Skip to main content
SpringerLink
Log in

Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997

  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

The taxonomic position of acidophilic actinomycetes selectively isolated from acidic soils and litter was examined using a polyphasic approach. The distinct 16S rDNA phyletic branch formed by representative strains was equated with related monophyletic clades that corresponded to the genera Kitasatospora and Streptomyces. The acidophilic isolates also exhibited a distinctive pH profile, a unique 16S rDNA signature, and contained major amounts of LL-diaminopimelic acid, galactose and rhamnose in whole-organism hydrolysates. It is proposed that these acidophilic actinomycetes be assigned to a new genus, Streptacidiphilus gen. nov., on the basis of genotypic and phenotypic differences. Three species were defined on the basis of DNA:DNA pairing and phenotypic data, namely, Streptacidiphilus albus sp. nov., the type species, Streptacidiphilus neutrinimicus sp. nov. and Streptacidiphilus carbonis sp. nov. Members of the genera Kitasatospora, Streptacidiphilus and Streptomyces share a number of key characteristics and form a stable monophyletic branch in the 16S rDNA tree. It is, therefore, proposed that the description of the family Streptomycetaceae be emended to account for properties shown by Kitasatospora and Streptacidiphilus species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Brosius J., Palmer M.L., Kennedy P.J. and Noller H.F. 1978. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75: 4801–4805.

    Article  PubMed  CAS  Google Scholar 

  • Chun J. 1995. Computer-assisted classification and identification of actinomycetes, PhD University of Newcastle, Newcastle upon Tyne.

    Google Scholar 

  • Corke C.T. and Chase F.E. 1964. Comparative studies of actinomycete populations in acid podzolic and neutral mull forest soils. Proc. Soil Sci. Soc. Am. 28: 68–70.

    Article  Google Scholar 

  • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368–376.

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791.

    Article  Google Scholar 

  • Felsenstein J. 1993. PHYLIP (phylogenetic inference package), version 3.5c. Department of Genetics, University of Washington, Seattle.

    Google Scholar 

  • Fitch W.M. and Margoliash E. 1967. Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155: 279–284.

    PubMed  CAS  Google Scholar 

  • Flowers T.H. and Williams S.T. 1977. Nutritional requirements of acidophilic streptomycetes. Soil. Biol. Biochem. 9: 225–226.

    Article  CAS  Google Scholar 

  • Goodfellow M. and Dawson D. 1978. Qualitative and quantitative studies of bacteria colonizing Picea sitchensis litter. Soil. Biol. Biochem. 10: 303–307.

    Article  Google Scholar 

  • Goodfellow M. and Simpson K.E. 1987. Ecology of streptomycetes. Frontiers Appl. Microbiol. 2: 97–125.

    Google Scholar 

  • Goodfellow M. and Williams S.T. 1983. Ecology of actinomycetes. Ann. Rev. Microbiol. 37: 189–216.

    Article  CAS  Google Scholar 

  • Hagedorn C. 1976. Influences of soil acidity on Streptomyces populations inhabiting forest soils. Appl. Environ. Microbiol. 32: 368–375.

    PubMed  CAS  Google Scholar 

  • Jensen H.L. 1928. Actinomyces acidophilus n. sp. – a group of acidophilus actinomycetes isolated from the soil. Soil Sci. 25: 225–236.

    CAS  Google Scholar 

  • Jones K.L. 1949. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J. Bacteriol. 57: 141–145.

    PubMed  CAS  Google Scholar 

  • Jukes T.H. and Cantor C.R. 1969. Evolution of protein molecules. In: Munro H.N. (ed.), Mammalian Protein Metabolism Vol. 3. Academic Press, New York, pp. 21–213.

    Google Scholar 

  • Kelly K.L. 1958. Centroid notations for the revised ISCC-NBS color name blocks. J. Res. Nat. Bur. Standards USA 61: 427.

    Google Scholar 

  • Khan M.R. and Williams S.T. 1975. Studies on the ecology of actinomycetes in soil-VIII. Distribution and characteristics of acidophilic actinomycetes. Soil Biol. Biochem. 7: 345–348.

    Article  Google Scholar 

  • Kim B., Sahin N., Minnikin D.E., Zakrzewska-Czerwinska J., Mordarski M. and Goodfellow M. 1999. Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalcalitolerans sp nov. Int. J. Syst. Bacteriol. 49: 7–17.

    PubMed  Google Scholar 

  • Kim D., Chun J., Sahin N., Hah Y.C. and Goodfellow M. 1996. Analysis of thermophilic clades within the genus Streptomyces by 16S ribosomal DNA sequence comparisons. Int. J. Syst. Bacteriol. 46: 581–587.

    CAS  Google Scholar 

  • Kim S.B. and Goodfellow M. 1999. Reclassification of Amycolatopsis rugosa Lechevalier (1986) as Prauserella rugosa gen. nov., comb. nov. Int. J. Syst. Bacteriol. 49: 507–512.

    PubMed  Google Scholar 

  • Kim S.B., Falconer C., Williams E. and Goodfellow M. 1998. Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int. J. Syst. Bacteriol. 48: 59–68.

    PubMed  Google Scholar 

  • Kim S.B., Brown R., Oldfield C., Gilbert S.C. and Goodfellow M. 1999. Gordonia desulfuricans sp. nov., a benzothiophene-de-sulphurizing actinomycete. Int. J. Syst. Bacteriol. 49: 1845–1851.

    PubMed  CAS  Google Scholar 

  • Kluge A.G. and Farris F.S. 1969. Quantitative phyletics and the acevolution of anurans. Syst. Zool. 18: 1–32.

    Article  Google Scholar 

  • Kroppenstedt R.M. 1985. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In: Goodfellow M. and Minnikin D.E. (eds), Chemical Methods in Bacterial Systematics. Academic Press, London, pp. 173–199.

    Google Scholar 

  • Labeda D.P. 1988. Kitasatosporia mediocidica sp. nov. Int. J. Syst. Bacteriol. 38: 287–290.

    Google Scholar 

  • Labeda D.P. 1993. DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. Int. J. Syst. Bacteriol. 43: 822–825.

    Google Scholar 

  • Labeda D.P. 1998. DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. Int. J. Syst. Bacteriol. 48: 829–832.

    CAS  Google Scholar 

  • Lechevalier M.P., de Biévre C. and Lechevalier H.A. 1977. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem. Syst. Ecol. 5: 249–260.

    Article  CAS  Google Scholar 

  • Lonsdale J.T. 1985. Aspects of the biology of acidophilic actinomycetes, PhD University of Newcastle, Newcastle upon Tyne.

    Google Scholar 

  • Mikami Y., Miyashita K. and Arai T. 1982. Diaminopimelic acid profiles of alkalophilic and alkaline-resistant strains of actinomycetes. J. Gen. Microbiol. 128: 1709–1712.

    PubMed  CAS  Google Scholar 

  • Minnikin D.E., Hutchinson I.G., Caldicott A.B. and Goodfellow M. 1980. Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. J. Chromatogr. 188: 221–233.

    Article  CAS  Google Scholar 

  • Minnikin D.E., O'Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A. et al. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2: 233–241.

    Article  CAS  Google Scholar 

  • Nakagaito Y., Yokota A. and Hasegawa T. 1992. Three new characspecies of the genus Streptomyces:Streptomyces cochleatus sp. nov., Streptomyces paracochleatus sp. nov., and Streptomyces azaticus sp. nov. J. Gen. Appl. Microbiol. 38: 105–120.

    CAS  Google Scholar 

  • National Bureau of Standards 1964. The ISCC-NBS Color Manual Charts Illustrated with Centroid Colours. Supplement to NBS, Circular 553.

  • O'Donnell A.G., Falconer C., Goodfellow M., Ward A.C. and Williams E. 1993. Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie Leeuwenhoek 64: 325–340.

    Article  PubMed  Google Scholar 

  • Ōmura S., Takahashi Y., Iwai Y. and Tanaka H. 1982. Kitasatosporia, a new genus of the order Actinomycetales. J. Antibiotics 35: 1013–1019.

    Google Scholar 

  • Ōmura S., Takahashi Y. and Iwai Y. 1989. Genus Kitasatosporia Ōmura et al. (1983), 672VP. In: Williams S.T., Sharpe M.E. and Holt J.G. (eds), Bergey's Manual of Systematic Bacteriology Vol. 4. Williams & Wilkins, Baltimore, pp. 2594–2598.

    Google Scholar 

  • Park Y.-H., Yim D.-G., Kim E., Kho Y.-H., Mheen T.-I., Lonsdale J. et al. 1991. Classification of acidophilic, neutrotolerant and neutrophilic streptomycetes by nucleotide sequencing of 5S ribosomal RNA. J. Gen. Microbiol. 137: 2265–2269.

    PubMed  CAS  Google Scholar 

  • Sahin N. 1995. Selective isolation, characterisation and classification of novel thermotolerant streptomycetes, PhD University of Newcastle, Newcastle upon Tyne.

    Google Scholar 

  • Saitou N. and Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.

    PubMed  CAS  Google Scholar 

  • Sembiring L., Ward A.C. and Goodfellow M. 2000. Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria. Antonie Leeuwenhoek 78: 353–366.

    Article  PubMed  CAS  Google Scholar 

  • Seong C.N., Goodfellow M., Ward A.C. and Hah Y.C. 1993. Numerical classification of acidophilic actinomycetes isolated from acid soil in Korea. Kor. J. Microbiol. 31: 355–363.

    CAS  Google Scholar 

  • Seong C.N., Park S.K., Goodfellow M., Kim S.B. and Hah Y.C. 1995. Construction of probability identification matrix and selective medium for acidophilic actinomycetes using numerical classification data. J. Microbiol. 33: 95–102.

    Google Scholar 

  • Shirling E.B. and Gottlieb D. 1966. Methods for characterization of Streptomyces species. Int. J. Syst. Bacteriol. 16: 313–340.

    Article  Google Scholar 

  • Shirling E.B. and Gottlieb D. 1976. Retrospective evaluation of International Streptomyces Project taxonomic criteria. In: Arai T. (ed.), Actinomycetes: The Boundary Microorganisms. University Park Press, Baltimore, pp. 9–41.

    Google Scholar 

  • Staneck J.L. and Roberts G.D. 1974. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl. Microbiol. 28: 226–231.

    PubMed  CAS  Google Scholar 

  • Stackebrandt E., Rainey F.A. and Ward-Rainey N.L. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47: 479–491.

    Google Scholar 

  • Takahashi Y., Iwai Y. and Ōmura S. 1983. Relationship between cell morphology and the types of diaminopimelic acid in Kitasatosporia setalba. J. Gen. Appl. Microbiol. 29: 459–465.

    CAS  Google Scholar 

  • Takahashi Y., Iwai Y. and Ōmura S. 1984. Two new species of the genus Kitasatosporia, Kitasatosporia phosalacinea sp. nov. and Kitasatosporia griseola sp. nov. J. Gen. Microbiol. 30: 377–387.

    CAS  Google Scholar 

  • Tamura T., Suzuki S. and Hatano K. 2000a. Arcocarpospora gen. nov., a new genus of the order Actinomycetales. Int. J. Syst. Evol. Microbiol. 50: 1163–1171.

    PubMed  CAS  Google Scholar 

  • Tamura T., Liu Z., Zhang Y. and Hatano K. 2000b. Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 50: 1435–1440.

    PubMed  CAS  Google Scholar 

  • Waksman S.A. and Henrici A.T. 1943. The nomenclature and classification of the actinomycetes. J. Bacteriol. 46: 337–341.

    PubMed  CAS  Google Scholar 

  • Wayne L.G., Brenner D.J. and Colwell R.R., & 9 other authors 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463–464.

    Google Scholar 

  • Wellington E.M.H., Stackebrandt E., Sanders D., Wolstrup J. and Jorgensen N.O.G. 1992. Taxonomic status of Kitasatosporia and proposed unification with Streptomyces on the basis of phenotypic and 16S rRNA analysis and emendation of Strep tomycesWaksman and Henrici (1943), 339AL. Int. J. Syst. Bacteriol. 42: 156–160.

    PubMed  CAS  Google Scholar 

  • Williams S.T. and Khan M.R. 1974. Antibiotics – a soil microbiologist's viewpoint. Post. Hig. I. Med. Dosw. 28: 395–408.

    CAS  Google Scholar 

  • Williams S.T. and Flowers T.H. 1978. The influence of pH on starch hydrolysis by neutrophilic and acidophilic actinomycetes. Microbios 20: 99–106.

    PubMed  CAS  Google Scholar 

  • Williams S.T. and Robinson C.S. 1981. The role of streptomycetes in decomposition of chitin in acidic soils. J. Gen. Microbiol. 127: 55–63.

    CAS  Google Scholar 

  • Williams S.T., Davies F.L., Mayfield C.I. and Khan M.R. 1971. Studies on the ecology of actinomycetes in soil II. The pH requirements of streptomycetes from two acid soils. Soil. Biol. Biochem. 3: 187–195.

    Article  CAS  Google Scholar 

  • Williams S.T., Goodfellow M., Alderson G., Wellington E.M.H., Sneath P.H.A. and Sackin M.J. 1983. Numerical classification of Streptomyces and related genera. J. Gen. Microbiol. 129: 1743–1813.

    PubMed  CAS  Google Scholar 

  • Williams S.T., Lanning S. and Wellington E.M.H. 1984. Ecology of actinomycetes. In: Goodfellow M., Mordarski M. and Williams S.T. (eds), The Biology of the Actinomycetes. Academic Press, London, pp. 481–528.

    Google Scholar 

  • Williams S.T., Goodfellow M. and Alderson G. 1989. Genus Streptomyces Waksman and Henrici (1943), 339AL. In: Williams S.T., Sharpe M.E. and Holt J.G. (eds), Bergey's Manual of Systematic Bacteriology Vol. 4. Williams Wilkins, Baltimore, pp. 2594–2598.

    Google Scholar 

  • Zhang Z., Wang Y. and Ruan J. 1997. A proposal to revive the genus Kitasatospora (Ōmura et al. 1982). Int. J. Syst. Bacteriol. 47: 1048–1054.

    PubMed  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Seung Bum Kim

    Present address: Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 52 Oun-Dong, Yusong, Daejon, 305-333, Republic of Korea

Authors and Affiliations

  1. Department of Agricultural and Environmental Science, University of Newcastle, Newcastle upon Tyne, NE1 7RU, UK

    Seung Bum Kim, John Lonsdale, Chi-Nam Seong & Michael Goodfellow

  2. Department of Biology, Suncheon National University, Suncheon, Republic of Korea

    Chi-Nam Seong

Authors
  1. Seung Bum Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John Lonsdale
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chi-Nam Seong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael Goodfellow
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Seung Bum Kim.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, S.B., Lonsdale, J., Seong, CN. et al. Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae (Waksman and Henrici (1943)AL) emend. Rainey et al. 1997. Antonie Van Leeuwenhoek 83, 107–116 (2003). https://doi.org/10.1023/A:1023397724023

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1023397724023

Search

Navigation