Scientists: All fungi matter, not just mushrooms

When fungi are mentioned, most people’s minds jump to images of the mushrooms they gather in autumn or the yeast used for baking and winemaking. 

For centuries, mycologists have been studying fungi for their applications in food and fermentation, as well as their roles in decay and disease. However, recent research has begun to challenge our traditional understanding of fungi and their behaviors.

Typically, we think of fungi as organisms that form physical structures, such as fruiting bodies, or yeast-like life forms that can be cultivated in our kitchens or laboratories. However, DNA sequencing studies conducted on environmental substrates like soil have revealed large groups of fungi that don’t appear to form fruiting bodies and can’t be grown in labs – yet they still exist. 

These elusive groups of fungi are often referred to as “dark fungi,” drawing a parallel with the concept of “dark matter” in astronomy. Both dark fungi and dark matter are known to be present but remain mostly unobservable.

A new study published in the journal MycoKeys has compared the accumulation of fungal species recovered using traditional mycological methods to those recovered using environmental DNA sequencing over time. 

The researchers found that species discovery through environmental sequencing has been growing at an increasingly rapid pace over the past five years. This study concludes that dark fungi are a defining feature of the fungal kingdom.

Lead author Henrik Nilsson of the University of Gothenburg, Sweden, explained the implications of these findings: 

“Under the current rules of nomenclature, these fungi cannot be given scientific names – they cannot be described formally. And species and groups that cannot be named formally, well, they tend to fall between the cracks. They’re typically not considered in nature conservation initiatives. They are often left out from efforts to estimate the evolutionary history of fungi, and their ecological roles and associations are largely overlooked when we try to figure out how mass and energy flow in ecosystems. They’re essentially treated as if they didn’t exist.”

Study second author Martin Ryberg from the University of Uppsala added to this sentiment: 

“And it’s not like we’re adding the few missing pieces to an otherwise nearly complete jigsaw puzzle. It seems to be the other way around. We’re talking about tens of large groups of fungi – and thousands upon thousands of species, some of which seem to be so common that we have yet to find a soil sample from which they’re absent. Indeed, we’re talking about what could well prove to be the dominant lifestyle in the fungal kingdom.”

Debating the fungal rules

The mycological community is currently engaged in a debate over whether the rules of fungal nomenclature should be modified to allow for the formal description of “dark fungi,” a group of elusive organisms that have remained mostly unobservable. The issue has yet to be resolved, and scientists are pushing for change in this area. 

“I think our study shows that it’s time to stop that debate, like, right away,” said Nilsson. “What we should be debating is how we should describe them. What criteria must be fulfilled for a dark fungus to be given a formal scientific name? Clearly, formation of a fruiting body or growth in the laboratory can’t be part of those criteria.”

Study co-author Alice Retter of the University of Vienna explainex the team’s approach to addressing this issue: “We figured we’d kickstart the how debate by listing criteria that we think make sense – criteria that would be stringent enough to allow for only particularly well-vetted dark fungi to be described, upholding a high level of scientific rigor and reproducibility in the process.”

“We blended our own observations with suggestions from the mycological community, culled from depositing a preprint of the manuscript at bioRxiv. We’re certainly not claiming that our suggestions form the final word in the debate. It’s more like they’re the first. We’re thinking that the mycological community will jointly be able to come up with a set of sound guiding principles on the matter – and here comes an initial set of well-meaning observations for nucleation.”

How researchers name fungi

The researchers propose making gentle modifications to the nomenclatural rules governing the naming of fungi, allowing for the formal naming of the most well-documented species and groups of dark fungi. However, these suggested changes would still exclude many rare or less well-documented dark fungi from formal description.

Senior author Kessy Abarenkov of the Tartu Natural History Museum commented on the importance of establishing rules for describing dark fungi. 

“By establishing rules for what’s needed to describe dark fungi, and specifying when we’ll have to refrain from describing such species at present, mycologists can do what they do best: doggedly gather enough research data to warrant naming of the dark fungi, group by group, and species by species,” said Abarenkov. “It’s what mycology has excelled at for hundreds of years. It’s just the setting that’s a bit new.”

Sten Anslan from the University of Tartu elaborated on the potential consequences of not updating the current rules:

“Much is at stake, obviously. The current rules governing the naming of fungi have served mycology well for a long time. We don’t want to upend or overthrow them. But we fear that if they’re not updated in this particular regard, there’s a risk that they grow increasingly obsolete over time. Having a book of rules that govern maybe only some few percent of the organisms it was originally conceived to govern – the fungal kingdom – would seem untenable in the long run.”

Marisol Sanchez-Garcia of the Swedish Agricultural University expressed hope for the future. “The nomenclatural aspects of dark fungi will presumably be discussed at some length at next year’s international mycological congress in Maastricht, the Netherlands,” said Sanchez-Garcia.

“We’re hopeful that the mycological community will reach meaningful agreement on integration of the dark fungi into the rules of nomenclature. After all, mycologists are used to negotiating and solving non-trivial questions on a day-to-day basis, and this one is hardly any different. Being part of tackling a huge, more or less unknown group of organisms where precious little is set in stone and where the rules will have to be adapted over time for the endeavor to stay attuned to recent developments, well, that’s what makes being a mycologist so interesting and rewarding in my eyes.”

This research highlights the need for a more comprehensive understanding of the vast and diverse world of fungi. Uncovering the mysteries of dark fungi could potentially lead to breakthroughs in various scientific fields, from ecology and evolution to nature conservation and ecosystem analysis. As we continue to explore this enigmatic domain, the full extent of fungi’s influence on our world may soon be brought to light.

The importance of fungi to Earth’s ecosystems

Fungi play a critical role in Earth’s ecosystems, contributing to various processes that maintain the health and balance of these environments. Some of the key functions of fungi in ecosystems include:

1. Decomposition: Fungi are essential decomposers in ecosystems, breaking down dead organic matter such as leaves, wood, and other plant materials. By decomposing organic matter, fungi release nutrients back into the soil, making them available for uptake by plants and other organisms. This process helps recycle essential nutrients and maintain soil fertility.
2. Mutualistic relationships: Fungi form symbiotic relationships with plants and other organisms, providing benefits to both parties. One example of this is the association between fungi and plant roots, known as mycorrhizae. In this relationship, fungi help plants absorb nutrients and water from the soil more efficiently, while the plants provide the fungi with carbohydrates produced through photosynthesis.
3. Carbon cycling: Fungi play a crucial role in the global carbon cycle. They decompose organic matter, releasing carbon dioxide back into the atmosphere. This process contributes to the regulation of atmospheric carbon dioxide levels and, subsequently, global climate patterns.
4. Food source: Fungi serve as a food source for various organisms, including insects, mammals, and other fungi. Their role in the food chain contributes to overall ecosystem stability and biodiversity.
5. Bioremediation: Some fungi possess the ability to break down environmental pollutants, such as heavy metals and chemicals. These fungi can help clean up contaminated environments through a process called bioremediation.
6. Production of bioactive compounds: Fungi produce a wide range of bioactive compounds, such as antibiotics, enzymes, and other molecules, which have potential applications in medicine, agriculture, and industry.

Overall, fungi play a critical role in maintaining the health and balance of Earth’s ecosystems. Their diverse functions contribute to nutrient cycling, soil fertility, symbiotic relationships, carbon cycling, and biodiversity, underscoring their importance in sustaining life on our planet.

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