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Review | Open Access

Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi

Bing Wu*,a, Muzammil Hussain*,a, Weiwei Zhanga, Marc Stadlerb, Xingzhong Liua,c, Meichun Xianga( )
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
University of Chinese Academy of Sciences, Beijing, China

*These authors contributed equally to this work.

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Abstract

The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7–13.2) million compared to 2.2–3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names’ type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded “unculturable fungi” could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the “digital type” could be assigned as the “clade” name + species name. The “clade” name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.

Keywords

biodiversityFungimolecular methodsnumbers of fungifungal phylogeny

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Mycology
Volume 10 Issue 3,
September 2019
Pages 127-140
DOI: 10.1080/21501203.2019.1614106
Cite this article:
Wu B, Hussain M, Zhang W, et al. Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi. Mycology, 2019, 10(3): 127-140. https://doi.org/10.1080/21501203.2019.1614106

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Received: 06 March 2019
Accepted: 22 April 2019
Published: 07 May 2019
© 2019 The Author(s).

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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