20 The Isolation and Study of Acidophilic Microorganisms

Methods in Microbiology

Volumn 35, Issue , 2006, Pages 471-510

  González Toril, Elena ^a   Gómez, Felipe ^a   Malki, Moustafa ^b   Amils, Ricardo ^a,b  

^a CENTRO DE ASTROBIOLOGÍA CSIC INTA   (Spain)

^b UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 35748934554     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0580-9517(08)70023-0     Document Type: Article

References (87)

1. Achenbach L., and Woese C. 16S and 23S rRNA-like primers. In: Sowers K.R., and Schreier H.J. (Eds). Archaea. A Laboratory Manual (1995), Cold Spring Harbor Laboratory Press, Cold Spring Harbor 521-523
2. Akkermans A.D.L., Mirza M.S., Harmsen H.J.M., Blok H.J., Herron P.R., Sessitsch A., and Akkermans W.M. Molecular ecology of microbes: A review of promises, pitfalls and true progress. FEMS Microbiol. Rev. 15 (1994) 185-194
3. Amann R.I. In situ identification of microorganisms by whole cell hybridization with rRNA-targeted nucleic acid probes. In: Akkermans A.D.L., Van Elsas J.D., and de Bruijn F.J. (Eds). Molecular Microbial Ecology Manual (1995), Kluwer Academic Publishers, Dordrecht 3.3.6.1-3.3.6.15
4. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., and Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56 (1990) 1919-1925
5. Amann R.I., Ludwig W., and Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59 (1995) 143-169
6. Amann R., Fuchs B.M., and Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Curr. Opin. Biotechnol. 12 (2001) 231-236
7. Amaral-Zettler L.A., Gómez F., Zettler E., Keenan B.G., Amils R., and Sogin M.L. Eukaryotic diversity in Spain's River of Fire. Nature 417 (2003) 137
8. Amils R., González-Toril E., Gómez F., Fernández-Remolar D., Rodríguez N., Malkim M., Aguilera A., and Amaral-Zettler L.A. Importance of chemolithotrophy for early life on earth: the Tinto River (Iberian Pyritic Belt) case. In: Seckbach J. (Ed). Origins (2004), Kluwer Academic Publishers, Dordrecht 463-480
9. Benison K.C., and Laclair D.A. Modern and ancient extreme acid saline deposits: terrestrial analogs for Martian environments. Astrobiology 3 (2003) 609-618
10. Benz M., Brune A., and Schink B. Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria. Arch. Microbiol. 169 (1998) 159-165
11. Bond P., Smriga S.P., and Banfield J.F. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66 (2000) 3842-3849
12. Bridge T.A.M., and Johnson D.B. Reduction of soluble iron and reductive dissolution of ferric iron-containing minerals by moderately thermophilic iron-oxidizing bacteria. Appl. Environ. Microbiol. 64 (1998) 2181-2186
13. Brierley C.L., and Brierley J.A. A chemoautotrophic and thermophilic microorganism isolated from an acid hot spring. Can. J. Microbiol. 19 (1973) 183-188
14. st Century (1999), Elsevier, Amsterdam 81-89 Part A
15. Brock T.D., and Gustafson J. Ferric iron reduction by sulfur- and iron-oxidizing bacteria. Appl. Environ. Microbiol. 32 (1976) 567-571
16. Brock T.D., Brock K.M., Belly R.T., and Weiss R.L. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch. Microbiol. 84 (1972) 54-68
17. Brosius J., Dull T.J., Sleeter D.D., and Noller H.F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148 (1981) 107-127
18. Chandler D.P., Fredrickson J.K., and Brockman F.J. Effect of the PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6 (1997) 475-482
19. Colmer A.R., Temple K.L., and Hinkle H.E. An iron-oxidizing bacterium from the acid drainage of some bituminous coal mines. J. Bacteriol. 59 (1950) 317-328
20. Corbett C.M., and Ingledew W.J. Is FeIII/FeII cycling an intermediate in sulphur oxidation by Thiobacillus ferrooxidans?. FEMS Microbiol. Lett. 41 (1987) 1-6
21. Daims H., Bruhl A., Amann R., Schleifer K.H., and Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. System. Appl. Microbiol. 22 (1999) 434-444
22. Daims H., Nielsen P., Nielsen J.L., Juretschko S., and Wagner M. Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology. Water Sci. Technol. 3 (2001) 416-523
23. DeLong E.F., Wickham G.S., and Pace N.R. Phylogenetic strains: ribosomal RNA-based probes for the identification of single cells. Science 243 (1989) 1360-1363
24. Edwards K.J., Bond P.L., Gihring T.M., and Banfield J.F. An archaeal iron-oxidizing extreme acidophile important in acidic mine drainage. Science 287 (2000) 1796-1798
25. Ehrlich, H. L. (2002). Geomicrobiology, 4th edn., Marcel Dekker, New York
26. Fernández-Remolar, D., Rodríguez, N., Gómez, F. and Amils, R. (2003). The geological record of an acidic environment driven by iron hydrochemistry: the Tinto River system. J. Geophys. Res. 108(2003)10.1029/2002JE001918
27. Fernández-Remolar, D., Morris, R. V., Gruener, J. E., Amils, R. and Knoll, A. H. (2005). The Río Tinto basin, Spain: mineralogy, sedimentary geobiology and implications for interpretation of outcrop rocks at Meridiani Planum, Mars. Earth Planet. Sci. Lett. 240, 179-189
28. Gehrke T., Hallmann R., and Sand W. Importance of exopolymers from Thiobacillus ferrooxidans and Leptospirillum ferrooxidans for bioleaching. In: Vargas T., Jérez C.A., Wiertz K.W., and Toledo H. (Eds). Biohydrometallurgical Processing 1 (1995), Universidad de Chile, Santiago 1-11
29. Giovannoni J.G., DeLong E.F., Olsen G.J., and Pace N.R. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170 (1988) 720-726
30. Giovannoni S.J., Britschgi T.B., Moyer C.L., and Field K.G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 (1990) 60-63
31. Golyshina O.V., Pivovarova T.A., Karavaiko G.I., Kondrateva T.F., Moore E.R., Abraham W.R., Lunsdorf H., Timmis K.N., Yakimov M.M., and Golyshina P.N. Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov. comprising a distinct lineage of the Archaea. Int. J. Syst. Evol. Microbiol. 50 (2000) 997-1006
32. González-Toril E., Gómez F., Rodríguez N., Fernández D., Zuluaga J., Marín I., and Amils R. Geomicrobiology of the Tinto river, a model of interest for biohydrometallurgy. In: Cuminielly V.S.T., and García O. (Eds). Biohydrometallurgy: Fundamentals, Technology and Sustainable Development (2001), Elsevier, Amsterdam 639-650 Part B
33. González-Toril E., Llobet-Brossa E., Casamayor E.O., Amann R., and Amils R. Microbial ecology of an extreme acidic environment, the Tito River. Appl. Environ. Microbiol. 69 (2003) 4853-4865
34. González-Toril, E., García-Moyano, A. and Amils, R. (2006). Phylogeny of prokaryotic microorganisms from the Tinto River. In Proceedings of the International Biohydrometallurgical Symposium - 2005 (D. Rawlings, ed.). Elsevier, Amsterdam, in press
35. Hallberg K.B., and Johnson D.B. Biodiversity of acidophilic prokaryotes. Adv. Appl. Microbiol. 49 (2001) 37-84
36. Hallberg K.B., and Johnson D.B. Novel acidophiles isolated from moderately acidic mine drainage waters. Hydrometallurgy 71 (2003) 139-148
37. Hallberg K.B., and Lindström E.B. Characterization of Thiobacillus caldus, sp. nov., a moderately thermophilic acidophile. Microbiology UK 140 (1994) 3451-3456
38. Harrison Jr. A.P. Genomic and physiological comparisons between heterotrophic thiobacilli and Acidiphilium cryptum, Thiobacillus versutus sp. nov., and Thiobacillus acidophilus nom. rev. Int. J. Syst. Bacteriol. 33 (1983) 211-217
39. Hiraishi A., and Kitamura H. Distribution of phototrophic purple nonsulfur bacteria in activated sludge systems and other aquatic environments. Bull. Jpn. Soc. Sci. Fish. 50 (1984) 1929-1937
40. st Century (1999), Elsevier, Amsterdam 645-656 Part A
41. Johnson D.B., and Roberto F.F. Heterotrophic acidophiles and their roles in the bioleaching of sulfide materials. In: Rawlings D.E. (Ed). Biomining: Theory, Microbes and Industrial Processes (1997), Springer, Berlin 259-279
42. Kelly D.P., and Harrison A.H. Genus Thiobacillus. In: Staley J.T., Bryant M.P., Pfennig N., and Holt J.G. (Eds). Bergey's Manual of Systematic Bacteriology. 1st 3 (1989), Williams & Wilkins, Baltimore 1842-1858
43. Kelly D.P., and Wood A.P. Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. Int. J. Syst. Evol. Microbiol. 50 (2000) 511-516
44. Leathen W.W., Kinsel N.A., and Braley Jr. S.A. Ferrobacillus ferrooxidans: a chemosynthetic autotrophic bacterium. J. Bacteriol. 72 (1956) 700-704
45. Llobet-Brossa E., Rosselló-Mora R., and Amann R. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64 (1998) 2691-2696
46. López-Archilla A.I., Marín I., and Amils R. Bioleaching and interrelated acidophilic microorganisms from Río Tinto, Spain. Geomicrobiol. J. 11 (1993) 223-233
47. López-Archilla A.I., Marín I., and Amils R. Microbial community composition and ecology of an acidic aquatic environment: the Tinto River, Spain. Microb. Ecol. 41 (2001) 20-35
48. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M., and Schleifer K.H. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19 (1998) 554-568
49. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüßmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., and Schleifer K.H. ARB: a software environment for sequence data. Nucl. Acids Res. 32 (2004) 1363-1371
50. Mackintosh M.E. Nitrogen fixation by Thiobacillus ferrooxidans. J. Gen. Microbiol. 105 (1978) 215-218
51. Manz W., Amann R., Ludwig W., Wagner M., and Schleifer K.H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. System. Appl. Microbiol. 15 (1992) 593-600
52. Manz W., Eisenbrecher M., Neu T.R., and Szewzyk U. Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol. Ecol. 25 (1998) 43-61
53. Margesin R., and Schinner F. Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5 (2001) 73-83
54. Marsh R.M., and Norris P.R. The isolation of some thermophilic, autotrophic, iron- and sulfur-oxidizing bacteria. FEMS Microbiol. Lett. 17 (1983) 311-315
55. Muyzer G., de Bruyn J.C., Schmedding D.J.M., Bos P., Westbroek P., and Kuenen J.G. A combined immunofluorescence-DNA-fluorescence staining technique for enumeration of Thiobacillus ferrooxidans in a population of acidophilic bacteria. Appl. Environ. Microbiol. 53 (1987) 660-664
56. Muyzer G., de Waal E.C., and Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59 (1993) 695-700
57. Muyzer G., Teske A., Wirsen C.O., and Jannasch H.W. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164 (1995) 165-172
58. Muyzer G., Hottenträger S., Teske A., and Wawer C. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - A new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans A.D.L., Van Elsas J.D., and de Bruijn F.J. (Eds). Molecular Microbial Ecology Manual. 2nd (1996), Kluwer Academic Publishers, Dordrecht 3.4.4.1-3.4.4.22
59. Myers R.M., Maniatis T., and Lerman L.S. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Meth. Enzymol. 155 (1987) 501-527
60. Neef, A. (1997). Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. Ph.D. Thesis, Technical University of Munich
61. Niehaus F., Bertoldo C., Kähler M., and Antranikian G. Extremophiles as a source of novel enzymes for industrial application. Appl. Microbiol. Biotechnol. 51 (1999) 711-729
62. Nogales B., Moore E.R., Llobet-Brossa E., Rossello-Mora R., Amann R., and Timmis K.N. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl. Environ. Microbiol. 67 (2001) 1874-1884
63. Norris P.R., Clark D.A., Owen J.P., and Waterhouse S. Characteristics of Sulfobacillus acidophilus sp. nov. and other moderately thermophilic mineral-sulphide-oxidizing bacteria. Microbiology UK 142 (1996) 775-783
64. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R., and Stahl D.A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40 (1986) 337-365
65. Peng J.B., Yan W.M., and Boo X.Z. Solid medium for the genetic manipulation of Thiobacillus ferrooxidans. J. Gen. Appl. Microbiol. 40 (1994) 243-253
66. Pernthaler A., Pernthaler J., and Amann R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68 (2002) 3094-3101
67. Pivovarova T.A., Markosyan G.E., and Karavaiko G.I. The auxotrophic growth of Leptospirillum ferrooxidans. Microbiology (English translation of Mikrobiologiya) 50 (1981) 339-344
68. Postgate, J. R. (1984). The Sulphate-Reducing Bacteria, 2nd edn., Cambridge University Press, Cambridge
69. Pronk J.T., Bruyn J.C., Bos P., and Kuenen J.G. Anaerobic growth of Thiobacillus ferrooxidans. Appl. Environ. Microbiol. 58 (1992) 2227-2230
70. Raskin L., Stromley J.M., Rittmann B.E., and Stahl D.A. Group specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60 (1994) 1232-1240
71. Rawlings D.E. Restriction enzyme analysis of 16S rRNA genes for a rapid identification of Thiobacillus ferrooxidans, Thiobacillus thiooxidans and Leptospirillum ferrooxidans strains in leaching environments. In: Vargas T., Jérez C.A., Wiertz J.V., and Toledo H. (Eds). Biohydrometallurgical Processing II (1997), University of Chile, Santiago 9-18
72. Rawlings D.E. Heavy metal mining using microbes. Annu. Rev. Microbiol 56 (2002) 65-91
73. Russell N.J. Toward a molecular understanding of cold activity of enzymes from psychrophiles. Extremophiles 4 (2000) 83-90
74. Sambrook J., and Russel D.W. Preparation of plasmid DNA by alkaline lysis with SDS: Minipreparation. In: Sambrook J., and Russel D.W. (Eds). Molecular Cloning. A Laboratory Manual. 3rd 1 (2001), Cold Spring Harbor Laboratory Press, New York 1.32-1.34
75. Sand W., Rhode K., Sobotke B., and Zenneck C. Evaluation of Leptospirillum ferrooxidans for leaching. Appl. Environ. Microbiol. 58 (1992) 85-92
76. Sand W., Gehrke T., Jozsa P.G., and Schippers A. (Bio)chemistry of bacterial leaching-direct vs. indirect bioleaching. Hydrometallurgy 59 (2001) 159-175
77. Schrenk M.O., Edwards K.J., Goodman R.M., Hamers R.J., and Bandfield J.F. Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans: Implications for generation of acidic mine drainage. Science 279 (1998) 1519-1522
78. Sheffield V.D., Cox D.R., Lerman L.S., and Meyers R.M. Attachment of a 40-base pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86 (1989) 232-236
79. Silverman M.N., and Lundgren D.G. Studies on chemoautotrophic iron bacterium Ferrobacillus ferrooxidans. J. Bacteriol. 77 (1959) 642-647
80. Stackebrandt E., and Rainey F.A. Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies. In: Akkermans A.D.L., van Elsas J.D., and de Bruijn F.J. (Eds). Molecular Microbial Ecology Manual (1998), Kluwer Academic Publishers, Dordrecht 3.1.1-3.1.17
81. Stahl D.A., and Amann R. Development and application of nucleic acid probes. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic Acid Techniques in Bacterial Systematics (1991), John Wiley & Sons, Chichester 205-248
82. Suzina N.E., Severina L.O., Senyushkin A.A., Karavaiko G.I., and Duda V.I. Ultrastructural organization of membrane system in Sulfobacillus thermosulfidooxidans. Mikrobiologiya 68 (1999) 429-436
83. Temple K.L., and Colmer A.R. The autotrophic oxidation of iron by a new bacterium Thiobacillus ferrooxidans. J. Bacteriol. 62 (1951) 605-611
84. 2-fixation and iron oxidation as measures of growth. Arch. Mikrobiol. 88 (1973) 285-298
85. Ward D.M., Weller R., and Bateson M.M. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345 (1990) 63-65
86. Widdel F., Schnell S., Heising S., Ehrenreich A., Assmus B., and Schink B. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362 (1993) 834-836
87. Wintzingerode F.V., Göbel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21 (1997) 213-229