scholar 

  • Barreto M, Quatrini R, Bueno S, Arriagada C, Valdes J, Silver S, Jedlicki E, Holmes D. 2003. Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence. Hydrometallurgy 71: 97-105.

    CrossRef  CAS  Google Scholar 

  • Barreto M, Jedlicki E, Holmes DS. 2005a. Identification of a Gene Cluster for the Formation of Extracellular Polysaccharide Precursors in the Chemolithoautotroph Acidithiobacillus ferrooxidans. Appl Environ Microbiol 71: 2902-2909.

    CrossRef  CAS  Google Scholar 

  • Barreto M, Gehrke T, Harneit K, Sand W, Jedlicki E, Holmes DS. 2005b. Unexpected Insights into Biofilm Formation by Acidithiobacillus ferrooxidans Revealed by Genome Analysis and Experimental Approaches. In: Harrison STL, Rawlings DE, Petersen J, eds. Proceedings of the 16th International Biohydrometallurgy Symposium, September 25–29, Cape Town, South Africa. Produced by Compress www.compress. co.za, 817-825.

    Google Scholar 

  • Brierley C. 2001. Bacterial succession in bioheap leaching. Hydrometallurgy 59: 249-255.

    CrossRef  CAS  Google Scholar 

  • Bro C, Knudsen S, Regenberg B, Olsson L, Nielsen J. 2005. Improvement of Galactose Uptake in Saccharomyces cerevisiae through Overexpression of Phosphoglucomutase: Example of Transcript Analysis as a Tool in Inverse Metabolic Engineering. Appl Environ Microbiol. 71: 6465-6472.

    PubMed  CrossRef  CAS  Google Scholar 

  • Broadbent JR, McMahon D, Welker DL, Ober CJ, Moineau S. 2003. Biochemistry, genetics, and applications of exopolysaccharide production in Streptococcus thermophilus: a review. J Dairy Sci 86: 407-423.

    PubMed  CAS  CrossRef  Google Scholar 

  • Coram-Uliana JN, van Hille RP, Kohr WJ, Harrison STL. 2005. Development Of A Method To Assay The Microbial Population In Heap Bioleaching Operations. In: Harrison STL, Rawlings DE, Petersen J, eds. Proceedings of the 16th International Biohydrometallurgy Symposium, September 25–29, Cape Town, South Africa. Produced by Compress www.compress. co.za, 647-656.

    Google Scholar 

  • Demergasso CS, Galleguillos PA, Escudero LV, Zepeda VJ, Castillo D, Casamayor EO. 2005a. Molecular characterization of microbial populations in a low-grade copper ore bioleaching test heap. Hydrometallurgy, in press.

    Google Scholar 

  • Demergasso CS, Echeverria A, Escudero L, Galleguillos P, Zepeda V, Castillo D. 2005b. Comparison of fluorescent in situ hybridization (FISH) and catalyzed reporter deposition (Card-Fish) for visualization and enumeration of Archaea and Bacteria Ratio in industrial heap bioleaching operations. In: Harrison STL, Rawlings DE, Petersen J, eds. Proceedings of the 16th International Biohydrometallurgy Symposium, September 25–29, Cape Town, South Africa. Produced by Compress www.compress. co.za, 843-851.

    Google Scholar 

  • Dopson M, Baker-Austin C, Bond PL. 2005. Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation. Microbiology 151: 4127-4137.

    PubMed  CrossRef  CAS  Google Scholar 

  • Farah C, Vera M, Morin D, Haras D, Jerez CA, Guiliani N. 2005. Evidence for a functional quorum-sensing type AI-1 system in the extremophilic bacterium Acidithiobacillus ferrooxidans. Appl Environ Microbiol. 71: 7033-7040.

    PubMed  CrossRef  CAS  Google Scholar 

  • Fry IJ, Garcia E. 1989. Cloning and characterization of Thiobacillus ferrooxidansgenes involved in sulfur assimilation. In: Salley J, McCready RGL, Wichlacz PL, eds. Biohydrometallurgy, CANMET, Ottawa, 171-185.

    Google Scholar 

  • Gehrke T, Telegdi J, Thierry D, Sand W. 1998. Importance of extracellular polymeric substances from Thiobacillus ferrooxidans for bioleaching. Appl Environ Microbiol 64: 2743-2747.

    PubMed  CAS  Google Scholar 

  • Goebel BM, Stackebrandt E. 1994. Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 60: 1614-1621.

    PubMed  CAS  Google Scholar 

  • Gonzalez-Toril E, Llobet-Brossa E, Casamayor EO, Amann R, Amils R. 2003. Microbial ecology of an extreme acidic environment, the Tinto River. Appl Environ Microbiol 69: 4853-4865.

    PubMed  CrossRef  CAS  Google Scholar 

  • Grossiord BP, Luesink EJ, Vaughan EE, Arnaud A, de Vos VM. 2003. Characterization, expression, and mutation of the Lactococcus lactis galPMKTE genes, involved in galactose utilization via the Leloir pathway. J Bacteriol 185: 870-878.

    PubMed  CrossRef  CAS  Google Scholar 

  • Handelsman J. 2004. Metagenomics: Application of Genomics to Uncultured Microorganisms Microbiol Molec Biol Revs 68: 669-685.

    CrossRef  CAS  Google Scholar 

  • Holmes DS. 1991. The Use of DNA Probes for the Identification and Enumeration of Biomining Microorganisms: An Overview for the Non-Specialist. In: Badilla-Ohlbaum R, Vargas T, Herrera L, eds. Bioleaching: From Molecular Biology to Industrial Applications. Editorial Universitaria, Santiago, Chile, 1-12.

    Google Scholar 

  • Holmes DS, Bonnefoy V. Genetic and Bioinformatic Insights into Iron and Sulfur Oxidation Mechanisms of Bioleaching Organisms. In: Rawlings DE, Johnson B, eds. Biomining: Practice, Theory and Microbiology. Springer (submitted, 2006).

    Google Scholar 

  • Johnson DB 1998. Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27: 307-317.

    CrossRef  CAS  Google Scholar 

  • Karavaiko GI, Bogdanova TI, Tourova TP, Kondrat’eva TP, Tsaplina IA, Egorova MA, Krasil’nikova EN, Zakharchuk LM. 2005. Reclassification of ‘Sulfobacillus thermosulfidooxidans subsp. thermotolerans’ strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus.Int J Syst Evol Microbiol 55: 941-947.

    PubMed  CrossRef  CAS  Google Scholar 

  • Kusano T, Sugawara K, Inoue C, Takeshima T, Numata M, Shiratori T. 1992. Electrotransformation of Thiobacillus ferrooxidans with plasmids containing a mer determinant. J Bacteriol 174: 6617-6623.

    PubMed  CAS  Google Scholar 

  • Leyh TS, Taylor JC, Markham GD. 1988. The sulfate activation locus of Escherichia coliK12. cloning, genetic, and enzymatic characterization. J Biol Chem. 263: 2409-2416.

    PubMed  CAS  Google Scholar 

  • Liu Z, Guiliani N, Appia-Ayme C, Borne F, Ratouchniak J, Bonnefoy V. 2000. Construction and characterization of a recA mutant of Thiobacillus ferrooxidans by marker exchange mutagenesis. J Bacteriol. 182: 2269-2276.

    PubMed  CrossRef  CAS  Google Scholar 

  • Lochowska A, Iwanicka-Nowicka R, Plochocka D, Hryniewicz MM. 2001. Functional dissection of the LysR-type CysB transcriptional regulator. Regions important for DNA binding, inducer response, oligomerization, and positive control. J Biol Chem 276: 2098-2107.

    PubMed  CrossRef  CAS  Google Scholar 

  • Lopez-Archilla AI, Mariın I, Amils R. 2001. Microbial community composition and ecology of an acidic aquatic environment: the Tinto River, Spain. Microb Ecol 41: 20-35.

    PubMed  CAS  Google Scholar 

  • Marchand E, Silverstein J. 2002. Influence of heterotrophic microbial growth on biological oxidation of pyrite. Environ Sci Technol 36: 5483-5490.

    PubMed  CrossRef  CAS  Google Scholar 

  • 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.

    PubMed  CrossRef  CAS  Google Scholar 

  • Payne SM. 1994. Detection, isolation, and characterization of siderophores. Methods Enzymol 235: 329-344.

    PubMed  CAS  CrossRef  Google Scholar 

  • Pronk JT, Liem K, Bos P, Kuenen JG. 1991. Energy transduction by anaerobic ferric iron respiration in Thiobacillus ferrooxidans. Appl Environ Microbiol 57: 2063-2068.

    PubMed  CAS  Google Scholar 

  • 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. 2006. Insights into the iron and sulfur energetic metabolism of Acidthiobacillus ferrooxidans by microarray transcriptome Profiling. Hydrometallurgy 83: 263-272.

    CrossRef  CAS  Google Scholar 

  • Quatrini R, Lefimil C, Holmes DS, Jedlicki E. 2005a. The Ferric Iron Uptake Regulator (Fur) from the Extreme Acidophile, Acidithiobacillus ferrooxidans.Microbiology 151: 2005-2015.

    CrossRef  CAS  Google Scholar 

  • Quatrini R, Jedlicki E, Holmes DS. 2005b. Genomic Insights into the Iron Uptake Mechanisms of the Biomining Microorganism Acidithiobacillus ferrooxidans. J Indust Microbiol Biotechnol 32: 606-614.

    CrossRef  CAS  Google Scholar 

  • Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC, Shah M, Hettich RL, Banfield JF. 2005. Community proteomics of a natural microbial biofilm. Science 308: 1915-1920.

    PubMed  CrossRef  ADS  CAS  Google Scholar 

  • Rawlings DE. 2002. Heavy metal mining using microbes. Annu Rev Microbiol 56: 65-91.

    PubMed  CrossRef  CAS  Google Scholar 

  • Rawlings DE. 2005. Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microbial Cell Factories. 4:13.

    PubMed  CrossRef  CAS  Google Scholar 

  • Rawlings DE, Tributsch H, Hansford GS. 1999. Reasons why “Leptospirillum”-like species rather than Thiobacillus ferrooxidansare the dominant iron-oxidizing bacteria in many commercial processes for the biooxidation of pyrite and related ores. Microbiology 145: 5-13.

    PubMed  CAS  CrossRef  Google Scholar 

  • Rivas M, Seeger M, Holmes DS, Jedlicki E. 2005. A Lux-like quorum sensing system in the extreme acidophile Acidithiobacillus ferrooxidans. Biological Res 38: 283-297.

    CAS  Google Scholar 

  • Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing-delta-proteobacteria. Genome Biol 5: R90.

    PubMed  CrossRef  Google Scholar 

  • Sand W, Gehrke T, Jozsa P-G, Schippers A. 2001. (Bio)chemistry of bacterial leaching-direct vs. indirect bioleaching. Hydrometallurgy. 59: 159-175.

    CrossRef  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Schloss PD, Handelsman J. 2003. Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14: 303-331.

    PubMed  CrossRef  CAS  Google Scholar 

  • Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M. 2000. Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. Proc Natl Acad Sci 97: 3509-3514.

    PubMed  CrossRef  ADS  CAS  Google Scholar 

  • Stoodley P, Sauer K, Davies DG, Costerton JW. 2002. Biofilms as complex differentiated communities. Annu Rev Microbiol 56: 187-209.

    PubMed  CrossRef  CAS  Google Scholar 

  • Streit WR, Schmitz RA, Perret X, Staehelin C, Deakin WJ, Raasch C, Liesegang H, Broughton WJ. 2004. An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234. J Bacteriol 186: 535-542.

    PubMed  CrossRef  CAS  Google Scholar 

  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Rachna JR, 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.

    PubMed  CrossRef  ADS  CAS  Google Scholar 

  • Tyson GW, Lo I, Baker BJ, Allen EE, HugenholtzP, Banfield JF. 2005. Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Appl Environ Microbiol 71: 6319-6324.

    PubMed  CrossRef  CAS  Google Scholar 

  • Valdes J, Veloso F, Jedlicki E, Holmes D. 2003. Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis. BMC Genomics 4: 51.

    PubMed  CrossRef  Google Scholar 

  • 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.

    PubMed  CrossRef  CAS  Google Scholar 

  • Vian M, Creo C, Dalmastri C, Gionni A, Palazzolo P, Levi G. 1986. Thiobacillus ferrooxidansselection in continuous culture. In: Lawrence RW, Branion RMR, Ebner HG, eds. Fundamental and Applied Biohydrometallurgy. Elsevier, Amsterdam, 395-406.

    Google Scholar 

  • Ward N, Fraser CM. 2005. How genomics has affected the concept of microbiology. Curr Opin Microbiol 8: 564-571.

    PubMed  CrossRef  CAS  Google Scholar 

  • Wylie JL, Bernegger-Egli C, O’Neil JD, Worobec EA. 1993. Biophysical characterization of OprB, a glucose-inducible porin of Pseudomonas aeruginosa. J Bioenerg Biomembr 25: 547-556.

    PubMed  CrossRef  CAS  Google Scholar 

  • Yates JR., Holmes DS. 1986a. Molecular Probes for the Identification and Quantification of Micro-organisms found in Mines and Mine Tailing. Biotechnol Bioeng Symp 16: 310-319.

    Google Scholar 

  • Yates JR, Holmes DS. 1986b. Construction and Use of Molecular Probes to Identify and Quantitate Bioleaching Microorganisms. In: Branion RMR, Ebner HG, eds. Fundamental and Applied Biohydrometallurgy, Elsevier Science Publ, Amsterdam, 409-418.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and Permissions

Copyright information

© 2007 Springer

About this chapter

Cite this chapter

Quatrini, R., Valdès, J., Jedlicki, E., Holmes, D.S. (2007). The Use Of Bioinformatics And Genome Biology To Advance Our Understanding Of Bioleaching Microorganisms. In: Donati, E.R., Sand, W. (eds) Microbial Processing of Metal Sulfides. Springer, Dordrecht. https://doi.org/10.1007/1-4020-5589-7_11

Download citation