While not immediately obvious, fungi are present in our everyday lives and play crucial roles in ecosystems, for instance by decomposing organic matter and recycling nutrients. And, as a new paper on the challenges of cataloguing fungal diversity just published in Nature Microbiology (doi.org/10.1038/s41564-021-00888-x), co-authored by the Leibniz Institute DSMZ’ researcher Dr. Andrey Yurkov, points out, there are many of them: 150,000 species currently known but 2.2 to 3.8 million estimated. Not all, however, is peaceful in the fungal realm. Many fungi are plant and animal (including human) pathogens, such as the stem rust (Puccinia graminis f.sp. tritici) attacking cereal crops or candidiasis in humans caused by species of Candida. On the other hand, the same unique physiological and biochemical traits that make fungi specialists in competing with or attacking other organisms also render them useful in diverse industrial and pharmaceutical applications, such as the food industry, the production of antibiotics, and biological pest control.
Given that fungi mostly grow hidden in and on a diversity of substrates, often visible only by their spore-producing structures, their study heavily relies on laboratory techniques ranging from sophisticated microscopy to the latest DNA sequencing technology. Particularly the advent of DNA sequencing technology has brought many surprises for mycologists, the scientists studying fungi, as an international group of experts, spearheaded by the International Commission on the Taxonomy of Fungi, outlines in the new paper. Presumably well-defined fungal groups, such as Candida yeasts, are turning out to represent numerous different genera and even families, requiring the introduction of new scientific names, which may cause confusion in the short term. Thus, fungi of importance for humans, long known under a particular name, may undergo name changes, much to the dismay of medical doctors, plant pathologists or farmers familiar with those names. Andrey Yurkov, mycologist at the German Leibniz Institute DSMZ summarises “The stability of taxonomy is crucial for many researchers and end-users alike. Names of Fungi are an integral part of quality standards, technical recommendations and legal compliances, and are used to communicate a potential infectious agent or quarantine organism. One of the major long-term goals of the taxonomic system is to ensure that naming adequately reflects both the scientific progress and information on properties of a species, be it an antifungal drug resistance or its potential biotechnological application.” On the other hand, the novel approach of environmental DNA sequencing is revealing a large number of previously unknown fungi from soil, water, air and other sources, which are only known from their DNA and have no physical specimen or living culture. However, the classification of fungi requires physical specimens that can be independently and repeatedly studied. Therefore, DNA sequences alone are insufficient to name perhaps millions of new fungi discovered from these environmental sources, several times as many as the total number of fungi currently known.
Background: How to name fungi
The rules that govern the naming of fungi, embedded in the International Code of Nomenclature for algae, fungi, and plants, date back more than 150 years. But they are being updated every four to six years to keep abreast with new scientific and technological developments. However, never has science and technology changed so fast as in the new millennium. Environmental sequencing alone has amassed enough data points to compare to the stars in our galaxy and this is growing exponentially. Mycologists therefore not only face the challenge to quickly, yet properly catalog the vast fungal diversity unveiled by these new approaches, but also to provide a stable naming system that enables accurate and precise communication between taxonomic experts and a diverse user community. To achieve this, the authors of the new paper, representing global expertise in all areas of mycology, elaborate on strategies how the naming of fungi is being adjusted to these new requirements, balancing between the need for names as an effective currency for communication and the huge amount of exciting new findings that emerge every day from the latest studies on fungal biodiversity.
The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures has a very rare expertise in the field of yeast ecology and systematics. Headed by mycologist Dr. Andrey Yurkov, the research group Fungi and Fungal Systematics works on the isolation of yeasts from soils, plant material and animal-related sources. In addition, Andrey Yurkov is a member of the International Commission on the Taxonomy of Fungi and contributes with his taxonomic expertise to the Heterobasidiomycetes and Yeast Working Groups.
Lücking, R., Aime, M.C., Robbertse, B., Miller, A.N., Aoki, T., Ariyawansa, H.A., Cardinali, G., Crous, P.W., Druzhinina, I.S., Geiser, D.M., Hawksworth, D.L., Hyde, K.D., Irinyi, L., Jeewon, R., Johnston, P.R., Kirk, P.M., Malosso, E., May, T.W., Meyer, W., Nilsson, H.R., Öpik, M., Robert, V., Stadler, M., Thines, M., Vu, D., Yurkov, A.M., Zhang, M., Schoch, C.L. (2021) Fungal taxonomy and sequence-based nomenclature. Nature Microbiology. doi.org/10.1038/s41564-021-00888-x
PhDr. Sven-David Müller, Head of Public Relations, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH
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About the Leibniz Institute DSMZ
The Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures is the world's most diverse collection of biological resources (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines). Microorganisms and cell cultures are collected, investigated and archived at the DSMZ. As an institution of the Leibniz Association, the DSMZ with its extensive scientific services and biological resources has been a global partner for research, science and industry since 1969. The DSMZ is the first registered collection in Europe (Regulation (EU) No. 511/2014) and certified according to the quality standard ISO 9001:2015. As a patent depository, it offers the only possibility in Germany to deposit biological material in accordance with the requirements of the Budapest Treaty. In addition to scientific services, research is the second pillar of the DSMZ. The institute, located on the Science Campus Braunschweig-Süd, accommodates more than 75,000 cultures and biomaterials and has around 200 employees. www.dsmz.de
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The Leibniz Association connects 96 independent research institutions that range in focus from the natural, engineering and environmental sciences via economics, spatial and social sciences to the humanities. Leibniz Institutes address issues of social, economic and ecological relevance. They conduct knowledge-driven and applied basic research, maintain scientific infrastructure and provide research-based services. The Leibniz Association identifies focus areas for knowledge transfer to policy-makers, academia, business and the public. Leibniz institutions collaborate intensively with universities – including in the form of “Leibniz ScienceCampi” – as well as with industry and other partners at home and abroad. They are subject to a transparent, independent evaluation. Because of their importance for the country as a whole, the Leibniz Association Institutes are funded jointly by Germany’s central and regional governments. The Leibniz Institutes employ around 20,000 people, including 10,000 researchers. The financial volume amounts to 1.9 billion euros. www.leibniz-gemeinschaft.de