Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Essay
  • Published:

Fungal systematics: is a new age of enlightenment at hand?

Nature Reviews Microbiology volume 11, pages 129–133 (2013)Cite this article

Subjects

Abstract

Fungal taxonomists pursue a seemingly impossible quest: to discover and give names to all of the world's mushrooms, moulds and yeasts. Taxonomists have a reputation for being traditionalists, but as we outline here, the community has recently embraced the modernization of its nomenclatural rules by discarding the requirement for Latin descriptions, endorsing electronic publication and ending the dual system of nomenclature, which used different names for the sexual and asexual phases of pleomorphic species. The next, and more difficult, step will be to develop community standards for sequence-based classification.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Two names, one fungus.
Figure 2: Unnamed diversity.

References

  1. Kirk, P. et al. (eds) Dictionary of the Fungi 10th edn (CABI, 2008).

    Google Scholar 

  2. Bass, D. & Richards, T. A. Three reasons to re-evaluate fungal diversity “on Earth and in the ocean”. Fungal Biol. Rev. 25, 159–164 (2011).

    Article  Google Scholar 

  3. McNeill, J. et al. (eds) International Code of Botanical Nomenclature (Vienna Code) (Gantner, 2006).

    Google Scholar 

  4. Hawksworth, D. L. et al. The Amsterdam declaration on fungal nomenclature. IMA Fungus 2, 105–112 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Hibbett, D. S. et al. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol. Rev. 25, 38–47 (2011).

    Article  Google Scholar 

  6. Taylor, J. W. One fungus = one name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2, 113–120 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Houbraken, J., Frisvad, J. C. & Samson, R. A. Taxonomy of Penicillium citrinum and related species. Fungal Divers. 44, 117–133 (2010).

    Article  Google Scholar 

  8. Crous, P. W. et al. Phylogenetic lineages in the Botryosphaeriaceae. Stud. Mycol. 55, 235–253 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Gräfenhan, T., Schroers, H.-J., Nirenberg, H. I. & Seifert, K. A. An overview of the taxonomy, phylogeny, and typification of nectriaceous fungi in Cosmospora, Acremonium, Fusarium, Stilbella, and Volutella. Stud. Mycol. 68, 79–113 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Norvell, L. L. Fungal nomenclature. 1. Melbourne approves a new Code. Mycotaxon 116, 481–490 (2011).

    Article  Google Scholar 

  11. Hawksworth, D. A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. IMA Fungus 2, 155–162 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Weresub, L. K. & Pirozynski, K. A. in The Whole Fungus: The Sexual-Asexual Synthesis (ed. Kendrick, B.) 17–30 (National Museum of Natural Sciences and National Museums of Canada, 1979).

    Google Scholar 

  13. Tulasne, L.-R. & Tulasne, C. Selecta Fungorum Carpologia. Vol. 1 (Imperial Typographer, 1861).

    Google Scholar 

  14. Kendrick, B. (ed.) The Whole Fungus: The Sexual-Asexual Synthesis. (National Museum of Natural Sciences and National Museums of Canada, 1979).

    Google Scholar 

  15. Houbraken, J. & Samson, R. A. Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud. Mycol. 70, 1–51 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Hawksworth, D. L. & Taylor, J. W. One fungus = which name? IMA Fungus 3, 10–14 (2012).

    Google Scholar 

  17. Rosling, A. et al. Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. Science 333, 876–879 (2011).

    Article  CAS  PubMed  Google Scholar 

  18. James, T. Y. & Berbee, M. L. No jacket required – new fungal lineage defies dress code: recently described zoosporic fungi lack a cell wall during trophic phase. Bioessays 34, 94–102 (2012).

    Article  CAS  PubMed  Google Scholar 

  19. Jones, M. D. et al. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474, 200–203 (2011).

    Article  CAS  PubMed  Google Scholar 

  20. Kirk, P. M. Index Fungorum no. 2. Index Fungorum [online] (2012).

    Google Scholar 

  21. Bidartondo, M. I. Preserving accuracy in GenBank. Science 319, 1616 (2008).

    Article  CAS  PubMed  Google Scholar 

  22. Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl Acad. Sci. USA 109, 6241–6246 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Abarenkov, K. et al. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytol. 186, 281–285 (2010).

    Article  PubMed  Google Scholar 

  24. Tindall, B. J., Rossello-Mora, R., Busse, H. J., Ludwig, W. & Kampfer, P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60, 249–266 (2010).

    Article  CAS  PubMed  Google Scholar 

  25. De Vos, P., Trüper, H. G. & Tindall, B. J. Judicial Commission of the International Committee on Systematics of Prokaryotes; Xth International (IUMS) Congress of Bacteriology and Applied Microbiology; Minutes of the meetings, 28, 29 and 31 July and 1 August 2002, Paris, France. Int. J. Syst. Evol. Microbiol. 55, 525–532 (2005).

    Article  Google Scholar 

  26. Lapage, S. et al. (eds) International Code Of Nomenclature Of Bacteria. (American Society for Microbiology, 1992).

    Google Scholar 

  27. Houbraken, J., Frisvad, J. C. & Samson, R. A. Fleming's penicillin producing strain is not Penicillium chrysogenum but P. rubens. IMA Fungus 2, 87–95 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Henk, D. A. et al. Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus. Mol. Ecol. 20, 4288–4301 (2011).

    Article  CAS  PubMed  Google Scholar 

  29. Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301, 976–978 (2003).

    Article  CAS  PubMed  Google Scholar 

  30. Cadillo-Quiroz, H. et al. Patterns of gene flow define species of thermophilic Archaea. PLoS Biol. 10, e1001265 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Gevers, D. et al. Re-evaluating prokaryotic species. Nature Rev. Microbiol. 3, 733–739 (2005).

    Article  CAS  Google Scholar 

  32. Rainey, F. A. & Oren, A. in Methods in Microbiology. Vol. 38 (eds Rainey, F. & Oren, A.) 1–5 (Academic, 2011).

    Google Scholar 

  33. Murray, R. G. E. & Stackebrandt, E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45, 186–187 (1995).

    Article  CAS  PubMed  Google Scholar 

  34. Murray, R. G. E. & Schleifer, K. H. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol. 44, 174–176 (1994).

    Article  CAS  PubMed  Google Scholar 

  35. Euzéby, J. P. Some names included in the category Candidatus. List of Prokaryotic Names with Standing in Nomenclature [online], (2012).

  36. Taylor, J. et al. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31, 21–32 (2000).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank their colleagues and members of their laboratories for discussions on the principles of fungal taxonomy, and the International Mycological Association and the Centraalbureau voor Schimmelcultures for hosting meetings addressing the revolution in fungal nomenclature. Research in the authors' laboratories is supported by the Open Tree of Life Project (http://opentreeoflife.org/), the US National Science Foundation (grant DEB-1208719 to D.S.H.), the US National Institutes of Health (grant U54-AI65359 to J.T.W.) and the Energy Biosciences Institute (grant EBI 001J09 to J.W.T.).

Author information

Authors and Affiliations

  1. David S. Hibbett is at The Biology Department, Clark University, Worcester, Massachusetts 01610, USA.,

    David S. Hibbett

  2. John W. Taylor is at The Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.,

    John W. Taylor

Authors
  1. David S. Hibbett
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. John W. Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David S. Hibbett.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

FURTHER INFORMATION

David S. Hibbett's homepage

John W. Taylor's homepage

GenBank

IndexFungorum

MycoBank

RefSeq

UNITE

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hibbett, D., Taylor, J. Fungal systematics: is a new age of enlightenment at hand?. Nat Rev Microbiol 11, 129–133 (2013). https://doi.org/10.1038/nrmicro2963

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro2963

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing