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Chapter 96 : Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria

Author: Jon L. Hobman
Content Type: Reference
Publication Year: 2007

Category: Environmental Microbiology

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Abstract:

Many toxic metals appear to be able to enter cells by import systems for essential elements or molecules, and although chromosomally encoded homeostasis systems for essential metals are widespread, in bacteria many toxic metal resistance genes are found on mobile genetic elements such as plasmids and transposons. Highthroughput methods in DNA sequencing, metagenomics, and the postgenomic technologies are going to revolutionize our understanding of toxic metal-bacterial cell interactions and the diversity of toxic metal(loid) resistances. With this in mind, this chapter talks about the options and potential workflows open to researchers wishing to use molecular techniques for the study of these resistance genes. Most of the techniques discussed in the chapter are equally applicable to the study of other nonmetal resistance phenotypes of environmental bacteria, because the techniques are generic. The chapter, however, focuses on and discusses the merits of molecular biology techniques that can be used to investigate bacterial resistance mechanisms. The outline of the experimental procedure and primary purpose of this technique is to culture toxic-metal-resistant bacteria, so that the genetic and biochemical basis for their resistance mechanisms can be further investigated. Although we are now entering a new phase in molecular research into toxic metal resistances, the techniques described in this chapter still have a valuable place in describing new metal-resistant bacteria.

Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
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Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria
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Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
/content/10.1128/9781555815882.ch96.ch96fig02
FIGURE 2
Diagrammatic representation of some metal resistance operons from bacteria: ( ), ( ), ( ), ( ), ( ), ( ), and ( ).
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10.1128/9781555815882/f1169-01.gif
Image of FIGURE 2
FIGURE 2

Diagrammatic representation of some metal resistance operons from bacteria: ( ), ( ), ( ), ( ), ( ), ( ), and ( ).

Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
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FIGURE 3
(a) Isolation and molecular techniques for the analysis of culturable toxic-metal-resistant bacteria. (b) Isolation and molecular techniques for the analysis of toxic metal resistance genes isolated directly from environmental samples. Modified from references and with permission.
10.1128/9781555815882/f1170-01_thmb.gif
10.1128/9781555815882/f1170-01.gif
Image of FIGURE 3
FIGURE 3

(a) Isolation and molecular techniques for the analysis of culturable toxic-metal-resistant bacteria. (b) Isolation and molecular techniques for the analysis of toxic metal resistance genes isolated directly from environmental samples. Modified from references and with permission.

Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
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References

/content/book/10.1128/9781555815882.ch96
1. Allen, E. E.,, and J. F. Banfield. 2005. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3: 489– 498.
2. Altschul, S. F.,, W. Gish,, W. Miller,, E. W. Myers, and, D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403– 410.
3. Altschul, S. F.,, T. L. Madden,, A. A. Schaffer,, J. Zhang,, Z. Zhang,, W. Miller, and, D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389– 3402.
4. Amann, R. I.,, W. Ludwig, and, K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143– 169.
5. Anderson, M. L. M. 1999. Nucleic Acid Hybridization. Bios Scientific Publishers, Oxford, England.
6. Atlas, R. M.,, and A. K. Bej. 1994. Polymerase chain reaction, p. 418–435. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
7. Bagdasarian, M.,, and M. M. Bagdasarian. 1994. Gene cloning and expression, p. 406–407. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
8. Ballatori, N. 2002. Transport of toxic metals by molecular mimicry. Environ. Health Perspect. 110: 689– 694.
9. Barkay, T.,, S. M. Miller, and, A. O. Summers. 2003. Bacterial mercury resistance from atoms to ecosystems. FEMS Microbiol. Rev. 27: 355– 384.
10. Barkley, W. E.,, and J. H. Richardson. 1994. Laboratory safety, p. 715–734. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
11. Bennett, P. M.,, J. Grinsted, and, T. J. Foster. 1988. Detection and use of transposons. Methods Microbiol. 21: 205– 232.
12. Berg, D. E.,, and M. M. Howe (ed.). 1989. Mobile DNA. American Society for Microbiology, Washington, D.C.
13. Beveridge, T. J.,, and S. F. Koval. 1981. Binding of metals to cell envelopes of Escherichia coli K-12. Appl. Environ. Microbiol. 42: 325– 335.
14. Beveridge, T. J.,, M. N. Hughes,, H. Lee,, K. T. Leung,, R. K. Poole,, I. Savvaides,, S. Silver, and, J. T. Trevors. 1997. Metal-microbe interactions: contemporary approaches. Adv. Microb. Physiol. 38: 177– 243.
15. Birnboim, H.,, and J. Doly. 1979. A rapid extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7: 1513– 1525.
16. Blencowe, D.,, and A. P. Morby. 2003. Zn(II) metabolism in prokaryotes. FEMS Microbiol. Rev. 27: 291– 312.
17. Bridson, E. 1994. The Development, Manufacture and Control of Microbiological Culture Media, p. 40–53. Unipath Limited, Basingstoke, England.
18. Brown, N. L.,, A. P. Morby, and, N. J. Robinson (guest ed.). 2003. Thematic issue: interactions of bacteria with metals. FEMS Microbiol. Rev. 27: 129– 447.
19. Brown, N. L.,, J. V. Stoyanov,, S. P. Kidd, and, J. L. Hobman. 2003. The MerR family of transcriptional regulators. FEMS Microbiol. Rev. 27: 145– 163.
20. Bruce, K. D.,, W. D. Hiorns,, J. L. Hobman,, A. M. Osborn,, P. Strike, and, D. A. Ritchie. 1992. Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl. Environ. Microbiol. 58: 3413– 3416.
21. Bruce, K. D.,, A. M. Osborn,, A. J. Pearson,, P. Strike, and, D. A. Ritchie. 1995. Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria. Mol. Ecol. 4: 605– 612.
22. Bruins, M. R.,, S. Kapil, and, F. W. Oehme. 2000. Microbial resistance to metals in the environment. Ecotoxicol. Environ. Safety 45: 198– 207.
23. Bürgmann, H.,, M. Pesaro,, F. Widmer, and, J. Zeyer. 2001. A strategy for optimizing quality and quantity of DNA extracted from soil. J. Microbiol. Methods 45: 7– 20.
24. Busenlehner, L. S.,, M. A. Pennella, and, D. P. Giedroic. 2003. The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance. FEMS Microbiol. Rev. 27: 131– 143.
25. Chance, M. R.,, A. Fiser,, A. Sali,, U. Pieper,, N. Eswar,, G. Xu,, J. E. Fajardo,, T. Radhakannan, and, N. Marin-kovic. 2004. High-throughput computational and experimental techniques in structural genomics. Genome Res. 14: 2145– 2154.
26. Chang, J. S.,, J. Hong,, O. A. Ogunseitan, and, B. H. Olson. 1993. Interaction of mercuric ions with the bacterialgrowth medium and its effects on enzymatic reduction of mercury. Biotechnol. Prog. 9: 526– 532.
27. Chaudhuri, R. R.,, A. M. Khan, and, M. J. Pallen. 2004. coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Res. 32: D296– D299.
28. Collins, C. H.,, and P. M. Lyne. 1984. Microbiological Methods, 5th ed. Butterworths, London, United Kingdom.
29. Crosa, J. H.,, M. E. Tomalsky,, L. A. Actis, and, S. Falkow. 1994. Plasmids, p. 366–386. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
30. Cutting, S. M.,, and P. Youngman. 1994. Gene transfer in gram-positive bacteria, p. 348–364. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
31. Daniel, R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3: 470- 478.
32. Davis, I. J.,, H. Richards, and, P. Mullaney. 2005. Isolation of silver- and antibiotic-resistant Enterobacter cloacae from teeth. Oral Microbiol. Immunol. 20: 191– 194.
33. De Bruijn, F. J.,, and S. Rossbach. 1994. Transposon mutagenesis p. 387–405. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
34. Dopson, M.,, C. Baker-Austin,, P. R. Koppineedi, and, P. L. Bond. 2003. Growth in sulfidic mineral environments: metal resistance mechanisms in acidophilic micro-organisms. Microbiology 149: 1959– 1970.
35. Duxbury, T. 1981. Toxicity of heavy metals to soil bacteria. FEMS Microbiol. Lett. 11: 217– 220.
36. Eckhardt, T. 1978. A rapid method for the identification of plasmid deoxyribonucleic acid in bacteria. Plasmid 1: 584– 588.
37. Egler, S.,, C. Große,, G. Grass, and, D. H. Nies. 2005. Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli. J. Bacteriol. 187: 2297– 2307.
38. Ellis, R. J.,, P. Morgan,, A. J. Weightman, and, J. C. Fry. 2003. Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl. Environ. Microbiol. 69: 3223– 3230.
39. Entcheva, P.,, W. Liebl,, A. Johann,, T. Hartsch, and, W. R. Streit. 2001. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl. Environ. Micro-biol. 67: 89– 99.
40. Essa, A. M. M.,, D. J. Julian,, S. P. Kidd,, N. L. Brown, and, J. L. Hobman. 2003. Mercury resistance determinants related to Tn 21, Tn 1696, and Tn 5053 in enterobacteria from the preantibiotic era. Antimicrob. Agents Chemother. 47: 1115– 1119.
41. Eyers, L.,, I. George,, L. Schuler,, B. Stenuit,, S. N. Agathos, and, S. El Fantroussi. 2004. Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Appl. Microbiol. Biotechnol. 66: 123– 130.
42. Farrell, R. E.,, J. J. Germida, and, P. M. Huang. 1993. Effects of chemical speciation in growth media on the toxicity of Hg(II). Appl. Environ. Microbiol. 59: 1507– 1514.
43. Ferianc, P.,, A. Farewell, and, T. Nystrom. 1998. The cadmium-stress stimulon of Escherichia coli K-12. Microbiology 144: 1045– 1050.
44. Field, D.,, E. J. Fell, and, G. A. Wilson. 2005. Databases and software for the comparison of prokaryotic genomes. Microbiology 151: 2125– 2132.
45. Finney, L. A.,, and T. V. O’Halloran. 2003. Transition metal speciation in the cell: insights from the chemistry of metal ion receptors. Science 300: 931– 936.
46. Gabor, E. M.,, E. J. de Vries, and, D. B. Jansenn. 2003. Efficient recovery of environmental DNA for expression cloning by indirect methods. FEMS Microbiol. Ecol. 44: 153– 163.
47. Gerhardt, P.,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.). 1994. Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
48. Glendinning, K. G. 2000. Studies on mercuric reductase and thermophilic mercury resistance. Ph.D. thesis. The University of Birmingham, Birmingham, United Kingdom.
49. Gonzalez, J. M.,, M. C. Portillo, and, C. Saiz-Jimenez. 2005. Multiple displacement amplification as a prepolymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ. Microbiol. 7: 1024– 1028.
50. Griffiths, R. I.,, A. S. Whiteley,, A. G. O’Donnell, and, M. J. Bailey. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66: 5488– 5491.
51. Grinsted, J.,, and P. Bennett (ed.). 1988. Plasmid technology. Methods Microbiol. 21: 129– 142.
52. Gupta, A.,, L. T. Phung,, D. E. Taylor, and, S. Silver. 2001. Diversity of silver resistance genes in IncH incompatibility group plasmids. Microbiology 147: 3393– 3402.
53. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured organisms. Microbiol. Mol. Biol. Rev. 68: 669– 685.
54. Handelsman, J.,, M. R. Rondon,, S. F. Brady,, J. Clardy, and, R. M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: R245- R249.
55. Hendrickson, W. G.,, and T. K. Misra. 1994. Nucleic acid analysis, p. 436–460. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (ed.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington, D.C.
56. Hobman, J. L.,, and N. L. Brown. 1997. Bacterial mercury-resistance genes, p. 527–568. In A. Sigel and, H. Sigel (ed.), Metal Ions in Biological Systems, vol. 34. Marcel Dekker, New York, N.Y.
57. Hobman, J. L.,, J. R. Wilson, and, N. L. Brown. 2000. Microbial mercury reduction, p. 177–197. In D. R. Lovley, (ed.), Environmental Microbe-Metal Interactions. ASM Press, Washington, D.C.
58. Hu, Y.,, G. Wang,, G. Y. J. Chen,, X. Fu, and, S. Q. Yao. 2003. Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 24: 1458– 1470.
59. Hughes, M. N.,, and R. K. Poole. 1989. Metals and Micro-Organisms. Chapman and Hall, London, United Kingdom.
60. Juhnke, S.,, N. Peitzsch,, N. Hübener,, C. Große, and, D. H. Nies. 2002. New genes involved in chromate resistance in Ralstonia metallidurans CH34. Arch. Microbiol. 179: 15– 25.
61. Katayama, A.,, A. Tsujii,, A. Wada,, T. Nishino, and, A. Ishihama. 2002. Systematic search for zinc-binding proteins in Escherichia coli. Eur. J. Biochem. 269: 2403– 2413.
62. Kell, D. B. 2004. Metabolomics and systems biology—making sense of the soup. Curr. Opin. Microbiol. 7: 296– 307.
63. Kershaw, C. J.,, N. L. Brown,, C. Constantinidou,, M. D. Patel, and, J. L. Hobman. 2005. The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations. Microbiology 151: 1187– 1198.
64. Kröning, B.,, and T. Paul. 1897. The chemical foundations of the study of disinfection and of the action of poisons. Translated into English in T. D. Brock (ed.), Milestones in Microbiology ( 1961). Prentice-Hall, Inc., Englewood Cliffs, N.J.
65. LaRossa, R. A.,, and T. K. Van Dyk. 2000. Applications of stress responses to environmental monitoring and molecular toxicology, p. 454–468. In G. Storz and, R. Hengge-Aronis (ed.), Bacterial Stress Responses. ASM Press, Washington, D.C.
66. Leadbetter, J. R. 2003. Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr. Opin. Microbiol. 6: 274– 281.
67. Lenihan, J. 1988. The Crumbs of Creation—Trace Elements in History, Medicine, Industry, Crime and Folklore, p. 44–75. Adam Hilger, Bristol, United Kingdom.
68. Lide, D. R. ( ed. in chief). 2004. CRC Handbook of Chemistry and Physics, 85th ed. CRC Press, Inc., Boca Raton, Fla.
69. Lippard, S. J.,, and J. M. Berg. 1994. Principles of Bio-inorganic Chemistry, p. 1–19. University Science Books, Mill Valley, Calif.
70. Lippard, S. J.,, and J. M. Berg. 1994. Principles of Bioinorganic Chemistry, p. 139–173. University Science Books, Mill Valley, Calif.
71. Lloyd, J. R.,, and D. R. Lovley. 2001. Microbial detoxification of metals and radionuclides. Curr. Opin. Biotechnol. 12: 248– 253.
72. Lloyd-Jones, G.,, and D. W. F. Hunter. 2001. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol. Biochem. 33: 2053– 2059.
73. Lovley, D. R. (ed.). 2000. Environmental Microbe-Metal Interactions. ASM Press, Washington, D.C.
74. Martin-Laurent, F.,, L. Phillipot,, S. Hallet,, R. Chaussod,, J. C. Germon,, G. Soulas, and, G. Catroux. 2001. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67: 2354– 2359.
75. Mergeay, M. 2000. Bacteria adapted to industrial biotopes: metal resistant Ralstonia, p. 403–414. In G. Storz and, R. Hengge-Aronis (ed.), Bacterial Stress Responses. ASM Press, Washington, D.C.
76. Mergeay, M.,, S. Monchy,, T. Vallaeys,, V. Auquier,, A. Benotmane,, P. Bertin,, S. Taghavi,, J. Dunn,, D. van der Lelie, and, R. Wattiez. 2003. Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal responsive genes. FEMS Microbiol. Rev. 27: 385– 410.
77. Miller, D. N.,, J. E. Bryant,, E. L. Madsen, and, W. C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65: 4715– 4724.
78. Moore, C. M.,, A. Gaballa,, M. Hui,, R. W. Ye, and, J. D. Helmann. 2005. Genetic and physiological responses of Bacillus subtilis to metal ion stress. Mol. Microbiol. 57: 27– 40.
79. Niedhardt, F. C.,, and R. A. VanBogelen. 2000. Proteomic analysis of bacterial stress responses, p. 445–452. In G. Storz and, R. Hengge-Aronis (ed.), Bacterial Stress Responses. ASM Press, Washington, D.C.
80. Nies, D. H. 1999. Microbial heavy-metal resistance. Appl. Microbiol. Biotechnol. 51: 730– 750.
81. Nies, D. H. 2003. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol. Rev. 27: 313– 339.
82. Nies, D. H.,, and N. L. Brown. 1998. Two-component systems in the regulation of heavy metal resistance, p. 77–103. In S. Silver and, W. Walden (ed.), Metal Ions in Gene Regulation. Chapman and Hall, New York, N.Y.
83. Noël-Georis, I.,, T. Vallaeys,, R. Chauvaux,, S. Monchy,, P. Falmagne,, M. Mergeay, and, R. Wattiez. 2004. Global analysis of the Ralstonia metallidurans proteome: prelude for the large-scale study of heavy metal response. Proteomics 4: 151– 179.
84. Oger, C.,, T. Berthe,, L. Quillet,, S. Barray,, J. F. Chiffoleau, and, F. Pettit. 2001. Estimation of the abundance of the cadmium resistance gene cadA in microbial communities in polluted estuary water. Res. Microbiol. 152: 671– 678.
85. O’Neill, M. J.,, A. Smith,, P. E. Heckelman, and, S. Budavari (ed.). 2003. The Merck Index, 13th ed. Merck and Company Inc., Rahway, N.J.
86. Outten, F. W.,, C. Outten, and, T. V. O’Halloran. 2000. Metalloregulatory systems at the interface between bacterial metal homeostasis and resistance, p. 145–178. In G. Storz and, R. Hengge-Aronis (ed.), Bacterial Stress Responses. ASM Press, Washington, D.C.
87. Phelps, T. J.,, A. V. Palumbo, and, A. S. Beliaev. 2002. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr. Opin. Biotechnol. 13: 20– 24.
88. Poretsky, R. S.,, N. Bano,, A. Buchan,, G. LeClair,, J. Kleikemper,, M. Pickering,, W. M. Pate,, M. A. Moran, and, J. T. Hollibaugh. 2005. Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71: 4121– 4126.
89. Provence, D.H.,, and R. Curtiss III. 1994. Gene transfer in gram-negative bacteria, p. 317–347. In P. Gerhardt,, R. G. E. Murray,, W. A. Wood, and, N. R. Krieg (eds.), Methods for General and Molecular Bacteriology. ASM Press, Washington, D.C.
90. Pumpel, T.,, B. Pernfuss,, B. Pigher,, L. Diels, and, F. Schinner. 1995. A rapid screening method for the isolation of metal accumulating microorganisms. J. Ind. Microbiol. 14: 213– 217.
91. Qiu, X.,, L. Wu,, H. Huang,, P. E. McDonel,, A. V. Palumbo,, J. M. Tiedje, and, J. Zhou. 2001. Evaluation of PCR generated chimeras, mutations and heteroduplexes with the 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67: 880– 887.
92. Ramamoorthy, S.,, and D. J. Kushner. 1975. Binding of mercuric and other heavy metal ions by microbial growth media. Microb. Ecol. 2: 162– 176.
93. Riesenfeld, C. S.,, P. D. Schloss, and, J. Handelsman. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525– 552.
94. Riley, J.,, R. Butler,, R. Finniear,, D. Jenner,, S. Powell,, R. Anand,, J. C. Smith, and, A. F. Markham. 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18: 2887– 2890.
95. Rosen, B. P. 2002. Transport and detoxification systems for transition metals, heavy metals and metalloids in eukaryotic and prokaryotic microbes. Comp. Biochem. Physiol. Part A 133: 689– 693.
96. Rouch, D. A.,, and N. L. Brown. 1997. Copper-inducible transcriptional regulation at two promoters in the Escherichia coli copper resistance determinant pco. Microbiology 143: 1191– 1202.
97. Saltikov, C. W.,, and B. H. Olson. 2002. Homology of Escherichia coli R773 arsA, arsB, and arsC genes in arsenic-resistant bacteria isolated from raw sewage and arsenic-enriched creek waters. Appl. Environ. Microbiol. 68: 280– 288.
98. Sambrook, J.,, P. MacCallum, and, D. Russell. 2001. Molecular Cloning: a Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
99. Schloss, P. D.,, and J. Handelsman. 2003. Biotechnological prospects for metagenomics. Curr. Opin. Biotechnol. 14: 303– 310.
100. Silver, S. 1996. Bacterial resistances to toxic metal ions—a review. Gene 179: 9– 19.
101. Silver, S. 1996. Transport of inorganic cations, p. 1091–1102. In F. C. Niedhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter, and, H. E. Umbarger (ed.), Escherichia coli and Salmonella; Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, D.C.
102. Silver, S. 1998. Genes for all metals; a bacterial view of the periodic table. J. Ind. Microbiol. Biotechnol. 20: 1– 12.
103. Silver, S. 2003. Bacterial silver resistance: molecular biology and uses and misuses of silver compounds. FEMS Microbiol. Rev. 27: 341– 354.
104. Silver, S.,, and L. T. Phung. 1996. Bacterial heavy metal resistance: new surprises. Annu. Rev. Microbiol. 50: 753– 789.
105. Silver, S.,, and L. T. Phung. 2005. A bacterial view of the periodic table: genes and proteins for toxic inorganic ions. J. Ind. Microbiol. Biotechnol. 32: 587– 605.
106. Speksnijder, A. G. C. L.,, G. A. Kowalchuk,, S. de Jong,, E. Kline,, J. R. Stephen, and, H. J. Laanbroek. 2001. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl. Environ. Microbiol. 67: 469– 472.
107. Stach, J. E. M.,, S. Bathe,, J. Clapp, and, R. G. Burns. 2001. PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA, using different isolation and purification methods. FEMS Microbiol. Ecol. 36: 139– 151.
108. Stormo, G. D.,, and K. Tan. 2002. Mining genome databases to identify and understand new gene regulatory systems. Curr. Opin. Microbiol. 5: 149– 153.
109. Storz, G.,, and R. Hengge-Aronis (ed.). 2000. Bacterial Stress Responses. ASM Press, Washington, D.C.
110. Streit, W. R.,, and R. A. Schmitz. 2004. Meta-genomics—the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492– 498.
111. Sun, Y.,, E. A. Polishchuk,, U. Radoja, and, W. R. Cullen. 2004. Identification and quantification of arsC genes in environmental samples by using real-time PCR. J. Microbiol. Methods 58: 335– 349.
112. Szpunar, J. 2005. Advances in analytical methodology for bioinorganic speciation analysis: metallomics, metal-loproteomics and heteroatom-tagged proteomics and metabolomics. Analyst 130: 442– 465.
113. Tam, R.,, and M. H. Saier, Jr. 1993. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57: 320– 346.
114. Trajanovska, S.,, M. L. Britz, and, M. Bhave. 1997. Detection of heavy metal ion resistance genes in Gram-positive and Gram-negative bacteria isolated from a lead-contaminated site. Biodegradation 8: 113– 124.
115. Treusch, A. H.,, A. Kletzin,, G. Raddatz,, T. Ochsenreiter,, A. Quaiser,, G. Meurer,, S. C. Schuster, and, C. Schleper. 2004. Characterization of large insert DNA libraries from soil for environmental genomic studies of Archaea. Environ. Microbiol. 6: 970– 980.
116. Trevors, J. T.,, K. M. Oddie, and, B. H. Belliveau. 1985. Metal resistance in bacteria. FEMS Microbiol. Rev. 32: 39– 54.
117. Tringe, S. G.,, C. von Mering,, A. Kobayashi,, A. A. Salamov,, K. Chen,, H. W. Chang,, M. Podar,, J. M. Short,, E. J. Mathur,, J. C. Detter,, P. Bork,, P. Hugenholtz, and, E. M. Rubin. 2004 Comparative genomics of microbial communities. Science 308: 554– 557.
118. Tyson, G. W.,, J. Chapman,, P. Hugenholtz,, E. E. Allen,, R. J. Ram,, P. M. Richardson,, V. V. Solovyev,, E. M. Rubin,, D. S. Rokshar, and, J. F. Banfield. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37– 43.
119. Valentin, K.,, U. John, and, L. Medlin. 2005. Nucleic acid isolation from environmental aqueous samples. Methods Enzymol. 395: 15– 37.
120. Vertriani, C.,, Y. S. Chew,, S. M. Miller,, J. Yagi,, J. Coombs,, R. A. Lutz, and, T. Barkay. 2005. Mercury adaptation among bacteria from a deep-sea hydrothermal vent. Appl. Environ. Microbiol. 71: 220– 226.
121. Wackett, L. P.,, A. G. Dodge, and, L. B. M. Ellis. 2004. Microbial genomics and the periodic table. Appl. Environ. Microbiol. 70: 647– 655.
122. Wang, G. G. Y.,, and Y. Wang. 1997. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol. 63: 4645– 4650.
123. Wheatcroft, R.,, and P. A. Williams. 1981. Rapid methods for the study of both stable and unstable plasmids in Pseudomonas. J. Gen. Microbiol. 124: 433– 437.
124. White, C.,, J. A. Sayer, and, G. M. Gadd. 1997. Microbiological solubilization and immobilization of toxic metals: key biogeochemical processes for treatment of contamination. FEMS Microbiol. Rev. 20: 503– 516.
125. Wiatrowski, H.,, and T. Barkay. 2005. Monitoring of microbial metal transformations in the environment. Curr. Opin. Biotechnol. 16: 261– 268.
126. Willetts, N. 1988. Conjugation. Methods Microbiol. 21: 49– 78.
127. Wilmes, P.,, and P. L. Bond. 2004. The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ. Microbiol. 6: 911– 920.
128. Yamamoto, K.,, and A. Ishihama. 2005. Transcriptional response of Escherichia coli to external copper. Mol. Microbiol. 56: 215– 227.

Tables

Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria
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Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
/content/10.1128/9781555815882.ch96.ch96fig01a
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Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96
/content/10.1128/9781555815882.ch96.ch96tab01
TABLE 1
PCR primers used to amplify specific resistance genes from toxic-metal-resistant bacteria
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TABLE 1

PCR primers used to amplify specific resistance genes from toxic-metal-resistant bacteria

Citation: Hobman J. 2007. Molecular Techniques for the Study of Toxic Metal Resistance Mechanisms in Bacteria, p 1166-1182. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch96

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