F Rosa Rubicondior: Creationism in Crisis - No Fun for Creationists in Evolving Fungi

Tuesday 24 October 2023

Creationism in Crisis - No Fun for Creationists in Evolving Fungi

Mycena purpureofusca
Fungal evolution discovered: Mycena can now invade living hosts – University of Copenhagen

An international team of mycologists led by Christoffer Bugge Harder of the Department of Biosciences, University of Oslo, Oslo, Norway has discovered that a family of fungi, the Mycena or Mycenaceae, also known as the bonnet mushrooms, is in the process of evolving a change of life style from that of a saprophyte (i.e., feeding on dead and decaying plant matter, mostly wood) to becoming a symbiont, living in cooperative alliance with other plants, or even a parasite able to invade and live on living plant tissues.

First a brief background on the Mycena:
Tell me about the Mycena family of fungi. The Mycena family, also known as the Mycenaceae, is a group of fungi that belongs to the order Agaricales, which includes many of the familiar gilled mushrooms. Mycena fungi are characterized by their small to medium-sized fruiting bodies with distinct features that set them apart from other mushroom families. Here are some key characteristics and information about the Mycena family of fungi:
  1. Size and Appearance: Mycena mushrooms typically have small to medium-sized fruiting bodies. They often have slender stems and caps with a conical to bell-shaped or convex shape. The caps can range in color from white and pale shades to various hues of brown, red, or yellow. The gills underneath the cap are usually closely spaced and attached to the stem.
  2. Ecology: Mycena fungi are saprobic, which means they primarily decompose dead organic matter, such as leaf litter, twigs, and decaying wood. Some Mycena species are known to form mycorrhizal associations with trees and other plants. They are commonly found in forested areas, particularly in temperate and tropical regions.
  3. Bioluminescence: One of the distinctive features of some Mycena species is their ability to produce bioluminescence. These luminescent species are often referred to as "foxfire" or "fairy fire." The bioluminescence is a result of a chemical reaction that occurs in specialized cells within the mushroom. Mycena species with this feature are found in various parts of the world, and their soft glow in the dark has intrigued and fascinated people for centuries.
  4. Diversity: The Mycena family is diverse, with hundreds of known species. Identifying individual species can be challenging due to the subtle differences in morphology and the presence of many closely related species. DNA sequencing and microscopic examination are often necessary for accurate identification.
  5. Edibility: While some Mycena species are considered edible and are consumed by foragers in some parts of the world, many are small and not commonly harvested for food. Due to the difficulty in identifying specific species and the potential for toxic look-alikes, caution is advised when considering the edibility of Mycena mushrooms.
  6. Taxonomy: The taxonomy and classification of Mycena mushrooms have evolved over the years with advancements in mycological research. Taxonomists continue to study and revise the classification of this fungal group.
In summary, the Mycena family of fungi is a diverse and interesting group of mushrooms known for their small to medium-sized fruiting bodies, bioluminescent capabilities in some species, and ecological roles in decomposing organic matter and forming mycorrhizal associations. While some Mycena species are edible, it's crucial to exercise caution and seek expert guidance when foraging for wild mushrooms, as some can be toxic or difficult to distinguish from toxic species.

Tell me more about the mycorrhizal associations.

Mycorrhizal associations are mutually beneficial symbiotic relationships between fungi and the roots of most vascular plants, including trees, shrubs, and many other types of plants. These associations play a crucial role in both the plant kingdom and the fungal kingdom and have significant ecological and agricultural importance. Mycorrhizal associations are essential for nutrient exchange, plant growth, and ecosystem health. There are several different types of mycorrhizal associations, with the two most common types being ectomycorrhizae and arbuscular mycorrhizae.
  1. Ectomycorrhizae (ECM): In ectomycorrhizal associations, the fungal mycelium forms a sheath around the plant's root tips and enters between the root cells, creating a complex network of fungal hyphae. This type of association is most commonly observed in trees, such as oaks, pines, and beeches. Ectomycorrhizal fungi are usually Basidiomycetes, including many species of the genera Amanita, Boletus, and Tricholoma. The mycorrhizal fungi provide the plant with nutrients, primarily nitrogen and phosphorus, and also improve the plant's ability to absorb water. In return, the plant provides the fungus with carbohydrates produced through photosynthesis. Ectomycorrhizal fungi do not penetrate the plant's root cells.
  2. Arbuscular Mycorrhizae (AM): Arbuscular mycorrhizal associations are the most widespread type of mycorrhizae, and they are formed between plants and fungi from the Glomeromycota phylum. These associations are found in a wide range of plant species, including agricultural crops, grasses, and many wild plants. In arbuscular mycorrhizal associations, the fungal hyphae penetrate the plant's root cells, forming specialized structures called arbuscules, where nutrient exchange takes place. These associations are especially important for nutrient uptake, particularly phosphorus, which is often present in the soil in forms that are difficult for plants to access. Arbuscular mycorrhizal fungi are obligate mutualists, meaning they can only survive in association with plants.
The benefits of mycorrhizal associations for plants include:
  1. Enhanced Nutrient Uptake: Mycorrhizal fungi can access and absorb nutrients, such as nitrogen, phosphorus, and other minerals, from the soil more efficiently than plant roots. They transfer these nutrients to the host plant, improving its nutrient supply.
  2. Improved Water Uptake: Mycorrhizal associations also enhance the plant's ability to absorb water from the soil, which can be especially valuable during drought conditions.
  3. Disease Resistance: Some mycorrhizal fungi can provide a degree of protection against soil-borne pathogens and diseases, helping to boost the plant's immune system.
  4. Soil Structure and Stability: The fungal mycelium helps create a stable soil structure, increasing soil porosity and reducing erosion.
Mycorrhizal associations are vital components of healthy ecosystems, as they facilitate plant growth and contribute to overall ecosystem stability. In agriculture, understanding and promoting mycorrhizal associations can lead to improved crop yields and reduced reliance on synthetic fertilizers and pesticides, which can have negative environmental impacts.

The team's research is published, open access in the journal Environmental Microbiology and explained in a press release from Oslo University:
Fungal evolution discovered: Mycena can now invade living hosts

FUNGI Biologists have long known mushrooms of the genus Mycena, commonly known as bonnet mushrooms, as fungi that live off of dead trees and plants. New research from the University of Copenhagen demonstrates that bonnets can also find their way into young, healthy trees and plants, where they try to cooperate. In doing so, they have made an evolutionary leap which challenges our understanding of the ecological roles of fungi.
Mycena can be recognized by their beenie-shaped mushroom caps - here it is Mycena haematopus.

Photo: Getty
Fungal spores float through the air. Thin strands of their mycelia creep along surfaces. They seek out defenseless hosts to wrap themselves around in webs of fungal growth. Their victims can then be used to satisfy their own need to devour and disperse.

That fungi have begun to invade the living is a horrific thought for anyone who ever thought that fungi only dined upon the dead. Or, at least for those who stream The Last of Us, a post-apocalyptic series in which humans battle relentless fungal-infected zombies.

Facts: Mycena

Most species of the Mycena genus are small, often only a few centimeters wide. Mycena caps are conical or bell-shaped and look like their common namesake – bonnets. Most are brown or gray but can also be whitish or almost transparent.

The fungi are generally not edible and can lead to poisoning and slight hallucinations.
Fortunately, reality is rarely so dramatic. But after Danish mycologists targeted local Mycena, known as bonnet mushrooms, it turned out that certain similarities emerged nevertheless.

New research from the University of Copenhagen’s Department of Biology suggests that this genus of fungi, which has traditionally been considered saprotrophic – i.e., a decomposer of nonliving organic matter – is in the midst of an evolutionary leap.

"Using DNA studies, we found that Mycena fungi are consistently found in the roots of living plant hosts. This suggests that bonnets are in the process of an evolutionary development, from uniquely being decomposers of nonliving plant material to being invaders of living plants, under favourable conditions," explains Christoffer Bugge Harder, the study’s lead author.

Photo: Getty
The research also demonstrates that some of these bonnet mushrooms species even show early signs of being able to act as mutualists – i.e., live in symbiosis with trees. Unlike the terrifying fungi in The Last of Us, the researchers believe that Mycena are primarily out to do good, as seen from the plant's perspective. This comes in the form of a kind of evolutionary courtship in which they live in harmony with their living hosts.

PCR and DNA sequencing used to find the Mycena

Using the PCR method that most people are familiar with from viral testing, the researchers found Mycena in samples of living trees in forests, meadows and Arctic mountain heaths around the world. In the method, strands of DNA are propagated when present in a sample so that they can be easily identified.

By sequencing the DNA strands so that part of the code is known, researchers were then able to search international databases of the most known fungal DNA and in doing so, determine whether the samples contained Mycena, for example.
"We see that a some Mycena appear to exchange nitrogen, an indispensable nutrient for plants, with carbon from plants," says the researcher.

"Once having penetrated a living plant, fungi can choose three strategies. They can be harmful parasites and suck the life out of their new hosts; they can lurk like vultures, waiting harmlessly for the plant to die, and be the first to feast upon the "carrion"; or, they can begin working together. Some Mycena species are gradually developing the ability to collaborate, though it has yet to be finely tuned," says Christoffer Bugge Harder.

Good deeds challenge traditional roles

"Other fungi, the Amanita genus for example, are known to work together with living plants, an ability that they developed many millions of years ago. But Amanita have long since lost their ability to survive without their hosts. And that’s how we traditionally divided fungi into strictly separate ecological groups: mutualistic, parasitic or saprophytic," explains Christoffer Bugge Harder.

Mycena seem to fall somewhere in between the ecological niches.

"The strict division has been increasingly called into question, and our Mycena research supports a blurring of the lines. Some Mycena have found their own solution and span several different ecological roles," says Harder.
Mycena leptocephala.
Photo: Arne Aronsen
Evidence of collaboration

Isotopes are versions of a chemical element that have a different number of neutrons, and therefore can be light or heavy depending on their composition.

E.g. as trees and mutualistic fungi work together, a larger proportion of heavy nitrogen isotopes are left in the fungi, as heavy isotopes are more difficult to move.

Because they are left to a greater extent when a fungus has shared nitrogen with its host plant, it is something that researchers can measure.
By looking at carbon isotopes in Mycena, the researchers were able to conclude that these fungi are saprotrophic decomposers, as well as mutualistic. And perhaps even parasitic.

"Mycena are opportunists. Unlike Amanita, they can easily grow without needing to invade plants, but should the opportunity arise, it’s a nifty bonus. They also seek out living roots, where they have nitrogen to offer – as fungi can take up nitrogen easier than a tree – for a reasonable price," explains Christoffer Bugge Harder.

Payment comes either in the form of carbon from the host while it is living, or when their friendly host dies, and the patient decomposer gets to work. Or perhaps both.

Seizing a human created opportunity

The favourable conditions sought after by Mycena seem to be related to human activity.

"It is reasonable to believe that we humans have played a role in this adaptation, because our monocultural plantations, stands of forest for example, have provided fungi with optimal conditions for adapting. The fungi seem to have seized upon this opportunity," he says.
Facts: The fungal kingdom’s three ecological niches
  • Species that have specialized in living off of nonliving vegetation for millions of years are known as saprotrophic fungi.
  • Species that feed on living vegetation are called parasitic fungi.
  • Fungi that coexist symbiotically with living trees and plants and exchange nutrients with their host are known as mutualistic.
However, the traditionally strict division of fungi into three ecological niches is increasingly being called into question. Mycena is a new example of a fungus that blurs the lines.
"Specialists thrive in old-growth forest. In this scenario, there aren’t many chances for Mycena to settle on living trees because specialized fungi are already present in this natural setting and don’t allow others in," says the mycologist.

On the other hand, human cultivated homogeneous plantations with young plants of the same age give Mycena a chance, because specialized fungi have yet to establish themselves. The same applies to harsh environments, such as in the Arctic, or disturbed environments, e.g., where there are many grazing animals about.

"These places present challenging conditions for many organisms, but Mycena are among those that seem to benefit," says Christoffer Bugge Harder.

The researcher and Mycena in the field.
Photo: Jacob Heilmann-Clausen
Extra info: Fear not fungi

Recent research has demonstrated that many trees bear the seeds of their own destruction – or at least those of an effective funeral director, as some of the fungi that thrive at their roots are also ready to begin decomposing them once they die.

After we humans die, fungi often play an important role in our decomposition as well. However, Christoffer Bugge Harder assures that we should not be worried about fungi invading us while we are still alive.

"The human body, unlike trees, is exceptionally adept at protecting us from the enormous amounts of spores that we are exposed to on a daily basis," he says.

Nevertheless, there has been an increased global focus on fungal infections as a threat to human health in recent years. This is because an essential aspect of the human body's defenses is our body heat, which is intolerable to many fungi. There is now speculation that climate change, and rising temperatures in particular, could lead to an adaptation in the fungal kingdom that would allow them to survive at our body temperature.

"It isn’t inconceivable that groups of fungi relevant to the ecological niche of humans could develop. But, there are lots of fungi in tropical regions which have already adapted to high temperatures. When they're not in our bodies anyway, it is due to our effective immune system. So, I don't see any reason to fear fungi – or at least not worry about Mycena," says Christoffer Bugge Harder.
Behind the research

In addition to Christoffer Bugge Harder, the following researchers have contributed to the study:
  • Emily Hesling - University of Aberdeen, UK
  • Synnøve S. Botnen - University of Oslo and Oslo Metropolitan University, Norway
  • Kelsey E. Lorberau - University of Oslo and UiT - The Arctic University of Norway, Norway
  • Bálint Dima - Eötvös Loránd University, Hungary and University of Helsinki, Finland
  • Tea von Bonsdorff-Salminen - University of Helsinki, Finland
  • Tuula Niskanen University of Helsinki, Finland and Royal Botanic Gardens, Kew, UK
  • Susan G. Jarvis - UK Centre for Ecology & Hydrology, UK
  • Andrew Ouimette - University of New Hampshire, USA
  • Alison Hester - The James Hutton Institute, UK
  • Erik A. Hobbie - University of New Hampshire, USA
  • Andy F. S. Taylor - University of Aberdeen, UK The James Hutton Institute, UK
  • Håvard Kauserud - University of Oslo, Norway
To summarise, by analysing samples from different ecosystems around the world and comparing DNA sequences with a database of fungal DNA, the team were able to show the fungi of the Mycena family are in the process of changing from purely saprophytes living on dead wood, to becoming symbionts with living plants or even parasitic on them.

In their open access paper in Environmental microbiology they say:

Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of 13C/15N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published 13C/15N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.


The investigation of the trophic status of the genus Mycena using sequence data from wild plant roots and δ15N and δ13C signatures yielded the following: (1) In 9 of 10 analysed herbaceous and ericaceous plants and tree mycorrhizal host plants from temperate, alpine and Arctic environments, Mycena was consistently present in living plant roots across species and in different environments, while other saprotrophic taxa were only occasionally present. (2) The stable isotopic data on carpophores suggested that, although the genus Mycena is indeed mostly saprotrophic, strains of certain Mycena species can display an ecological versatility in the field and exchange nutrients with plants, consistent with previous results from in vitro resynthesis experiments. (3) Mycena infections were not generally more prevalent in Arctic environments or at higher altitudes, but we hypothesize that infection may be more prevalent under conditions of disturbance. (4) The ability to invade living plant roots is a feature of multiple Mycena species that do not discriminate between plant hosts. The evidence that fungal trophic modes may be variable on the species level and that within a large genus such as Mycena, there may be several potential trophic options in addition to pure free-living saprotrophy, raises intriguing questions about the general understanding and study of fungal ecology and the evolution of plant-fungus interactions. More research directly targeting root-associated fungi with unclear or unknown ecologies is required to resolve these questions. This study highlights the importance of continued detailed studies on interactions among organisms at the species level. Such studies would enhance data usage from broad, environmental metabarcoding approaches to community characterization.
Harder, C.B., Hesling, E., Botnen, S.S., Lorberau, K.E., Dima, B., von Bonsdorff-Salminen, T. et al. (2023)
Mycena species can be opportunist-generalist plant root invaders.
Environmental Microbiology, 25(10), 1875–1893. DOI: 10.1111/1462-2920.16398

Copyright: © 2023 The authors.
Published by Applied Microbiology International. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
The significance of the fact that the scientists explain these changes by reference to the process of evolution and not to a magic entity intelligently redesigning the fungi will probably be ignored by creationists determined to believe the absurdity that scientists are abandoning the Theory of Evolution in favour of their magical fairy tale.

What they probably won't want to understand either is that a perfectly designed organism should not need to change, especially, as in this case, simply to exploit an available niche, and yet here we have a whole family of fungi apparently making an evolutionary 'leap' from being purely saprophytic to mutualism ad even parasitism.

And of course, they will need to ignore the fact that mutualism between fungi and plants from which both benefit, would not have been necessary if they had been perfectly designed because neither of them would be deficient in some way.

Also to be ignored, is the fact that this is an example of the needless complexity which refutes the notion of intelligent design, which is characterised by minimal complexity. In a way typical of evolved systems, we have a ridiculously complex system for plants and fungi to obtain the nutrients they need, which would not even have been necessary if they had been intelligently designed in the first place.

Thank you for sharing!

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