When Candida is not Candida – the challenge of naming of Fungi

Light microscope images of the yeast fungus Candida albicans (DSM 1386) Source: DSMZ

Dr. Andrey Yurkov Source: DSMZ

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.

Original publication
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

Press contact:
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Mail: press@dsmz.de

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