1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 44, Issue 2

A Phylogenetic Analysis of the Family and the Genera and with 16S rRNA Sequences and a Proposal To Combine the Genera and in an Emended Genus Free

Abstract

Abstract

The 16S rRNAs of 15 species of actinomycetes belonging to the genera and and the family including and species, were sequenced by using reverse transcriptase. The sequences were analyzed along with the sequences of reference actinomycetes by using distance matrix and parsimony methods. The wall chemotype IV genus was found to be closely related to species of the genus which have chemotype III walls. Together, these two genera formed a clade which was closely related to members of the family which have chemotype IV walls. However, the phylogenetic branching pattern did not unambiguously resolve whether the members of all three taxa should be placed in a single family. We suggest, therefore, that the genera and should remain outside the family until additional sequence or phenotypic data are available to decide the issue. The sequences of species belonging to the genera and were always recovered as a mixed group in phylogenetic trees, and we propose that these organisms should be classified in an emended genus This proposal is strongly supported by previously published lipid, ribosomal protein, and ultrastructure data.

  • Published Online:
Copyright 1994, International Union of Microbiological Societies
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-44-2-293
1994-04-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/44/2/ijs-44-2-293.html?itemId=/content/journal/ijsem/10.1099/00207713-44-2-293&mimeType=html&fmt=ahah

References

  1. Bowen T., Stackebrandt E., Dorsch M., Embley T. M. 1989; The phylogeny of Amycolata autotrophica, Kibdelosporangium ari- dum and Saccharothrix australiensis. J. Gen. Microbiol. 135 2529 2536
    [Google Scholar]
  2. Brosius J., Palmer J. L., Kennedy J. P., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75 4801 4805
    [Google Scholar]
  3. Collins M. D., Jones D. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45 316 354
    [Google Scholar]
  4. Collins M. D., Kroppenstedt R. M., Tamaoka J., Komagata K., Kinoshita T. 1988; Structures of the tetrahydrogenated menaquinones from Actinomadura angiospora, Faenia rectivirgula and Saccharothrix australiensis. Curr. Microbiol. 17 275 279
    [Google Scholar]
  5. Collins M. D., Smida J., Dorsch M., Stackebrandt E. 1988; Tsukamurella gen. nov. harboring Corynebacterium paurometabolum and Rhodococcus aurantiacus. Int. J. Syst. Bacteriol. 38 385 391
    [Google Scholar]
  6. Collins M. D., Smida J., Stackebrandt E. 1990; Phylogenetic evidence for the transfer of Caseobacter polymorphus (Crombach) to the genus Corynebacterium. Int. J. Syst. Bacteriol. 39 7 9
    [Google Scholar]
  7. DeBoer L., Dijkhuizen L., Grobben G., Goodfellow M., Stackebrandt E., Parlett J. H., Whitehead D., Witt D. 1990; Amycolatopsis methanolica sp. nov., a facultatively methylotrophic actinomycete. Int. J. Syst. Bacteriol. 40 194 204
    [Google Scholar]
  8. DeBorde D. C., Naeve C. W., Herlocher M. L., Maassab H. F. 1986; Resolution of a common RNA sequencing ambiguity by terminal deoxynucleotidyl transferase. Anal. Biochem. 157 275 282
    [Google Scholar]
  9. Embley T. M. 1991; The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett. Appl. Microbiol. 13 171 174
    [Google Scholar]
  10. Embley T. M. 1992; The family Pseudonocardiaceae,. 996 1027 Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. The prokaryotes Springer Verlag; Berlin:
    [Google Scholar]
  11. Embley T. M., O’Donnell A. G., Rostron J., Goodfellow M. 1988; Chemotaxonomy of wall type IV actinomycetes which lack mycolic acids. J. Gen. Microbiol. 134 953 960
    [Google Scholar]
  12. Embley T. M., Smida J., Stackebrandt E. 1988; Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, three wall type IV actinomycetes which lack mycolic acids. J. Gen. Microbiol. 134 961 966
    [Google Scholar]
  13. Embley T. M., Smida J., Stackebrandt E. 1988; The phylogeny of mycolateless wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst. Appl. Microbiol. 11 44 52
    [Google Scholar]
  14. Evtushenko L. I., Akimov V. N., Dobritsa S. V., Taptykova S. D. 1989; A new species of actinomycete, Amycolata alni. Int. J. Syst. Bacteriol. 39 72 77
    [Google Scholar]
  15. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783 791
    [Google Scholar]
  16. Felsenstein J. 1993 PHYLIP (phylogenetic inference package) version 3.5c Department of Genetics, University of Washington; Seattle:
    [Google Scholar]
  17. Felsenstein J., Kishino H. 1993; Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42 193 200
    [Google Scholar]
  18. Fox G., Stackebrandt E. 1987; The application of 16S rRNA cataloguing and 5S rRNA sequencing in bacterial systematics. Methods Microbiol. 19 405 458
    [Google Scholar]
  19. Fiy N. K., Warwick S., Saunders N. A., Embley T. M. 1991; The use of ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae. J. Gen. Microbiol. 137 1215 1222
    [Google Scholar]
  20. Goodfellow M., Cross T. 1984; Classification,. 7 146 Goodfellow M., Mordarski M., Williams S. T. The biology of the actinomycetes Academic Press; London:
    [Google Scholar]
  21. Goodfellow M., Lacey J., Athalye M., Embley T. M., Bowen T. 1989; Saccharopolyspora gregorii and Saccharopolyspora hordei: two new actinomycete species from fodder. J. Gen. Microbiol. 135 2125 2139
    [Google Scholar]
  22. Greiner-Mai E., Korn-Wendisch F., Kutzner H. J. 1988; Taxonomic revision of the genus Saccharomonospora and description of Saccharomonospora glauca sp. nov. Int. J. Syst. Bacteriol. 38 398 405
    [Google Scholar]
  23. Greiner-Mai E., Kroppenstedt R. M., Korn-Wendisch F., Kutzner H. J. 1987; Morphological and biochemical characterisation and emended descriptions of thermophilic actinomycete species. Syst. Appl. Microbiol. 9 97 109
    [Google Scholar]
  24. Grund E., Kroppenstedt R. 1989; Transfer of five Nocardiopsis species to the genus Saccharothrix Labeda et al. 1984. Syst. Appl. Microbiol. 12 267 274
    [Google Scholar]
  25. Hasegawa T. 1988; Actinokineospora: a new genus of the Actinomycetales. Actinomycetologica 2 31 45
    [Google Scholar]
  26. Henssen A. 1957; Beitrage zur Morphologie und Systematik der thermophilen Actinomyceten. Arch. Mikrobiol. 26 373 414
    [Google Scholar]
  27. Henssen A., Happach-Kasan C., Renner B., Vobis G. 1983; Pseudonocardia compacta sp. nov. Int. J. Syst. Bacteriol. 33 829 836
    [Google Scholar]
  28. Henssen A., Kothe H. W., Kroppenstedt R. M. 1987; Transfer of Pseudonocardia azurea and “Pseudonocardia fastidiosa” to the genus Amycolatopsis with emended species descriptions. Int. J. Syst. Bacteriol. 37 292 295
    [Google Scholar]
  29. Henssen A., Schafer D. 1971; Emended description of the genus Pseudonocardia Henssen and description of a new species, Pseudonocardia spinosa Schafer. Int. J. Syst. Bacteriol. 21 29 34
    [Google Scholar]
  30. Hillis D. M., Bull J. J. 1993; An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42 182 192
    [Google Scholar]
  31. Hirsch P. 1960; Einige weitere von Luftverunreinigungen lebende Actinomyceten und ihre Klassifizierung. Arch. Mikrobiol. 35 391 414
    [Google Scholar]
  32. Johnson K. G., Lanthier P. H., Gochnauer M. B. 1986; Cell walls from Actinopolyspora halophila, an extremely halophilic actinomycete. Arch. Microbiol. 143 365 369
    [Google Scholar]
  33. Jukes T. H., Cantor C. R. 1969; Evolution of protein molecules,. 21 132 Munro H. N. Mammalian protein metabolism Academic Press; New York:
    [Google Scholar]
  34. Kothe H. W., Vobis G., Kroppenstedt R. M., Henssen A. 1989; A taxonomic study of mycolateless, wall chemotype IV actinomycetes. Syst. Appl. Microbiol. 12 61 69
    [Google Scholar]
  35. Kroppenstedt R. M. 1985; Fatty acids and menaquinone analysis of actinomycetes and related organisms,. 173 189 Goodfellow M., Minnikin D. E. Chemical methods in bacterial systematics Academic Press; London:
    [Google Scholar]
  36. Labeda D. P., Lechevalier M. P. 1989; Amendment of the genus Saccharothrix Labeda et al. 1984 and descriptions of Saccharothrix espanaensis sp. nov., Saccharothrix cryophilis sp. nov., and Saccharothrix mutabilis comb. nov. Int. J. Syst. Bacteriol. 39 420 423
    [Google Scholar]
  37. Labeda D. P., Testa R. T., Lechevalier M. P., Lechevalier H. A. 1984; Saccharothrix•. a new genus of the Actinomycetales related to Nocardiopsis. Int. J. Syst. Bacteriol. 34 426 431
    [Google Scholar]
  38. Lacey J. 1971; The microbiology of moist barley storage in unsealed silos. Ann. Appl. Biol. 69 187 212
    [Google Scholar]
  39. Lane D. J., Field K., Olsen G. J., Pace N. R. 1988; Reverse transcriptase sequencing of ribosomal RNA for phylogenetic analysis. Methods Enzymol. 167 138 144
    [Google Scholar]
  40. Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. 1993; The ribosomal database project. Nucleic Acids Res. 21 3021 3023
    [Google Scholar]
  41. Lechevalier H. A. 1989; A practical guide to generic identification of actinomycetes,. 2344 2347 Williams S. T., Sharpe M. E., Holt J. G. Bergey’s manual of systematic bacteriology 4 Williams & Wilkins; Baltimore:
    [Google Scholar]
  42. Lechevalier M. P., De Bievre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem. Syst. Ecol. 5 249 260
    [Google Scholar]
  43. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int. J. Syst. Bacteriol. 20 435 443
    [Google Scholar]
  44. Lechevalier M. P., Prauser H., Labeda D. P., Ruan J. S. 1986; Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int. J. Syst. Bacteriol. 36 29 37
    [Google Scholar]
  45. McVeigh H., Embley T. M. Unpublished data
  46. Mertz F. P., Yao R. C. 1990; Saccharopolyspora spinosa sp, nov. isolated from soil collected from a sugar mill rum still. Int. J. Syst. Bacteriol. 40 34 39
    [Google Scholar]
  47. Nonomura H., Takagi S. 1977; Distribution of actinoplanetes in soils of Japan. J. Ferment. Technol. 55 423 428
    [Google Scholar]
  48. Ochi K., Yoshida M. 1991; Polyacrylamide gel electrophoresis analysis of mycolateless wall chemotype IV actinomycetes. Int. J. Syst. Bacteriol. 41 402 405
    [Google Scholar]
  49. Rogall T., Wolters J., Flohr T., Bottger E. C. 1990; Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int. J. Syst. Bacteriol. 40 323 330
    [Google Scholar]
  50. Runmao H. 1987; Saccharomonospora azurea sp. nov., a new species of the genus Saccharomonospora. Int. J. Syst. Bacteriol. 37 60 61
    [Google Scholar]
  51. Runmao H., Lin C., Guizhen W. 1988; Saccharomonospora cyanea sp. nov. Int. J. Syst. Bacteriol. 38 444 446
    [Google Scholar]
  52. Saitou N., Nei M. 1987; The neighbour joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4 406 425
    [Google Scholar]
  53. Schatz A., Isenberg H. D., Angrist A., Schatz V. 1954; Microbial metabolism of carbamates. I. Isolation of Streptomyces nitrificans spec, nov., and other organisms which grow on urethane. J. Bacteriol. 68 1 4
    [Google Scholar]
  54. Shearer M. C., Colman P. M., Ferrin R. M., Nisbet L. J., Nash C. H. 1986; New genus of the Actinomycetales: Kibdelosporangium aridum gen. nov., sp. nov. Int. J. Syst. Bacteriol. 36 47 54
    [Google Scholar]
  55. Stackebrandt E., Smida J., Collins M. D. 1988; Evidence of phylogenetic heterogeneity within the genus Rhodococcus: revival of the genus Gordona (Tsukamura). J. Gen. Appl. Microbiol. 34 341 348
    [Google Scholar]
  56. Stahl D. A., Urbance J. W. 1990; The division between fast-and slow-growing species corresponds to natural relationships among the mycobacteria. J. Bacteriol. 172 116 124
    [Google Scholar]
  57. Swofford D. 1993 PAUP: phylogenetic analysis using parsimony, version 3.1.1 Illinois Natural History Survey; Champaign:
    [Google Scholar]
  58. Takeuchi M., Nishii T., Yokota A. 1992; Taxonomic significance of arabinose in the family Pseudonocardiaceae. Actinomycetologica 6 79 90
    [Google Scholar]
  59. Wallace D. M. 1987; Large- and small-scale phenol extractions. Methods Enzymol. 152 33 41
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-44-2-293
Loading
A Phylogenetic Analysis of the Family Pseudonocardiaceae and the Genera Actinokineospora and Saccharothrix with 16S rRNA Sequences and a Proposal To Combine the Genera Amycolata and Pseudonocardia in an Emended Genus Pseudonocardia
Int J Syst Evol Microbiol 44, 293 (1994); https://doi.org/10.1099/00207713-44-2-293
/content/journal/ijsem/10.1099/00207713-44-2-293
/content/journal/ijsem/10.1099/00207713-44-2-293
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error