DNA sequencing turns fungal taxonomy upside down

While not immediately obvious, fungi are present in our everyday lives and play crucial roles in ecosystems and, as a new paper on the challenges of cataloguing fungal diversity in Nature Microbiology points out, there are many of them: 150,000 species currently known but 2.2 to 3.8 million estimated. Particularly with the help of DNA sequencing technology, presumably well-defined fungal groups, such as Candida yeasts, are turning out to represent numerous different genera and even families. This requires the introduction of new scientific names to accommodate them. In their paper, the authors elaborate on strategies how the naming of fungi can be adjusted, without causing a Babylonian confusion of tongues.

The classic picnic in the countryside is unthinkable without fungi. No bread and wine without baker’s and brewer’s yeasts (Saccharomyces), no camembert or blue cheese without Penicillium fungi, all rounded off with tasteful chanterelles (Cantharellus), porcini (Boletus) and truffles (Tuber). The blanket, still smelling a bit mouldy (Cladosporium) from the previous summer, now spread over patchily tannish grass (caused by Rhizoctonia fungi), under the shadow of trees associated with mycorrhizal fungi, such as the fly agaric (Amanita muscaria). Attached to the trees a diversity of lichens (a symbiosis between fungi and algae or cyanobacteria), indicating clean air, and the occasional bracket fungus slowly causing wood decay.

From ethanol to antibiotics

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) 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.

Pedro Crous, director of the Westerdijk Fungal Biodiversity Institute and professor in Evolutionary Phytopathology at Wageningen University in the Netherlands, one of the co-authors of the new paper on the challenges of cataloguing fungal diversity published in Nature Microbiology, states that “fungi are not only important in the ripening of cheese and processing of other products, but are otherwise widely used commercially, producing a range of products from ethanol to antibiotics. Fungi express a range of secondary metabolites or enzymes and present a cost-effective and environmentally friendly solution for numerous industrial applications”.

New scientific names

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.

Co-author Wieland Meyer, professor for Molecular Medical Mycology and Head of the Molecular Mycology Research Laboratory at the Center for Infectious Diseases and Microbiology, The University of Sydney says about the benefits of fungal names reflecting current science: “A precise and stable name of a disease-causing fungal agent is critical for a successful treatment of patients. As a well-circumscribed and informative fungal name is indicative for possible drug resistance and pathogenicity. It enables an informed and targeted treatment if a diagnosis is obtained in a timely manner, leading to better disease outcomes, resulting in a drastic reduction of morbidity and mortality, and health care cost. It also allows for the introduction of appropriate public health responses to reduce the impact of diseases on society and the establishment of quarantine restrictions to stop the spread of diseases. In addition, it avoids unnecessary antifungal drug exposure, which in turn reduces the risk to develop drug resistance.”

Previously unknown fungi

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.

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.

Naming is essential for communication

David Hawksworth, co-author of the current version of the Code of Nomenclature, also a contributor to this paper, comments: “This is a major contribution to increasing awareness of the issues involved in documenting the world’s fungi and how we can approach learning about the around 85% that still have no names. Naming is essential for communication about them in research to elucidate their roles in key ecosystem processes pertinent to climate change, including the global carbon cycle and forest health, and further to human welfare, food security, and the discovery of potentially exploitable properties. This aspect of basic science remains grossly under-resourced in relation to its importance to both human well-being and global health. I see this contribution, by revealing what has been and is being achieved, identifying issues still to be addressed, and indicating future directions of travel, as a call-to-arms that needs to be addressed by pertinent funding bodies at all levels.”

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