When the topic of fungi arises, the majority of people would likely think about the mushrooms they gather in the autumn, or possibly the yeast they use in baking or wine-making.
Some might even recollect the rotten bread or cucumbers they stumbled upon in their refrigerator last week. For ages, mycologists have researched these fungi not only as a source of food and fermentation but also as the cause of decay and disease.
As we commonly know, fungi are organisms that can develop into physical structures like fruiting bodies or yeast-like life forms that we can cultivate in our laboratories or kitchens. However, recent discoveries indicate that fungi are not restricted to these two classifications. Environmental substrates like soil have been studied using DNA sequencing, revealing vast evidence of extensive fungal groups that do not produce fruiting bodies and are not cultivable in labs. These groups are referred to as “dark fungi,” drawing an analogy with the concept of “dark matter” in astronomy. Despite our inability to observe them directly, we are aware of their existence.
According to a recent study published in the journal MycoKeys, researchers have found a significant contrast between the accumulation of fungal species using traditional mycological approaches and environmental DNA sequencing over time. The study found that, despite accounting for various types of biases, species discovery through environmental sequencing has exceeded traditional species recovery in a strongly increasing trend over the past five years. As a result, the authors concluded that dark fungi, which thrive in extreme environments, play a defining role in the fungal kingdom.
“And that’s where it gets interesting,” remarks lead author Henrik Nilsson.
In accordance with the current nomenclature guidelines, according to the author, these fungi are unable to receive formal scientific names, rendering them nameless. Consequently, they tend to be neglected and overlooked, often slipping through the cracks of nature conservation initiatives. Their exclusion from efforts to estimate fungal evolutionary history leads to an incomplete understanding of their ecological roles and associations, and their significance in mass and energy flow within ecosystems is disregarded. In essence, they are treated as if they do not exist.
“They’re essentially treated as if they didn’t exist.”
In a recent statement, Martin Ryberg, a second author from the University of Uppsala in Sweden, emphasized the significance of their recent findings regarding fungi.
According to second author Martin Ryberg, their research reveals that fungi are not just adding a few missing pieces to an almost complete puzzle. Instead, the puzzle seems to be far from complete, with tens of large groups of fungi and thousands of species remaining undiscovered. In fact, some species of fungi are so widespread that they have yet to come across a soil sample without them.
These findings, according to the author, suggest that fungi may be the dominant life form in the fungal kingdom, a discovery that could have significant implications for the field of mycology.
The mycological community has been engaged in an ongoing debate about whether the rules of fungal nomenclature should be adapted to accommodate the formal description of dark fungi. However, according to Nilsson, the matter has not yet been resolved in the affirmative. Based on their recent study, Nilsson believes that it is time to put an end to this debate and shift the focus towards discussing how dark fungi should be described. Specifically, there needs to be a discussion about the criteria that must be met for a dark fungus to receive a formal scientific name.
“Clearly, formation of a fruiting body or growth in the laboratory can’t be part of those criteria.”
Alice Retter, a co-author from the University of Vienna in Austria, stated that their team has compiled a list of criteria that they believe would be suitable for describing dark fungi. The aim of this list is to uphold a high level of scientific rigor and reproducibility in the process, ensuring that only well-vetted dark fungi are formally described. The criteria were formulated by combining their own observations with suggestions gathered from the mycological community, which were collected after depositing a preprint of their manuscript at bioRxiv. Retter clarified that their suggestions are not meant to be the final word on the matter, but rather a starting point for the ongoing debate. They hope that the mycological community will collaborate to develop a set of guiding principles that will be sound and effective. This initial set of well-intentioned observations is intended to serve as a foundation for that discussion.
According to the authors, it is necessary to make slight modifications to the current nomenclatural rules that govern the naming of fungi, to enable the formal naming of the most extensively documented species and groups of dark fungi. However, it should be noted that the proposed modifications would not include many of the rare or less thoroughly documented dark fungi from receiving a formal description.
Senior author Kessy Abarenkov of the Tartu Natural History Museum in Estonia argues that it is not necessary to have a theory of everything to have a theory of something. According to Abarenkov, mycologists can establish rules that define what is required to describe dark fungi and identify when it is necessary to hold back from describing such species. By adopting this approach, mycologists can diligently gather research data to support the naming of dark fungi, group by group, and species by species, which has been the cornerstone of mycology for hundreds of years.
“It’s what mycology has excelled at for hundreds of years. It’s just the setting that’s a bit new.”
“Much is at stake, obviously,” adds Sten Anslan from the University of Tartu.
Although the current rules that govern the naming of fungi have been beneficial to mycology for a significant period, there is a growing concern that they may become outdated if they are not revised to include the description of dark fungi. The authors do not intend to discard or dismantle the existing rules entirely. However, they fear that if these rules are not updated, they may only regulate a small percentage of the organisms they were intended to govern, namely those belonging to the fungal kingdom. This scenario would be unsustainable in the long run, as having a rule book that does not account for the vast majority of fungi would be untenable.
Marisol Sanchez-Garcia, from the Swedish Agricultural University, anticipates that the nomenclatural aspects of dark fungi will be extensively discussed at the forthcoming international mycological congress in Maastricht, the Netherlands. Sanchez-Garcia is optimistic that the mycological community will come to a meaningful agreement on the integration of dark fungi into the rules of nomenclature. Given that mycologists are accustomed to resolving complex questions daily, Sanchez-Garcia believes that this issue is hardly any different. In her opinion, being part of the solution to a vast, relatively unknown group of organisms, where very little is known, and where the rules must be updated regularly to keep up with the latest developments, is “what makes being a mycologist so interesting and rewarding.”
Image Credit: Henrik Nilsson