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Fungal taxonomy and sequence-based nomenclature

Nature Microbiology volume 6, pages 540–548 (2021)Cite this article

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An Author Correction to this article was published on 27 May 2021

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Abstract

The identification and proper naming of microfungi, in particular plant, animal and human pathogens, remains challenging. Molecular identification is becoming the default approach for many fungal groups, and environmental metabarcoding is contributing an increasing amount of sequence data documenting fungal diversity on a global scale. This includes lineages represented only by sequence data. At present, these taxa cannot be formally described under the current nomenclature rules. By considering approaches used in bacterial taxonomy, we propose solutions for the nomenclature of taxa known only from sequences to facilitate consistent reporting and communication in the literature and public sequence repositories.

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Fig. 1: Fungal diversity.
Fig. 2: Timeline of important events in fungal taxonomy and nomenclature.
Fig. 3: Visualization of new lineages.

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Acknowledgements

Work by C.L.S. and B.R. was supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health in Bethesda, Maryland, USA. D.M.G. received support through the National Science Foundation (NSF) grant DEB-1655980 and Project 4655 of the Pennsylvania State Agricultural Experiment Station. E.M. acknowledges CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil) and FACEPE (Fundação de Amparo à Ciência e Tecnologia de Pernambuco, Brazil). K.D.H. thanks the Thailand Research Fund, grant RDG6130001, entitled “Impact of Climate Change on Fungal Diversity and Biogeography in the Greater Mekong Subregion”. The USDA Hatch project 1010662 is acknowledged for support to M.C.A. M.Ö. was supported by the European Regional Development Fund (Centre of Excellence EcolChange). M.T. acknowledges LOEWE for funding in the framework of the Centre for Translational Biodiversity Genomics (TBG) and the German Science Foundation. N.Z. acknowledges the NSF of the United States (DEB-1452971). P.R.J. was supported through the Manaaki Whenua Biota Portfolio with funding from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment. R.J. thanks the University of Mauritius for research support. We thank S. Redhead for nomenclatural advice. R. Sanders provided the update for the fungal ITS data in the SRA.

Author information

Authors and Affiliations

  1. Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany

    Robert Lücking

  2. International Commission on the Taxonomy of Fungi (ICTF) https://www.fungaltaxonomy.org/

    Robert Lücking, M. Catherine Aime, Andrew N. Miller, Takayuki Aoki, Hiran A. Ariyawansa, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Peter R. Johnston, Elaine Malosso, Tom W. May, Maarja Öpik, Marc Stadler, Marco Thines, Andrey M. Yurkov, Ning Zhang & Conrad L. Schoch

  3. Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA

    M. Catherine Aime

  4. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Barbara Robbertse & Conrad L. Schoch

  5. Illinois Natural History Survey, University of Illinois, Champaign, IL, USA

    Andrew N. Miller

  6. National Agriculture and Food Research Organization, Genetic Resources Center, Ibaraki, Japan

    Takayuki Aoki

  7. Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan

    Hiran A. Ariyawansa

  8. Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy

    Gianluigi Cardinali & Vincent Robert

  9. Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands

    Pedro W. Crous, Vincent Robert & Duong Vu

  10. Laboratory of Phytopathology, Wageningen University and Research Centre (WUR), Wageningen, The Netherlands

    Pedro W. Crous

  11. Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing, China

    Irina S. Druzhinina

  12. Institute of Chemical, Environmental and Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria

    Irina S. Druzhinina

  13. Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA

    David M. Geiser

  14. Department of Life Sciences, The Natural History Museum, London, UK

    David L. Hawksworth

  15. Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, UK

    David L. Hawksworth

  16. Geography and Environment, University of Southampton, Southampton, UK

    David L. Hawksworth

  17. Jilin Agricultural University, Changchun, China

    David L. Hawksworth

  18. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China

    Kevin D. Hyde

  19. Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand

    Kevin D. Hyde

  20. World Agroforestry Centre, East and Central Asia, Kunming, China

    Kevin D. Hyde

  21. Mushroom Research Foundation, Chiang Rai, Thailand

    Kevin D. Hyde

  22. Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia

    Laszlo Irinyi & Wieland Meyer

  23. Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia

    Laszlo Irinyi & Wieland Meyer

  24. Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia

    Laszlo Irinyi & Wieland Meyer

  25. Westmead Hospital (Research and Education Network), Westmead, New South Wales, Australia

    Laszlo Irinyi & Wieland Meyer

  26. Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius

    Rajesh Jeewon

  27. Manaaki Whenua—Landcare Research, Auckland, New Zealand

    Peter R. Johnston

  28. Royal Botanic Gardens, Kew, Richmond, UK

    Paul M. Kirk

  29. Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil

    Elaine Malosso

  30. Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia

    Tom W. May

  31. Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden

    Henrik R. Nilsson

  32. Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia

    Maarja Öpik

  33. Department Microbial Drugs, Helmholtz Center for Infection Research, Braunschweig, Germany

    Marc Stadler

  34. German Centre for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany

    Marc Stadler

  35. Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany

    Marco Thines

  36. Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany

    Marco Thines

  37. Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany

    Andrey M. Yurkov

  38. Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA

    Ning Zhang

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  1. Robert Lücking
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Contributions

The present manuscript was first discussed among members of the ICTF. Based on contributions from this initial discussion, a first version of the manuscript was drafted by R.L., C.L.S., M.C.A., B.R. and A.N.M. This version was distributed among the ICTF and to selected colleagues outside the ICTF, and all comments were recorded and incorporated. Based on these initial comments, lead and co-authorship was determined, additional co-authors then including T.A., H.A.A., G.C., P.W.C., I.S.D., D.M.G., D.L.H., K.D.H., L.I., R.J., P.R.J., P.M.K., E.M., T.W.M., W.M., M.Ö., V.R., M.S., M.T., D.V., A.M.Y. and N.Z. The revised draft was circulated two more times among all authors for additional comments before submission. After the first review, H.R.N. was invited as an additional co-author to provide specific input regarding dark taxa and the role of the UNITE database in the proposed alternatives for dark taxa nomenclature. Apart from contributing generally to the manuscript, D.L.H. and T.W.M. revised the nomenclatural details included in Box 1 and Fig. 1. B.R. and D.V. also assisted in technical aspects regarding the SRA and Fig. 3. P.W.C., R.L., W.M., M.T. and A.M.Y. organized the photographs used in Fig. 2 from their working groups. The final draft was approved by all authors.

Corresponding author

Correspondence to Conrad L. Schoch.

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References for the timeline events depicted in Fig. 2.

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Lücking, R., Aime, M.C., Robbertse, B. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6, 540–548 (2021). https://doi.org/10.1038/s41564-021-00888-x

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