Techniques for detecting and identifying acidophilic mineral-oxidizing microorganisms

Biomining

Volumn , Issue , 2007, Pages 237-261

  Johnson, D Barrie ^a   Hallberg, Kevin B ^a  

^a BANGOR UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84920081524     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-540-34911-2_12     Document Type: Chapter

References (75)

1. Adamczyk J, Hesselsoe M, Iversen N, Horn M, Lehner A, Nielsen PH, Schloter M, Roslev P, Wagner M (2003) The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function. Appl Environ Microbiol 69:6875-6887
2. Amann R, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990a) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919-1925
3. Amann RI, Krumholz L, Stahl DA (1990b) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762-770
4. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169
5. Amaro AM, Hallberg KB, Lindström EB, Jerez CA (1994) An immunological assay for detection and enumeration of thermophilic biomining microorganisms. Appl Environ Microbiol 60:3470-3473
6. Apel WA, Dugan PR, Filppi JA, Rheins MS (1976) Detection of Thiobacillus ferrooxidans in acid mine environments by indirect fluorescent-antibody staining. Appl Environ Microbiol 32:159-165
7. Arredondo R, Jerez CA (1989) Specific dot-immunobinding assay for detection and enumeration of Thiobacillus ferrooxidans. Appl Environ Microbiol 55:2025-2029
8. Bergamo RF, Novo MTM, Verissimo RV, Paulino LC, Stoppe NC, Sato MIZ, Manfio GP, Prado PI, Garcia O, Ottoboni LMM (2004) Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S-23S rDNA spacer polymorphism analysis. Res Microbiol 155:559-567
9. Bond PL, Banfield JF (2001) Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. Microb Ecol 41:149-161
10. Bond PL, Smriga SP, Banfield JF (2000a) Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl Environ Microbiol 66:3842-3849
11. Bond PL, Druschel GK, Banfield JF (2000b) Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl Environ Microbiol 66:4962-4971
12. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107-127
13. De Bruyn JC, Boogerd FC, Bos P, Kuenen JG (1990) Floating filters, a novel technique for isolation and enumeration of fastidious, acidophilic, iron-oxidizing, autotrophic bacteria. Appl Environ Microbiol 56:2891-2894
14. Demergasso C, Echeverria A, Escudero L, Galleguillos P, Zepeda V, Castillo D (2005) 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. 16th International Biohydrometallurgy Symposium, Cape Town, pp 843-851
15. De Wulf-Durand P, Bryant LJ, Sly LI (1997) PCR-mediated detection of acidophilic, bioleaching-associated bacteria. Appl Environ Microbiol 63:2944-2948
16. Dziurla M-A, Achouak W, Lam B-T, Heulin T, Berthelin J (1998) Enzyme-linked immunofiltration assay to estimate attachment of thiobacilli to pyrite. Appl Environ Microbiol 64:2937-40
17. Edwards KJ, Bond PL, Banfield JF (2000a) Characteristics of attachment and growth of Thiobacillus caldus on sulphide minerals: a chemotactic response to sulphur minerals? Environ Microbiol 2:324-332
18. Edwards KJ, Bond PL, Gihring TM, Banfield JF (2000b) An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796-1799
19. Ehrlich HL (2002) Geomicrobiology, 4th edn. Taylor and Francis, New York
20. Felsenstein J (1985) Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39:783-791
21. Friedrich MW (2002) Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms. J Bacteriol 184:278-289
22. Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwig W, Amann R (1998) Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 64:4973-4982
23. Fuchs BM, Glockner FO, Wulf J, Amann R (2000) Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 66:3603-3607
24. 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
25. Hallberg KB, Coupland K, Kimura S, Johnson DB (2006) Macroscopic acid streamer growths in acidic, metal-rich mine waters in north Wales consist of novel and remarkably simple bacterial communities. Appl Environ Microbiol 72:2022-2030
26. Hallberg KB, Johnson DB (2003) Novel acidophiles isolated from moderately acidic mine drainage waters. Hydrometallurgy 71:139-148
27. Hallberg KB, Lindström EB (1996) Multiple serotypes of the moderate thermophile Thiobacillus caldus, a limitation of immunological assays for biomining microorganisms. Appl Environ Microbiol 62:4243-4246
28. Harneit K, Göksel A, Kock D, Klock JH, Gehrke T, Sand W (2005) Adhesion to metal sulphide surfaces by cells of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans. In: Harrison STL, Rawlings DE, Petersen J (eds) Proceedings of the 16th international biohydrometallurgy symposium. 16th International Biohydrometallurgy Symposium, Cape Town, pp 635-646
29. Head IM, Saunders JR, Pickup RW (1998) Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35:1-21
30. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765-4774
31. Jerez CA, Arredondo R (1991) A sensitive immunological method to enumerate Leptospirillum ferrooxidans in the presence of Thiobacillus ferrooxidans. FEMS Microbiol Lett 78:99-102
32. Johnson DB (1995) Selective solid media for isolating and enumerating acidophilic bacteria. J Microbiol Methods 23:205-218
33. Johnson DB, McGinness S (1991) A highly efficient and universal solid medium for growing mesophilic and moderately thermophilic iron-oxidizing acidophilic bacteria. J Microbiol Methods 13:113-122
34. Johnson DB, Okibe N, Hallberg KB (2005) Differentiation and identification of iron-oxidizing acidophilic bacteria using cultivation techniques and amplified ribosomal DNA restriction enzyme analysis (ARDREA). J Microbiol Methods 60:299-313
35. Karan G, Natarajan KA, Modak JM (1996) Estimation of mineral adhered biomass of Thiobacillus ferrooxidans by protein assay - some problems and remedies. Hydrometallurgy 42:169-175
36. Kolmert Å, Wikström P, Hallberg KB (2000) A fast and simple turbidimetric method for the determination of sulfate in sulfate-reducing bacterial cultures. J Microbiol Methods 41:179-184
37. Koppe B, Harms H (1994) Antigenic determinants and specificity of antisera against acidophilic bacteria. World J Microbiol Biotechnol 10:154-158
38. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115-175
39. Leclerc M, Delbes C, Moletta R, Godon J-J (2001) Single strand conformation polymorphism monitoring of 16S rDNA archaea during start-up of an anaerobic digester. FEMS Microbiol Ecol 34:213-220
40. Lindström EB, Sehlin HM (1989) High efficiency plating of the thermophilic sulfur-dependent archaebacterium Sulfolobus acidocaldarius. Appl Environ Microbiol 55:3020-3021
41. Lovley DR, Phillips EJP (1987) Rapid assay for microbially reduced ferric iron in aquatic sediments. Appl Environ Microbiol 53:1536-1540
42. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG (1998) Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64:795-799
43. Marsh TL (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2:323-327
44. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek J Microbiol 73:127-41
45. Muyzer G, Hottenträger S, Teske A, Wawer C (1996) Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - a new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer, Dordrecht, pp 1-23
46. Orita M, Suzuki Y, Sekiya T, Hayashi K (1989) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5:874-879
47. Orphan VJ, Taylor, LT, Hafenbradl D, De Long EF (2000) Culture-dependent and cultureindependent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66:700-711
48. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
49. Parro V, Moreno-Paz M (2003) Gene function analysis in environmental isolates: The nif regulon of the strict iron oxidizing bacterium Leptospirillum ferrooxidans. Proc Natl Acad Sci USA 100:7883-7888
50. Peccia J, Marchand EA, Silverstein J, Hernandez M (2000) Development and application of small-subunit rRNA probes for assessment of selected Thiobacillus species and members of the genus Acidiphilium. Appl Environ Microbiol 66:3065-40
51. Pernthaler A, Pernthaler J, Amann R (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-3101
52. Pizarro J, Jedlicki E, Orellana O, Romero J, Espejo RT (1996) Bacterial populations in samples of bioleached copper ore as revealed by analysis of DNA obtained before and after cultivation. Appl Environ Microbiol 62:1323-1328
53. Ramsay B, Ramsay J, De Tremblay M, Chavarie C (1988) A method for quantification of bacterial protein in the presence of jarosite. Geomicrobiol J 6:171-177
54. Raskin L, Stromley JM, Rittmann BE, Stahl DA (1994) Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl Environ Microbiol 60:1232-1240
55. Rawlings DE (1995) Restriction enzyme analysis of 16S rDNA genes for the rapid identification of Thiobacillus ferrooxidans, Thiobacillus thiooxidans and Leptospirillum ferrooxidans strains in leaching environments. In: Vargas T, Jerez CA, Wiertz JV, Toledo H (eds) Biohydrometallurgical processing. University of Chile, Santiago, pp 9-18
56. Rawlings DE, Coram NJ, Gardner MN, Deane SM (1999) Thiobacillus caldus and Leptospirillum ferrooxidans are widely distributed in continuous flow biooxidation tanks used to treat a variety of metal containing ores and concentrates. In: Amils R, Ballester A (eds) Biohydrometallurgy and the environment toward the mining of the 21st century. Elsevier, Amsterdam, pp 777-786
57. Rohwerder T, Schippers A, Sand W (1998) Determination of reaction energy values for biological pyrite oxidation by calorimetry. Thermochim Acta 309:79-85
58. 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
59. Sasaki K, Ida C, Ando A, Matsumoto N, Saiki H, Ohmura N (2003) Respiratory isozyme, two types of rusticyanin of Acidithiobacillus ferrooxidans. Biosci Biotechnol Biochem 67:1039-1047
60. Schippers A, Bosecker K (2005) Bioleaching: analysis of microbial communities dissolving metal sulfides. In: Barredo JL (ed) Methods in biotechnology: microbial processes and products. Humana, Totowa, pp 405-412
61. Schrenk MO, Edwards KJ, Goodman RM, Hamers RJ, Banfield JF (1998) Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: implications for generation of acid mine drainage. Science 279:1519-1522
62. Silverman MP, Lundgren DG (1959) Studies on the chemoautotrophic iron bacterium Ferrobacillus ferrooxidans. I. An improved medium and harvesting procedure for securing high yields. J Bacteriol 77:642-647
63. Stackebrandt E, Goebel BM (1994) A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849
64. Stahl DA, Amann R (1991) Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 205-248
65. Stoner DL, Browning CK, Bulmer DK, Ward TE, MacDonell MT (1996) Direct 5S rRNA assay for monitoring mixed-culture bioprocesses. Appl Environ Microbiol 62:1969-1976
66. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
67. Tributsch H, Rojas-Chapana J (2004) Comparative study on pit formation and interfacial chemistry induced by Leptospirillum and Acidithiobacillus ferrooxidans during FeS2 leaching. In: Tsezos M, Hatzikioseyian A, Remoudaki E (eds) Biohydrometallurgy; a sustainable technology in evolution. National Technical University of Athens, Zografou, pp 1047-1055
68. 2 fixation and iron oxidation as measures of growth. Arch Microbiol 88:285-298
69. 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
70. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P, 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
71. Von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213-229
72. Wagner M, Roger AJ, Flax JL, Brusseau GA, Stahl DA (1998) Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180:2975-2982
73. White DC, Pinkhart HC, Ringelberg DB (1997) Biomass measurements: biochemical approaches. In: Hurst CJ, Knudsen GR, McInerney MJ, Stetzenbach LD, Walter MV (eds) Manual of environmental microbiology. American Society for Microbiology, Washington, D. C, pp 91-101
74. Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288-294
75. Zumstein E, Moletta R, Godon J-J (2000) Examination of two years of community dynamics in an anaerobic bioreactor using fluorescent-PCR single strand conformation polymorphism analysis. Environ Microbiol 2:69-78