How to name dark fungal taxa outside the Code: The International Standard to Catalogue Dark Fungal Taxa (ISCDFT)

There is an exponential increase in the number of fungal OTUs being documented by environmental DNA (eDNA) metabarcoding. Many of these, the so-called dark fungal taxa (DFT), are known only from eDNA data, with no associated physical specimen or derived culture. Of the millions of fungal species predicted to exist, only ~205,000 are currently described, making it likely that many of these unknown or undescribed fungi are represented only by eDNA data. For more than a decade mycologists have struggled with whether the International Code of Nomenclature for algae, fungi, and plants (the Code ) should allow for formal description of fungal taxa from eDNA data alone, i.e. with a DNA sequence serving as a type. It is, however, unlikely that an amendment to the Code with this provision will pass in the near future. It is therefore imperative to establish an informal yet structured naming system to allow unified communication about DFT. The system proposed herein applies most of the principles of the Code to generate designations that, while nomenclatorially invalid, can nonetheless be integrated into fungal classifications and diversity assessments. We used the 2025 Westerdijk Spring Symposium "DNA Sequences as Type" to bring mycologists together to work out community consensus-driven conventions and standards for what we call the International Standard to Catalogue Dark Fungal Taxa (ISCDFT). The established guidelines principally refer to naming conventions, quality and standards for the underlying data, and standards regarding the underlying analysis leading to the detection of new DFT. The ISCDFT does not compete with the Code but enables the community to catalogue DFT and integrate these into fungal classifications while adhering to broadly established principles. For ease of immediate implementation, we provide examples to illustrate these newly established guidelines, a checklist for publishing new DFTs under the ISCDFT, and convert some previously published fungal names based on eDNA sequences to ISCDFT-compliant names.

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Published
2026-11-03
DOI
https://doi.org/10.3897/arphapreprints.e221892
Primary Topic
Mycorrhizal Fungi and Plant Interactions
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preprint
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preprint

How to name dark fungal taxa outside the Code: The International Standard to Catalogue Dark Fungal Taxa (ISCDFT)

Maria S. Chuvochina, R. Henrik Nilsson, Urmas Kõljalg, Kessy Abarenkov et al.
Mycorrhizal Fungi and Plant Interactions
preprint

How to name dark fungal taxa outside the Code: The International Standard to Catalogue Dark Fungal Taxa (ISCDFT)

Maria S. Chuvochina, R. Henrik Nilsson, Urmas Kõljalg, Kessy Abarenkov, Pedro Willem Crous, Paul M. Kirk, Laura Guzmán‐Dávalos, Jos A. M. P. Houbraken, Tom W. May, Marco Thines, Michael Bradshaw, Yasmina Marín-Felix, Konstanze Bensch, J.Z. Groenewald, M. Catherine Aime, Gareth Wyn Griffith, Wieland Meyer, Elizabet D’hooge, Aída M. Vasco‐Palacios, David L. Hawksworth, Brendan Furneaux, Mika Bendiksby, Ioanna Pyrri, Jianping Xu, Robert Lücking, Duong Vu, Marc Stadler, Mounes Bakhshi, Nathan Schoutteten, Cobus M. Visagie, Angela Conti, Nalin N. Wijayawardene, Andrey M. Yurkov, Margarita Hernández‐Restrepo, Leho Tedersoo, Gianluigi Cardinali, Jacob Lucas Steenwyk, Anna Rosling, David S. Hibbett, Elaine Malosso, Christiane Baschien, João P. M. Araújo, Teppo Rämä, Kevin D. Hyde, Ning Zhang, Hiran Anjana Ariyawansa, Vincent Robert, David Sánchez Hernández, Valeria Flores-Almaraz, Dylan Stephens, Gareth Jones
preprint en

Abstract

There is an exponential increase in the number of fungal OTUs being documented by environmental DNA (eDNA) metabarcoding. Many of these, the so-called dark fungal taxa (DFT), are known only from eDNA data, with no associated physical specimen or derived culture. Of the millions of fungal species predicted to exist, only ~205,000 are currently described, making it likely that many of these unknown or undescribed fungi are represented only by eDNA data. For more than a decade mycologists have struggled with whether the International Code of Nomenclature for algae, fungi, and plants (the Code ) should allow for formal description of fungal taxa from eDNA data alone, i.e. with a DNA sequence serving as a type. It is, however, unlikely that an amendment to the Code with this provision will pass in the near future. It is therefore imperative to establish an informal yet structured naming system to allow unified communication about DFT. The system proposed herein applies most of the principles of the Code to generate designations that, while nomenclatorially invalid, can nonetheless be integrated into fungal classifications and diversity assessments. We used the 2025 Westerdijk Spring Symposium "DNA Sequences as Type" to bring mycologists together to work out community consensus-driven conventions and standards for what we call the International Standard to Catalogue Dark Fungal Taxa (ISCDFT). The established guidelines principally refer to naming conventions, quality and standards for the underlying data, and standards regarding the underlying analysis leading to the detection of new DFT. The ISCDFT does not compete with the Code but enables the community to catalogue DFT and integrate these into fungal classifications while adhering to broadly established principles. For ease of immediate implementation, we provide examples to illustrate these newly established guidelines, a checklist for publishing new DFTs under the ISCDFT, and convert some previously published fungal names based on eDNA sequences to ISCDFT-compliant names.

Rutgers, The State University of New Jersey (US), Goethe University Frankfurt (DE), Uppsala University (SE), University of Copenhagen (DK), Clark University (US), Natural History Museum (GB), North Carolina State University (US), Universität Hamburg (DE), Aberystwyth University (GB), Royal Botanic Garden Edinburgh (GB), National Taiwan University (TW), Universidad de Guadalajara (MX), National and Kapodistrian University of Athens (GR), Norwegian University of Science and Technology (NO), Purdue University West Lafayette (US), Universidade Federal de Pernambuco (BR), University of Perugia (IT), Fisher College (US), Royal Botanic Gardens, Kew (GB), Universidad de Antioquia (CO), Botanic Garden and Botanical Museum Berlin (DE), Carnegie Department of Plant Biology (US), Qujing Normal University (CN), Senckenberg Biodiversity and Climate Research Centre (DE), Westerdijk Fungal Biodiversity Institute (NL), Helmholtz Centre for Infection Research (DE), University of Tartu Natural History Museum and Botanical Garden (EE), Jilin Agricultural University (CN), Instituto Canario de Investigaciones Agrarias (ES), University of Southampton (GB), Natural History Museum of Denmark (DK), Royal Botanic Gardens Victoria (AU), University of Tartu (EE), University of Pretoria (ZA), Freie Universität Berlin (DE), Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE), University of Gothenburg (SE), Aalborg University (DK), Technische Universität Braunschweig (DE), University of Jyväskylä (FI), University of California, Berkeley (US), McMaster University (CA)
Mycorrhizal Fungi and Plant Interactions
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