The fungal kingdom and decomposition

Old drawing showing several mushrooms. — Mushrooms drawn in brown wash and gouache by Georg Wilhelm Baurenfeind in 1751. Georg Wilhelm Baurenfeind (c. 1710–1763); The Cleveland Museum of Art, CC0, source

A fungus is not a plant. It is closer to us than to a tree.

This sentence sounds absurd. Yet it is rigorously established, as we shall see.

What was believed, and why it was reasonable

Fungi were long classed with plants.

The reasons are clear: they do not move about, they grow in the soil, they have no mouth, no eyes and no legs, and they spring up after rain like shoots in spring. Everything that could be observed with the naked eye pointed towards the plant world.

It was only in the twentieth century that they were given a kingdom of their own — the kingdom Fungi — and only later that their true place in the tree of life was discovered.¹

The group’s name comes from a wonderful detail

Fungi and animals form a single phylogenetic group, called the opisthokonts.

This learned name comes from a microscopic observation: their flagellated cells bear a single flagellum located at the rear — a filament used for propulsion, placed behind rather than in front.²

This same rear flagellum today propels the spores of certain aquatic fungi (such as the chytrids) and the sperm cells of animals. A detail of locomotion preserved since a common ancestor that no one has ever seen.

How it was established: four separate paths

It was not a single isolated measurement that settled the question. Four different proteins, examined separately — actin, alpha-tubulin, beta-tubulin and elongation factor — all place animals and fungi together, to the exclusion of plants.³

Added to this is a decisive signature: an insertion of twelve amino acids in a key protein, shared only by animals and fungi, and absent from plants, protists and bacteria. A signature of this length does not occur twice by chance. One last clue, a metabolic one this time: fungi store their energy in the form of glycogen, like animals, whereas plants store starch.⁴

The approach is the same as Jean Perrin’s: he established the existence of atoms through thirteen distinct methods that all converged on the same value. If the result came from an artefact, why would four different methods produce exactly the same bias?

The consensus is solid, which does not mean that everything agrees: certain genes analysed in isolation place animals closer to plants, and certain datasets show accelerated rates of evolution that can be misleading. Science advances by integrating these anomalies rather than by hiding them.

Decomposition: who can break down wood?

A dead tree eventually disappears. This seems obvious, but it is not obvious at all.

Wood contains lignin, a complex molecule that gives it its rigidity and that is extremely difficult to break down. Very few organisms can do this: essentially the so-called “white rot” fungi. Brown rot fungi, for their part, slightly modify the lignin in order to attack the cellulose and hemicellulose of the wood.⁵

Without these saprotrophic organisms, dead organic matter would not be recycled. It would accumulate indefinitely, blocking the carbon and nutrient cycles.

An attractive thesis (2012)

There is a geological period, the Carboniferous, during which enormous quantities of plant matter did not decompose: they accumulated and formed the coal that we burn today.

A study published in 2012 proposed an elegant explanation: the ability to degrade lignin by means of peroxidases is thought to have appeared about 295 million years ago, roughly coinciding with the end of this period of accumulation. Before the decomposer fungi, wood piled up; after them, it rotted.⁶

A decisive refutation (2016)

In 2016, a team of palaeontologists and geologists reopened the case. It raised four objections, and they are worth following, because each one is of a different kind.⁷

First objection — the material was not what was thought. A large proportion of Carboniferous coal is made up of unlignified plant tissue. Lignin was therefore not the dominant component.⁸

Second objection — the natural experiment. Over the course of this period, the vegetation changed several times: lignin-poor plants gave way to lignin-rich plants, and vice versa. Yet coal continued to accumulate at the same rate through these shifts.⁹

This point is worth dwelling on. If lignin was the cause, the rate should have varied with it. It did not vary. Nature had carried out the experiment for us, and the result is negative.

Third objection — the traces. Marks of decay are present everywhere in the fossil record, on all organic matter exposed to the air during deposition. Organisms already knew how to break down wood.¹⁰

Fourth objection — reasoning by reductio ad absurdum, and it is the strongest. If lignin had accumulated for a hundred million years without ever decomposing, all the world’s carbon would have ended up buried. The authors calculate that a much smaller imbalance would have been enough to strip the atmosphere of its carbon dioxide in less than a million years. Nothing of the kind happened. The hypothesis is therefore untenable.¹¹

One last fact, simple and decisive: coal is still forming today, wherever conditions allow.¹²

What, then, is the explanation? It is geographical and climatic: a constantly wet tropical climate, and vast areas where sediments accumulated, brought together at the time when the supercontinent Pangaea was forming.¹³

The coincidence of dates was real. It was not a cause.

A methodological bias as a bonus

Why did it take so long to map the history of fungi?

Fungal fossils are greatly under-represented in the records: at the Permian–Triassic boundary, for example, palynologists focused mainly on plant pollen and spores, and left fungal remains unidentified, or set aside. They were passed over because people were looking for something else. An absence in the data was simply an absence in the method.¹⁴

The safeguards: parasites, regulators and threats

While fungi are essential to the recycling of matter, they are also agents of regulation and formidable pathogens.

Crop pathogens: microscopic fungi such as wheat stem rust (Puccinia graminis) can wipe out a large part of a harvest; a fungus-like organism, the agent of potato late blight, caused the Irish famine of the 1840s.
The threat to biodiversity: the chytrid Batrachochytrium dendrobatidis causes chytridiomycosis, a skin disease that is decimating amphibian populations worldwide (see Entry 5.5).
The danger of foraging: morphological confusion is common. The death cap (Amanita phalloides) resembles several edible species and causes severe, sometimes fatal liver damage. ¹⁵

How many species, and since when?

How many species? A long-accepted estimate gave 1.5 million species; the 2017 reassessment, based on environmental sequencing, gives between 2.2 and 3.8 million, and others go as high as 5. In 2017, only about 120,000 had been described.
Since when? Reliable fungal fossils went back only to the middle of the Palaeozoic era. Fossils from Canada, 900 million to 1 billion years old, may already be fungi, which is consistent with the molecular clocks (between 760 million and 1.06 billion years). The two methods do not measure the same thing: one dates the genetic separation, the other the presence of preserved physical structures.¹⁶

Medical and safety warning

⚠ A mushroom must never be eaten on the strength of a web illustration or an app. Some deadly species are almost identical to edible species. No general information page can replace the expertise of a pharmacist or a qualified mycologist in the field. No foraging guidance is provided on this site.

Note 1

For hundreds of years, all fungi were considered to be plants. […] It wasn’t until the mid-20th century that fungi were moved from the Plant Kingdom to their own new Kingdom […]

Johnston, Eddie, “What in earth? Understanding what fungi really are”, Royal Botanic Gardens, Kew, 7 October 2022