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Volume 136, Issue 1

16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs Free

Abstract

16S ribosomal RNAs (rRNA) of 12 methylotrophic bacteria have been almost completely sequenced to establish their phylogenetic relationships. Methylotrophs that are physiologically related are phylogenetically diverse and are scattered among the purple eubacteria (class Proteobacteria). Group I methylotrophs can be classified in the -and the γ-subdivisions and group II methylotrophs in the α-subdivision of the purple eubacteria, respectively. Pink-pigmented facultative and non-pigmented obligate group II methylotrophs form two distinctly separate branches within the α-subdivision. The secondary structures of the 16S rRNA sequences of ‘’ strain OBBP, ‘’ strain OB3b, ‘’ strain 81Z and sp. strain DM2 are similar, and these non-pigmented obligate group II methylotrophs form one tight cluster in the α-subdivision. The pink-pigmented facultative methylotrophs, strain AM1, sp. strain DM4 and strain XX form another cluster within the α-subdivision. Although similar in phenotypic characteristics, strain XX and strain AM1 are clearly distinguishable by their 16S rRNA sequences. The group I methylotrophs, strain AS1 and methylotrophic species DM11, which do not utilize methane, are similar in 16S rRNA sequence to bacteria in the -subdivision. The methane-utilizing, obligate group I methanotrophs, strain BATH and , are placed in the γ-subdivision. The results demonstrate that it is possible to distinguish and classify the methylotrophic bacteria using 16S rRNA sequence analysis.

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© Society for General Microbiology 1990
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1990-01-01
2024-04-18
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References

  1. Anthony C. 1982 Biochemistry of Methylotrophs. New York: Academic Press;
     [Google Scholar]
  2. Chumakov K. M. 1987; Evolution of nucleotide sequences. Soviet Scientific Reviews, Section D, Physicochemical Biology 7:51–94
     [Google Scholar]
  3. Dalton H., Whittenbury R. 1976; The acetylene reduction technique as an assay for nitrogenase activity in the methane oxidizing bacterium Methylococcus capsulatus strain BATH. Archives of Microbiology 109:147–151
     [Google Scholar]
  4. De Soete G. 1983; A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48:621–626
     [Google Scholar]
  5. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368–376
     [Google Scholar]
  6. Fox G. E., Stackebrandt E., Hespell R. B., Gibson J., Maniloff J., Dyer T. A., Wolfe R. S., Balch W. E., Tanner R. S., Magrum L. J., Zablen L. B., Blakemore R., Gupta R., Bonen L., Lewis B. J., Stahl D. A., Luehrsen K. R., Chen K. N., Woese C. R. 1980; The phylogeny of prokaryotes. Science 209:457–463
     [Google Scholar]
  7. Gibson J., Stackebrandt E., Zablen L., Gupta R., Woese C. R. 1979; A phylogenetic analysis of the purple photosynthetic bacteria. Current Microbiology 3:59–64
     [Google Scholar]
  8. Green P. N., Bousfield I. J. 1981; The taxonomy of the pink-pigmented facultatively methylotrophic bacteria. In Microbial Growth on C-l Compounds pp 285–293 Dalton H. Edited by London: Heyden;
     [Google Scholar]
  9. Green P. N., Bousfield I. J. 1982; A taxonomic study of some Gram-negative facultatively methylotrophic bacteria. Journal of General Microbiology 128:623–638
     [Google Scholar]
  10. Green P. N., Gibson D. M. 1984; Carbohydrate metabolism in some methylotrophic bacteria. FEMS Microbiology Letters 23:31–34
     [Google Scholar]
  11. Higgins I. J., Aston W. J., Best D. J., Turner A.O.F., Jezequel S. G., Hill H.A.O. 1984; Applied aspects of methylotrophs: bioelectrochemical applications, purification of methanol dehydrogenase, and mechanism of methane monooxygenase. In Microbial Growth on C1 Compounds.Proceedings of the 4th International Symposium, pp 297–305 Crawford R. L., Hanson R. S. Edited by Washington, DC: American Society for Microbiology;
     [Google Scholar]
  12. Hori H., Osawa S. 1979; Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 54 5S rRNA species. Proceedings of the National Academy of Sciences of the United States of America 76:381–385
     [Google Scholar]
  13. Ingraham J. L., Maaloe O., Neidhardt F. C. 1983 Growth of the Bacterial Cell, pp 12–107 Sunderland, Massachusetts: Sinauer;
     [Google Scholar]
  14. Jenkins O., Jones D. 1987; Taxonomic studies on some Gramnegative methylotrophic bacteria. Journal of General Microbiology 133:453–473
     [Google Scholar]
  15. Jukes T. H., Canter C. R. 1969; Evolution of protein molecules. In Mammalian Protein Metabolism, pp 21–132, Muro H. N. Edited by New York: Academic Press;
     [Google Scholar]
  16. Kohler-Staub D., Hartmens S., Gälli R., Suter F., Leisinger T. 1987; Evidence for identical dichloromethane dehydrogenases in different methylotrophic bacteria. Journal of General Microbiology 132:2837–2843
     [Google Scholar]
  17. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. 1985; Rapid determination of 16S ribosomal RNA sequences for phylogenetic analysis. Proceedings of the National Academy of Sciences of the United States of America 82:6955–6959
     [Google Scholar]
  18. Olsen G. J. 1983 Comparative analysis of nucleotide sequence data. PhD thesis, Health Sciences Center, University of Colorado
    [Google Scholar]
  19. Olsen G. J., Lane D. J., Giovannoni S. J., Pace N. R. 1986; Microbial ecology and evolution: a ribosomal RNA approach. Annual Review of Microbiology 40:337–365
     [Google Scholar]
  20. Pace N. R., Stahl D. A., Lane D. J., Olsen G. J. 1986; The analysis of natural microbial populations by ribosomal RNA sequences. Advances in Microbial Ecology 9:1–55
     [Google Scholar]
  21. Patt T. E., Cole G. C., Bland J., Hanson R. S. 1974; Isolation and characterization of bacteria that grow on methane and organic compounds as sole sources of carbon and energy. Journal of Bacteriology 120:955–964
     [Google Scholar]
  22. Patt T. E., Cole G. C., Hanson R. S. 1976; Methylobacterium, a new genus of facultatively methylotrophic bacteria. International Journal of Systematic Bacteriology 26:226–229
     [Google Scholar]
  23. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74:5463–5467
     [Google Scholar]
  24. Scholtz R., Wackett , Egli C., Cook A. M., Leisinger T. 1988; Dichloromethane dehalogenase with improved catalytic activity isolated from a fast-growing dichloromethane-utilizing bacterium. Journal of Bacteriology 170:5698–5704
     [Google Scholar]
  25. Stackebrandt E., Murray , Trüper H. G. 1988; Proteobacteria classis nov., a name for the phylogenetic taxon that includes the ‘purple bacteria and their relatives’. International Journal of Systematic Bacteriology 38:321–325
     [Google Scholar]
  26. Stahl D. A., Lane D. J., Olsen G. J., Pace N. R. 1984; Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224:409–411
     [Google Scholar]
  27. Whittenbury R., Dalton H. 1980; The methylotrophic bacteria. In The Prokaryotes pp. 894–902 Edited by Starr M. P., Stolp H., Truper H. G. New York: Springer-Verlag;
     [Google Scholar]
  28. Whittenbury R., Dalton H. 1983; The obligate methane-oxidizing bacteria and their biotechnological potential. In Basic Biology of New Developments in Biotechnology, pp 439–460 Hollaender A., Laskin A. I., Rogers P. Edited by New York: Plenum Press;
     [Google Scholar]
  29. Whittenbury R., Krieg N. R. 1984; Methylococcaceae. In Bergey’s, Manual of Systematic Bacteriology, 1 pp 256–261 Krieg N. R. Edited by Baltimore: Williams & Wilkins;
     [Google Scholar]
  30. Whittenbury R., Phillips K. C., Wilkinson J. F. 1970; Enrichment, isolation and some properties of methane-utilizing bacteria. Journal of General Microbiology 61:205–218
     [Google Scholar]
  31. Woese C. R. 1987; Bacterial evolution. Microbiological Reviews 51:221–271
     [Google Scholar]
  32. Woese C. R., Stackebrandt E., Weisburg W. G., Paster B. J., Madigan M. T., Fowler V. J., Hahn C. M., Blanz P., Gupta R., Nealson K. H., Fox G. E. 1984a; The phylogeny of purple bacteria: the alpha subdivision. Systematic and Applied Microbiology 5:315–326
     [Google Scholar]
  33. Woese C. R., Weisburg , Paster B. J., Hahn C. M., Tanner R. S., Krieg N. R., Koops H. P., Harms H., Stackebrandt E. 1984b; The phylogeny of purple bacteria: the beta subdivision. Systematic and Applied Microbiology 5:327–336
     [Google Scholar]
  34. Woese C. R., Weisburg W. G., Hahn C. M., Paster B. J., Zablen L. B., Lewis B. J., Macke T. J., Ludwig W., Stackebrandt E. 1985; The phylogeny of purple bacteria: the gamma subdivision. Systematic and Applied Microbiology 6:25–33
     [Google Scholar]
  35. Wolfrum T., Stolp H. 1987; Comparative studies on 5S RNA sequences of RuMP-type methylotrophic bacteria. Systematic and Applied Microbiology 9:273–276
     [Google Scholar]
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16S ribosomal RNA sequence analysis for determination of phylogenetic relationship among methylotrophs
Microbiology 136, 1 (1990); https://doi.org/10.1099/00221287-136-1-1
/content/journal/micro/10.1099/00221287-136-1-1
/content/journal/micro/10.1099/00221287-136-1-1
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