Skip to main content

Advertisement

SpringerLink
Log in

Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A novel actinobacterium, designated isolate B204T, was isolated from a marine ascidian Didemnum sp., collected from São Paulo, Brazil, and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Gordonia and formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. It was closely related to Gordonia terrae DSM 43249T (99.9 % 16S rRNA gene sequence similarity) and Gordonia lacunae DSM 45085T (99.3 % 16S rRNA gene sequence similarity) but was distinguished from these strains by a moderate level of DNA–DNA relatedness (63.0 and 54.7 %) and discriminatory phenotypic properties. Based on the data obtained, the isolate B204T (=CBMAI 1069T = DSM 46679T) should therefore be classified as the type strain of a novel species of the genus Gordonia, for which the name Gordonia didemni sp. nov. is proposed.

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

Fig. 1

Similar content being viewed by others

References

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

    Article  CAS  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for specific tree topology. Syst Biol 20:406–416

    Article  Google Scholar 

  • Franzetti A, Caredda P, Ruggeri C, La-Colla P, Tamburini E, Papacchini M, Bestetti G (2009) Potential applications of surface active compounds by Gordonia sp. strain BS29 in soil remediation technologies. Chemosphere 75:801–807

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez JM, Saiz-Jimenez C (2002) A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4:770–773

    Article  CAS  PubMed  Google Scholar 

  • Goodfellow M, Kumar Y, Maldonado LA (2012) Genus 2. Gordonia Tsukamura 1971 emend. Stackebrandt, Smida and Collins 1988 345VP. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds), Bergey’s manual of systematic bacteriology, vol. 5, 2nd edn. The Actinobacteria, Part A. Springer, New York, pp 429–425

  • Gordon RE, Mihm JM (1962) The type species of the genus Nocardia. J Gen Microbiol 27:1–10

    Article  CAS  PubMed  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–123

    Chapter  Google Scholar 

  • Kageyama A, Iida S, Yazawa K, Kudo T, Suzuki S, Koga T, Saito H, Inagawa H, Wada A, Kroppenstedt RM, Mikami Y (2006) Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan. Int J Syst Evol Microbiol 56:1817–1821

    Article  CAS  PubMed  Google Scholar 

  • Kim SB, Brown R, Oldfield C, Gilbert SC, Goodfellow M (1999) Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete. Int J Syst Bacteriol 49:1845–1851

    Article  CAS  PubMed  Google Scholar 

  • Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M (2000) Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 50:2031–2036

    Article  CAS  PubMed  Google Scholar 

  • Kim KK, Lee KC, Klenk HP, Oh HM, Lee JS (2009) Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream. Int J Syst Evol Microbiol 59:1992–1996

    Article  CAS  PubMed  Google Scholar 

  • Kim BY, Stach JEM, Weon HY, Kwon SW, Goodfellow M (2010) Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil. Int J Syst Evol Microbiol 60:1813–1823

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kummer C, Schumann P, Stackebrandt E (1999) Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 49:1513–1522

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Goodfellow M, Stackebrandt E (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–147

    Google Scholar 

  • Le Roes M, Goodwin CM, Meyers PR (2008) Gordonia lacunae sp. nov., isolated from an estuary. Syst Appl Microbiol 31:17–23

    Article  PubMed  Google Scholar 

  • Linos A, Steinbüchel A, Spröer C, Kroppenstedt RM (1999) Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre. Int J Syst Evol Microbiol 49:1785–1791

    CAS  Google Scholar 

  • Menezes CBA, Bonugli-Santos RC, Miqueletto PB, Passarini MRZ, Silva CH, Justo MR, Leal RR, Fantinatti-Garboggini F, Oliveira VM, Berlinck RGS, Sette LD (2010) Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil. Microbiol Res 165:466–482

    Article  PubMed  Google Scholar 

  • Minnikin DE, Alshamaony L, Goodfellow M (1975) Differentiation of Mycobacterium, Nocardia and related taxa by thin-layer-chromatographic analyses of whole-cell methanolysates. J Gen Microbiol 88:200–204

    Article  CAS  PubMed  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoidquinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Saitou N, Nei M (1987) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Mol Biol Evol 4:404–425

    Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Tech Note 101. MIDI Inc., Newark, DE

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Article  Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Environ Microbiol 28:226–231

    CAS  Google Scholar 

  • Takeuchi M, Hatano K (1998) Gordonia rhizosphera sp. nov.isolated from the mangrove rhizosphere. Int J Syst Bacteriol 48:907–912

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526

    CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tsukamura M (1971) Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 68:15–26

    Article  CAS  PubMed  Google Scholar 

  • Uchida K, Kudo T, Suzuki K, Nakase T (1999) A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45:49–56

    Article  CAS  PubMed  Google Scholar 

  • van Soolinger D, de Haas PEW, Hermans PWM, Groenen P, van Embden JDA (1993) Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of M. tuberculosis. J Clin Microbiology 31:1987–1995

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Xue Y, Sun X, Zhou P, Liu R, Liang F, Ma Y (2003) Gordonia paraffinivorans sp. nov., a hydrocarbon-degrading actinomycete isolated from an oil-producing well. Int J Syst Evol Microbiol 53:1643–1646

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was kindly supported by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; Grants 2009/53320-7 and 2011/50243-1).We thank Roberto Gomes de Souza Berlinck at the Universidade de São Paulo, São Carlos, Brazil, by collection from marine macroorganisms.

Author information

Authors and Affiliations

  1. Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, UNICAMP, Av. Alexandre Cazelatto 999, Paulínia, SP, CEP 13148-218, Brazil

    Cláudia Beatriz Afonso de Menezes, Rafael Sanches Afonso & Fabiana Fantinatti-Garboggini

  2. Programa de Pós-Graduação em Genética e Biologia Molecular, UNICAMP, CP 6109, Campinas, SP, 13083-970, Brazil

    Cláudia Beatriz Afonso de Menezes & Fabiana Fantinatti-Garboggini

  3. Embrapa Meio Ambiente, Rodovia SP 340 km 127.5, CP 69, Jaguariúna, SP, CEP 13820-000, Brazil

    Wallace Rafael de Souza, Márcia Parma, Itamar Soares de Melo & Tiago Domingues Zucchi

  4. Agrivalle – Biotecnologia Agrícola, Rua Moisés Lopes Silva 50, Pouso Alegre, MG, CEP 37550-000, Brazil

    Tiago Domingues Zucchi

Authors
  1. Cláudia Beatriz Afonso de Menezes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rafael Sanches Afonso
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wallace Rafael de Souza
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Márcia Parma
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Itamar Soares de Melo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tiago Domingues Zucchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Fabiana Fantinatti-Garboggini
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fabiana Fantinatti-Garboggini.

Additional information

The GenBank accession number for the 16S rRNA sequence of Gordonia didemni CBMAI 1069T (=DSM 46679T) is JN615417.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

de Menezes, C.B.A., Afonso, R.S., de Souza, W.R. et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.. Antonie van Leeuwenhoek 109, 297–303 (2016). https://doi.org/10.1007/s10482-015-0632-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-015-0632-y

Keywords

Search

Navigation