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Volume 154, Issue 8

16S rDNA and 16S–23S internal transcribed spacer sequence analyses reveal inter- and intraspecific phylogeny Free

Abstract

In order to contribute to our understanding of taxonomy, we determined 16S rDNA sequences and the 16S–23S internally transcribed spacer (ITS) sequence of 35 Chinese isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polymorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter- and intraspecific genealogical relationships of the genus . Similarity values of the ITSs varied from 60.5 % to 84.7 % between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13 %. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese -like isolates represent one or two new species of the genus . The ITS may be a potential target for the development of fluorescent hybridization probes for more accurately detecting distinct ecotypes of strains and other closely related sulfur-oxidizing bacteria.

  • Received:
  • Accepted:
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Keyword(s): ITS, internal transcribed spacer , RAPD, randomly amplified polymorphic DNA and UPGMA, unweighted pair group method with arithmetic means
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2008-08-01
2025-04-27
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References

  1. Acharya C., Sukla L. B., Misra V. N. 2004; Biodepyritisation of coal. J Chem Technol Biotechnol 79:1–12
     [Google Scholar]
  2. Ageeva S. N., Kondrat'eva T. F., Karavaiko G. I. 2001; Phenotypic characteristics of Thiobacillus ferrooxidans strains. Mikrobiologiia 70:226–234 (in Russian
    [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410
     [Google Scholar]
  4. Amils R., Irazabal N., Moreira D., Avad J. P., Marin I. 1998; Genomic organization analysis of acidophilic chemolithotrophic bacteria using pulsed field gel electrophoretic techniques. Biochimie 80:911–921
     [Google Scholar]
  5. Baker B. J., Banfield J. F. 2003; Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44:139–152
     [Google Scholar]
  6. Barry T., Colleran G., Glennon M., Dunican L. K., Gannon F. 1991; The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1:51–56
     [Google Scholar]
  7. Berg K. L., Squires C., Squires C. L. 1989; Ribosomal operon antitermination: function of leader and spacer region BoxB-BoxA sequences and their conservation in diverse microorganisms. J Mol Biol 209:345–358
     [Google Scholar]
  8. Bergamo R. F., Novo M. T. M., Veríssimo R. V., Paulino L. C., Stoppe N. C., Sato M. I. Z., Manfio G. P., Prado P. I., Garcia O. Jr, Ottoboni L. M. M. 2004; Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S–23S rDNA spacer polymorphism analysis. Res Microbiol 155:559–567
     [Google Scholar]
  9. Bond P. L., Banfield J. F. 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
     [Google Scholar]
  10. Bouchez T, Jacob P, d'Hugues P, Durand A. 2006; Acidophilic microbial communities catalyzing sludge bioleaching monitored by fluorescent in situ hybridization. Antonie Van Leeuwenhoek 89:435–442
     [Google Scholar]
  11. Brenner D. J., Staley J. T., Krieg N. R. 2004; Classification of procaryotic organisms and the concept of bacterial speciation. In Bergey's Manual of Systematic Bacteriology, vol. 2 pp. 27–31 Edited by Brenner D. J., Krieg N. R., Staley J. T. , Garrity G. M. New York: Springer;
     [Google Scholar]
  12. Fox G. E., Wisotzkey J. D., Jurtshuk P. 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170
     [Google Scholar]
  13. Friedrich C. G. 1998; Physiology and genetics of sulfur-oxidizing bacteria. Adv Microb Physiol 39:235–289
     [Google Scholar]
  14. Goebel B. M., Stackebrandt E. 1994; Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 60:1614–1621
     [Google Scholar]
  15. Gurtler V., Stanisich V. A. 1996; New approaches to typing and identification of bacteria using the16S–23S rDNA spacer region. Microbiology 142:3–16
     [Google Scholar]
  16. Hallberg K. B., Lindstrom E. B. 1994; Characterization of Thiobacillus caldus sp. nov., a moderately thermophilic acidophile. Microbiology 140:3451–3456
     [Google Scholar]
  17. Harrison A. P. 1982; Genomic and physiological diversity amongst strains of Thiobacillus ferrooxidans, and genomic comparison with Thiobacillus thiooxidans . Arch Microbiol 131:68–76
     [Google Scholar]
  18. Johnson D. B. 1995; Selective solid media for isolating and enumerating acidophilic bacteria. J Microbiol Methods 23:205–218
     [Google Scholar]
  19. Johnson D. B., Okibe N., Hallberg K. B. 2005; Differentiation and identification of iron-oxidizing acidophilic bacteria using cultivation techniques and amplified ribosomal DNA restriction enzyme analysis. J Microbiol Methods 60:299–313
     [Google Scholar]
  20. Jonas D., Meyer H. G., Matthes P., Hartung D., Jahn B., Daschner F. D., Jansen B. 2000; Comparative evaluation of three different genotyping methods for investigation of nosocomial outbreaks of legionnaires' disease in hospitals. J Clin Microbiol 38:2284–2291
     [Google Scholar]
  21. Karavaiko G. I., Turova T. P., Kondrateva T. F., Lysenko A. M., Kolganova T. V., Ageeva S. N., Muntyan L. N., Pivovarova T. A. 2003; Phylogenetic heterogeneity of the species Acidithiobacillus ferrooxidians . Int J Syst Evol Microbiol 53:113–119
     [Google Scholar]
  22. Kelly D. P., Wood A. P. 2000; 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 50:511–516
     [Google Scholar]
  23. Kelly D. P., Wood A. P. 2005; Genus I. Acidithiobacillus. In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol. 2 The Proteobacteria), part B (The Gammaproteobacteria) pp 60–62 Edited by Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. New York: Springer;
     [Google Scholar]
  24. Kondratyeva T. F., Pivovarova T. A., Muntyan L. N., Karavaiko G. I. 1999; Strain diversity of Thiobacillus ferrooxidans and its significance in biohydrometallurgy. In Biohydrometallurgy and the Environment toward the Mining of the 21st Century, part B pp 89–98 Edited by Amils R., Balleter A. Amsterdam: Elsevier;
     [Google Scholar]
  25. Lado B. H., Yousef A. E. 2003; Selection and identification of a Listeria monocytogenes target strain for pulsed electric field process optimization. Appl Environ Microbiol 69:2223–2229
     [Google Scholar]
  26. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow M. New York: Wiley;
     [Google Scholar]
  27. Lane D. J., Harrison A. P. Jr, Stahl D., Pace B., Giovannoni S. J., Olsen G. J., Pace N. R. 1992; Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol 174:269–278
     [Google Scholar]
  28. Leblond-Bourget N., Philippe H., Mangin I., Decaris B. 1996; 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46:102–111
     [Google Scholar]
  29. Leduc L. G., Ferroni G. D. 1994; The chemolithotrophic bacterium Thiobacillus ferrooxidans . FEMS Microbiol Rev 14:103–120
     [Google Scholar]
  30. Merroun M. L., Selenska-Pobell S. 2001; Interactions of three eco-types of Acidithiobacillus ferrooxidans with U(VI. Biometals 14:171–179
     [Google Scholar]
  31. Ni Y.-Q., He K.-Y., Bao J. T., Yang Y., Wan D.-S., Li H.-Y. 2008; Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse environments in China. FEMS Microbiol Ecol 64:248–259
     [Google Scholar]
  32. Norris P. R. 2007; Acidophile diversity in mineral sulfide oxidization. In Biomining pp 199–216 Edited by Rawlings D. E., Johnson D. B. Berlin: Springer;
     [Google Scholar]
  33. Novo M. T. M., De Souza A. P., Garcia O. Jr, Ottoboni L. M. M. 1996; RAPD genomic fingerprinting differentiates Thiobacillus ferrooxidans strains. Syst Appl Microbiol 19:91–95
     [Google Scholar]
  34. Okabe S., Odagiri M., Ito T., Satoh H. 2007; Succession of sulfur-oxidizing bacteria in the microbial community on corroding concrete in sewer systems. Appl Environ Microbiol 73:971–980
     [Google Scholar]
  35. Paulino L. C., Bergamo R. F., de Mello M. P., Garcia O. Jr, Manfio G. P., Ottoboni L. M. M. 2001; Molecular characterization of Acidithiobacillus ferrooxidans and A. thiooxidans strains isolated from mine wastes in Brazil. Antonie Van Leeuwenhoek 80:65–75
     [Google Scholar]
  36. Peccia J., Marchand E. A., 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 66:3065–3072
     [Google Scholar]
  37. Rawlings D. E. 2005; Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates. Microb Cell Fact 4:13–17
     [Google Scholar]
  38. Rawlings D. E., Johnson D. B. 2007; The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153:315–324
     [Google Scholar]
  39. Rohlf F. J. 1997 Numerical Taxonomy and Multivariate Analysis System New York: Exeter;
     [Google Scholar]
  40. Rossello-Mora R., Amann R. 2001; The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
     [Google Scholar]
  41. Sagredo B., Jedlicki E., Orellana O. 1992; Organization of the 16S–23S intergenic spacer region of the two rRNA operons from Thiobacillus ferrooxidans . Geomicrobiol J 10:239–247
     [Google Scholar]
  42. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  43. Salazar O., Takamiya M., Orellana O. 1989; Characterization of the two rRNA gene operons present in Thiobacillus ferrooxidans . FEBS Lett 242:439–443
     [Google Scholar]
  44. Schrenk M. O., Edwards K. J., Goodman R. M., Hamers R. J., Banfield J. F. 1998; Distribution of Thiobacillus ferrooxidans and Leptospirillum ferrooxidans – implications for generation of acid mine drainage. Science 279:1519–1522
     [Google Scholar]
  45. Selenska-Pobell S., Otto A., Kutschke S. 1998; Identification and discrimination of thiobacilli using ARDREA, RAPD and rep-APD. J Appl Microbiol 84:1085–1091
     [Google Scholar]
  46. Simmons S., Norris P. R. 2002; Acidophiles of saline water at thermal vents of volcano, Italy. Extremophiles 6:201–207
     [Google Scholar]
  47. Sneath P. H. A., Sokal R. R. 1973 Numerical Taxonomy: the Principles and Practice of Numerical Classification San Fransisco: W. H. Freeman;
     [Google Scholar]
  48. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C., Nesme X., Rosselló-Mora R., Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047
     [Google Scholar]
  49. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega 4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599
     [Google Scholar]
  50. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
     [Google Scholar]
  51. Tyson G. W., Lo I., Baker B. J., Allen E. E., Hugenholtz P., Banfield J. F. 2005; Genome-directed isolation of the key nitrogen-fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71:6319–6324
     [Google Scholar]
  52. Valenzuela L., Chi A., Beard S., Orell A., Guiliani N., Shabanowitz J., Hunt D. F., Jerez C. A. 2006; Genomics, metagenomics and proteomics in bioming microorganisms. Biotechnol Adv 24:197–211
     [Google Scholar]
  53. van Belkum A., Struelens M., Quint W. 1993; Typing of Legionella pneumophila strains by polymerase chain reaction-mediated DNA fingerprinting. J Clin Microbiol 31:2198–2200
     [Google Scholar]
  54. Venegas A., Hevia E., Sanchez H. 1988; Sequence of two tRNA genes from a Thiobacillus ferrooxidans ribosomal operon. Nucleic Acids Res 16:8179
     [Google Scholar]
  55. Versalovic J., Koeuth T., Lupski J. R. 1991; Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831
     [Google Scholar]
  56. Welsh J., McClelland M. 1990; Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218
     [Google Scholar]
  57. Williams J. G. K., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. 1990; DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
     [Google Scholar]
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16S rDNA and 16S–23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Acidithiobacillus phylogeny
Microbiology 154, 2397 (2008); https://doi.org/10.1099/mic.0.2007/016295-0
/content/journal/micro/10.1099/mic.0.2007/016295-0
/content/journal/micro/10.1099/mic.0.2007/016295-0
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