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Genetically, this is a super fungus
Researchers found traces of the fungus in places where it shouldn't be. When they examined the genes, they found several surprises.
Carrying more than you need is rarely an advantage, not even in genetics. For this reason, genes and DNA that are not vital tend to disappear over time.
When researchers examined fungi in the Mycena genus, they found much more DNA compared to other fungi. Some species have four to five times more DNA.
Why is that?
“These fungi are like a mountain climber carrying a PlayStation. The best mountain climber is usually not the one with the biggest backpack,” says Christoffer Bugge Harder from the University of Copenhagen.
He explains that you carry what you require, but nothing more. That is why it is so peculiar that this fungus has kept all these genes.
At the same time, it turns out that this fungus can thrive in many different environments. It seems that its genetic baggage equips it for various lifestyles.
Found fungi in unexpected places
It all began when Professor Håvard Kauserud from the University of Oslo's Department of Biosciences and his colleagues were studying the collaboration between plants and fungi in Svalbard.
They discovered something they initially thought was a mistake. They found DNA from Mycena fungi in plant roots. Mycena fungi are known as decomposers. The researchers did not believe that Mycena fungi formed symbiotic relationships, known as mycorrhiza, with plants.
When they found traces of Mycena fungi in many root samples, they realised they had stumbled upon something intriguing.
Perhaps Mycena fungi had a secret life among plant roots?
Together with Bugge Harder, who was then a researcher at the University of Oslo, Kauserud wanted to find out what the Mycena fungi were up to.
Their work would result in several surprises.
“We didn't expect the Mycena fungi to have such enormously large genomes. We had assumed that the genomes would reflect their lifestyle as decomposers, but we didn't see this in the DNA,” says Bugge Harder.
In a study led by Ella Thoen, they also observed that nutrients could be transferred between Mycena fungi and plants, somewhat like mycorrhizal fungi.
Record-breaking amount of DNA for a fungus
To better understand the Mycena fungi, researchers examined the genetic material of 24 different species in the genus. They discovered that Mycena fungi have an unusually large amount of DNA for fungi.
On average, they had double the DNA of other fungi. The species with the most DNA had four to five times more than the average for other fungi.
The study also revealed a record: The largest fungal genome found in this group of fungi so far. The record-holder was Mycena olivaceomarginata, which has 501 million base pairs.
“This could seemingly be an advantage for them if living conditions were to suddenly change,” says Bugge Harder.
The large genome suggests a secret life of the fungi
One of the surprises was that a large portion of their DNA appeared to have no function.
“They have long, repeating sequences without any known function. In some of the fungi, 40 to 50 per cent of the genetic material consisted of such sequences,” explains Bugge Harder.
“Many of the fungi are also equipped with genes for almost everything, along with genes that seem to have no known function – a duplicate of a functioning gene. Theoretically, this means they are equipped to live in various ways. This is quite unusual among fungi. They usually don’t have all possible adaptations,” he says.
Therefore, he believes that the Mycena fungi might have a secret life that researchers know little about.
“We can see how some of them invade plants and become parasites, even though they’re not supposed to, since they are primarily decomposers,” says Bugge Harder.
He explains that fungi that live symbiotically with plants typically don't have genes for breaking down plant material because they don't need them. However, researchers see that these fungi, which are decomposers, have genes for both roles.
This fungus has used all the tricks in the genetic toolbox
To acquire all these genes, the Mycena fungi have used all the strategies known to researchers:
“These fungi have used all the tricks in the genetic toolbox,” says Bugge Harder.
They have employed what researchers call horizontal gene transfer, which is best known among bacteria. They have mobile DNA elements that shift around and have duplicated some of their genes – possibly even the entire genome.
The horizontal gene transfer, or theft of genes from other fungi, is particularly surprising. While it is common in bacteria, it is much rarer in organisms with a cell nucleus, like fungi.
“One of the fungal groups they've taken genes from is Ascomycota, a sac fungi. They are as distantly related to Mycena fungi as humans are to insects or echinoderms. It's as if we were to acquire genes from a butterfly or a starfish,” says Bugge Harder.
He adds that how this genetic transfer occurs between these fungal species remains unknown.
Genes from other species
Researchers know that the genes come from other species.
When analysed, the software identifies structures in the DNA and compares them with DNA from other species.
“When you suddenly find genes in Mycena fungi that do not exist in their closer relatives but are instead identical to genes found in entirely different parts of the tree of life with which they are not closely related, it most likely comes from there,” he explains.
The large genomes equip them for all conditions
Mycena fungi are found everywhere – on all continents, including Antarctica. They live in forests, grasslands, meadows, the tropics, and the tundra. However, not all species are found everywhere.
“Some Mycena fungi are very specialised, while others seem to be highly adaptable,” says Bugge Harder.
The five to six most adaptable species can be found in many different locations. Several of these are also among those with the largest genomes.
Two of these fungi are Mycena galopus and Mycena leptocephala. They are decomposers but seem to act as opportunists, invading plant roots.
Arctic fungi have exceptionally large genomes
The researchers found the largest genomes among Mycena fungi in the Arctic.
“The Mycena fungi from Svalbard have nearly 100,000 genes and 400-500 million base pairs. In comparison, most fungi have a genome of about 30-60 million base pairs,” says Bugge Harder.
It is already known that plants living in Arctic regions tend to have large genomes.
Researchers believes this makes them more robust against extreme and challenging conditions.
“We believe the Mycena fungi in Svalbard invade plant roots and go dormant while waiting for food to be provided, meaning for the plant to die,” explains Bugge Harder.
He notes that the fungi grow a little but let the plant live. If they do not need to compete with others for food, they can afford this strategy.
“The large genetic backpack prevents them from being fast. In return, they have genetic preparedness, giving them a greater chance of survival. In other places with more competition, it's about being the fastest,” he says.
The downside of the large genome is that every time a cell divides, it has to copy all the genetic material. This takes time and resources, making cell division slower than in fungi with smaller genomes.
One possible explanation for why the fungi have retained their large genomes despite the disadvantages is that Arctic conditions make it useful to experiment a bit, suggests Bugge Harder.
“If you have only one copy of a gene, you'll run into problems if it doesn't work or gets altered. If you have multiple copies, you can experiment without facing vital issues,” he says.
Genetic experimentation can give rise to new adaptations and functions.
“We also see that some genes seem to hitch a ride with the repeating sequences. Maybe it's a method that causes certain genes to be copied more than others?” wonders Bugge Harder.
Globally, many fungal species are under threat
“Some fungi grow only on old logs of dead wood,” explains Bugge Harder.
Other fungi grow exclusively in symbiosis with rare plants. The more specialised they are, the more threatened such fungi become.
Even though many fungi are endangered, Bugge Harder says that no Mycena fungi are listed as threatened.
“On the contrary, we see that clear-cut forests have plenty of Mycena fungi. They lie and wait within living plants and emerge to become dominant, like vultures, after logging. They seem to fare well in disturbed areas,” he says.
“In relation to evolutionary history, humans have introduced significant changes in a short period. Perhaps this is an advantage for these fungi,” he concludes.
References:
Harder et al. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations, Cell Genomics, vol. 4, 2024. DOI: 10.1016/j.xgen.2024.100586
Harder et al. Mycena species can be opportunist-generalist plant root invaders, Environmental Microbiology, vol. 25, 2023. DOI: 10.1111/1462-2920.16398
Thoen et al. In vitro evidence of root colonization suggests ecological versatility in the genus Mycena, New Phytologist, vol. 227, 2020. DOI: 10.1111/nph.16545
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Read the Norwegian version of this article on forskning.no
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