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Dark fungi: discovery and recognition of unseen fungal diversity

Fig. 1 from Khan et al./  CC BY 4.0 / Image resizedHigh throughput sequencing has opened the door to exciting new approaches to detect and classify unknown fungal diversity, particularly of ecologically cryptic fungi. Both the methodological approaches to accurately delimit and recognize fungal taxa from these data and the nomenclatural hurdles to describe them formally have posed challenges to advance the classification of these "dark fungi", lineages only known from sequence data for which no physical voucher material or cultures are available.

This topical collection, compiled by Robert Lücking and David Hawksworth, flags papers that in some way relate to dark fungi taxonomy and nomenclature, including methodological approaches, nomenclature, and associated topics such as important resources, the extent of unknown fungal diversity, or aspects of species concepts in lineages only known from sequence data.

Other relevant articles include: 

Lücking, R., Aime, M.C., Robbertse, B. et al. Fungal taxonomy and sequence-based nomenclature. Nat Microbiol 6, 540–548 (2021). (See also this blog post, Naming the fungal universe.)

Lücking, R., Moncada, B. Dismantling Marchandiomphalina into Agonimia (Verrucariaceae) and Lawreymyces gen. nov. (Corticiaceae): setting a precedent to the formal recognition of thousands of voucherless fungi based on type sequences. Fungal Diversity 84, 119–138 (2017). 

Image: Figure 1 from Khan et al., used under CC BY 4.0. Image resized.

  1. Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environ...

    Authors: Faheema Kalsoom Khan, Kerri Kluting, Jeanette Tångrot, Hector Urbina, Tea Ammunet, Shadi Eshghi Sahraei, Martin Rydén, Martin Ryberg and Anna Rosling
    Citation: IMA Fungus 2020 11:23
  2. A revised version of Chapter F of the International Code of Nomenclature for algae, fungi, and plants is presented, incorporating amendments approved by the Fungal Nomenclature Session of the 11th International M...

    Authors: Tom W. May, Scott A. Redhead, Konstanze Bensch, David L. Hawksworth, James Lendemer, Lorenzo Lombard and Nicholas J. Turland
    Citation: IMA Fungus 2019 10:21
  3. Procedures, appointments and outcomes of the Fungal Nomenclature Session (FNS) of the 11th International Mycological Congress (IMC11) are summarized, including the composition of the Fungal Nomenclature Bureau...

    Authors: Tom W. May, Scott A. Redhead, Lorenzo Lombard and Amy Y. Rossman
    Citation: IMA Fungus 2018 9:BF03449448
  4. We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus 9: 167–175, 2018) and Thines et al. (IMA Fungus 9: 177–183, 2018). W...

    Authors: Robert Lücking, Paul M. Kirk and David L. Hawksworth
    Citation: IMA Fungus 2018 9:901185
  5. The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be ...

    Authors: Marco Thines, Pedro W. Crous, M. Catherine Aime, Takayuki Aoki, Lei Cai, Kevin D. Hyde, Andrew N. Miller, Ning Zhang and Marc Stadler
    Citation: IMA Fungus 2018 9:901177
  6. Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artific...

    Authors: Juan Carlos Zamora, Måns Svensson, Roland Kirschner, Ibai Olariaga, Svengunnar Ryman, Luis Alberto Parra, József Geml, Anna Rosling, Slavomír Adamčík, Teuvo Ahti, M. Catherine Aime, A. Martyn Ainsworth, László Albert, Edgardo Albertó, Alberto Altés García, Dmitry Ageev…
    Citation: IMA Fungus 2018 9:901167
  7. A commentary is provided on the seven formally published proposals to modify the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN) that will be dealt with by the Fungal Nomen...

    Authors: Tom W. May and Scott A. Redhead
    Citation: IMA Fungus 2018 9:BF03449482
  8. Seven proposals to modify the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN) at the 11th International Mycological Congress (IMC11) in July 2018 had been received by the p...

    Authors: Luis A. Parra, Juan C. Zamora, David L. Hawksworth, David S. Hibbett, Paul M. Kirk, Robert Lücking, Gerhard Rambold, Konstanze Bensch, Yi-Jian Yao, Vincent Robert and Dagmar Triebel
    Citation: IMA Fungus 2018 9:BF03449481
  9. Authors: David L. Hawksworth and Sharon A. Cantrell Rodríguez
    Citation: IMA Fungus 2016 7:BF03449418
  10. The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (...

    Authors: David L. Hawksworth, Pedro W. Crous, Scott A. Redhead, Don R. Reynolds, Robert A. Samson, Keith A. Seifert, John W. Taylor, Michael J. Wingfield, Özlem Abaci, Catherine Aime, Ahmet Asan, Feng-Yan Bai, Z. Wilhelm de Beer, Dominik Begerow, Derya Berikten, Teun Boekhout…
    Citation: IMA Fungus 2011 2:2010105