Discovering the world of fossil fungi

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Violeta de Anca Prado and Stephen McLoughlin (Sweden)

When people think of fossils, they usually picture slabs of rock bristling with bones, or the shells of ammonites or trilobites. Most do not even consider that delicate organisms, such as fungi or bacteria, can even fossilize – they seem too fragile to be preserved as they lack a hard skeleton. In many cases this is true. Microscopic organisms that lack hard parts have fewer chances of being fossilised but, despite the odds, delicate fungi have a fossil record that is more extensive than generally thought.

The fossil record of fungi goes all the way back to the Proterozoic. Identifying the oldest fossil fungus is difficult because many reports of early fungi have later been reinterpreted as filaments of green algae or cyanobacteria. Nevertheless, increasing reports of fungi from the late Proterozoic are consistent with DNA comparisons (the so-called “molecular clock” method) that suggests fungi, plants and animals diverged about 1,600 million years ago. What is more certain, is that fungi were actively diversifying in terrestrial habitats as soon as plants gained a foothold on land.

Fungi are fossilised in diverse styles. Usually, the best examples are preserved inside permineralized (petrified) wood or peats. The process of permineralization involves the organic tissues becoming entombed within mineral matter (usually calcium carbonate or silica), which is precipitated from solution in groundwaters. More rarely, we encounter fungi preserved as impressions, which are like a “fingerprint” of the organism – the original fungus has decayed but the imprint remains. Another style of preservation is compression. Plants are commonly preserved in this manner – coal being an example of plant remains becoming compressed and homogenised. Sometimes we find fungi, either parasites or decomposers, preserved as distinctive dots and irregular patches on the surfaces of leaf compressions.

A rare but amazing type of fossilisation that we encounter is mummified fungi. Mummification occurs when the specimen is buried very quickly in a dry, cold or acidic environment, where it can avoid being broken down by bacteria. As this process does not involve mineralisation, details of the original soft tissues can be observed and, in young fossils, even DNA can be recovered, providing insights into the evolution of fungi.

But what are fungi? And why should we care about them? Fungi occur everywhere from the highest mountains to the deep crust. They are heterotrophs – that is, they do not generate their own food like plants, but need to feed on organic matter. Like plants, fungi are largely immobile, although they can move very slowly by producing a network of hyphae (thread-like cells) that you may see creeping through leaf litter. They reproduce either asexually (by budding off clones) or sexually (just like animals). Their reproductive structures, called sporophores, come in many shapes and sizes and release clouds of tiny spores that provide another means for fungi to disperse.

Fungi are ecologically important as they play a vital role in nutrient cycling. One key function in ecosystems is as decomposers, in which they have a direct impact on the carbon cycle. By decomposing organic matter, they break down complex macromolecules into simpler mineral nutrients that plants can re-use. About 95% of modern plants are known to have symbiotic (mycorrhizal) associations with fungi through their root systems for the uptake of nutrients. Within these associations, plants provide complex sugars to the fungus, while the fungus provides water and key mineral nutrients to the plant. Some fungi are also serious parasites and pathogens of plants and animals. For the fossil collector, it is important to know that some of these interactions with plants and animals can be traced back to the dawn of life on land.

Now that the importance of fungi is clear, how are they classified? Fungi are divided into several major groups – all with long and difficult-to-pronounce names: for example, Chytridiomycota, Zygomycetes, Glomeromycota, Ascomycota and Basidiomycota.

  • Chytridiomycota are saprotrophs (decomposers) and parasites. This group diverged early in the evolutionary tree of fungi. They are very ancient and retain a motile stage (spore with a whip-like tail) in their lifecycle. Many are aquatic and occur as parasites on plants back to the Devonian.
  • Zygomycetes are also saprotrophs, parasites and mycorrhizal forms. The parasitic species often attack insects. Mycorrhizal species live in symbiosis with plants, promoting growth by exchange of nutrients. A characteristic of this group is that they lack septa (cross-walls) in their thread-like hyphae. This means that all the “cells” are connected into a continuous tube.
  • Glomeromycota are mainly obligatory symbionts, forming arbuscular mycorrhizae. They penetrate plant root cells and form tightly knotted masses of hyphae called arbuscles that provide the plant with phosphorus, nitrogen, sulphur and other key micronutrients. Glomeromycota are similar to Zygomycetes in lacking septa in their hyphae and having spores of similar form.
  • Ascomycota, the largest group of modern fungi, is characterised by production of asci (sac-like reproductive structures) that typically contain eight ascospores. This group includes one of the most important fungi in human culinary history, Saccharomyces cerevisiae (a type of yeast). This yeast is fundamentally important in the fermentation process and is crucial to baking the bread, brewing the beer and fermenting the wine we consume every day. Penicillium, from which we obtain the antibiotic, penicillin, is another economically vital member of the Ascomycota.
  • The last group, Basidiomycota is probably the most well-known, as it includes all the mushrooms, puffballs and bracket fungi we are generally familiar with. The group is very diverse, ranging from microscopic to enormous. Indeed, a single specimen of Armillaria fungus in Oregon is commonly argued to be the largest living organism on Earth – its underground hyphal network spanning 9.6km2 and weighing greater than 30,000 tonnes.

Now that we know a little bit about fungi, what are some examples in the fossil record? If you ever dig in Quaternary peat bogs looking for leaf or animal fossils, you may encounter mummified bracket fungi (Fig. 1). These are the reproductive structures of Basidiomycota that were decomposing the dead plants before being buried themselves in the peat swamp. Quaternary peat bogs typically contain many fungal groups, including Ascomycota, Basidiomycota and Zygomycetes, but you may need a microscope to see some of the smaller forms.

Fig. 1. Fossil bracket fungi from Quaternary peat deposits: (A) Polyporus fromentarius from Åskammen, Sweden; and (B) Polyporus igniarius from Robenhausen, Switzerland. Scale bars = 10mm.

In rare cases where plant fossils have been preserved rapidly by permineralization, fungi of the Chytridiomycota can be found as parasites on or within plant tissues. These fungi are extremely small, so thin-sections need to be cut from the permineralized wood or peat and studied with a transmitted-light microscope to be able to detect the parasitic fungi. In Permian strata, it is common to find chytrid fungi parasitizing pollen grains (Fig. 2).

Fig. 2. Parasitic chytrid fungi within a Permian pollen grain from the Prince Charles Mountains, Antarctica. Scale bar =10µm.

Other fossils that you will find with a light microscope are fungal spores (Fig. 3). These are among the most common fossil one can find. Since they are dispersed by the wind in their millions, dispersed fungal spores have accumulated in sedimentary rocks the world over.

Fig. 3. Cluster of fungal spores in a Permian permineralized peat from the Prince Charles Mountains, Antarctica. Scale bar = 20µm.

If you are lucky, you might find delicate fungal hyphae (filamentous cells) in fossil woods. Many hyphae together form a mycelium – the ‘vegetative’ part of the fungus. Hyphae can either contain septa (cross-walls) or be non-septate. If you follow a hypha, you may find distinctive branching patterns, such as H- or Y-shaped connections (Fig. 4), or clamp connections, which develop in the hyphae of reproductive tissues.

Fig. 4. Fossil fungal hypha with Y-branching (arrowed) from the Permian of Antarctica. Scale bar = 20µm.

If invasive pathogenic fungi are preserved inside wood, you may see how they penetrate from cell to cell (Fig. 5) and also how the plant defended itself by reinforcing the walls of cells that were infected by fungi (Fig. 6).

Fig. 5. Fungal hyphae in the stem tissue of a Tempskya tree fern from the Paleocene of Kent, UK: (A) sinuous and branched fungal hyphae penetrating cell walls; and (B) hypha with a terminal reproductive body (arrowed). Scale bar = 10µm.
Fig. 6. A wall thickening (apposition) providing defence for neighbouring cells from fungal infection. Scale bar = 10µm.

Distinctive cavities may be left in fossil wood caused by the decomposing activities of ancient fungi. A good example is pocket rot in 260 million-year-old (Permian) Glossopteris wood from Antarctica (Fig. 7), which is similar to white pocket rot in modern trees.

Fig. 7. Fungal pocket rot in Permian glossopterid wood from Antarctica. Scale bar = 10mm.

Plant roots are commonly fossilised by permineralization. In these, you may find evidence of ancient symbiosis. Mycorrhizal fungi are found inside root cells as far back as the Devonian and prove just how ancient the interactions between plants and fungi really are.

Lichens are a special case of symbiosis. They represent a mutually beneficial relationship between a fungus and an alga (or, in some cases, a cyanobacterium). Lichen fossils are especially rare. However, in a few places where spring water is rich in calcium carbonate, the lichens growing on surrounding damp soil can become encrusted with minerals that faithfully preserve the shape of the branching thallus (Fig. 8).

Fig. 8. Fossil lichen (Peltigera canina) impression in Quaternary calcrete, Filsta, Sweden. Scale bar = 10mm.

In many cases, we must resort to the microscope to find fossil fungi. However, there is one type of fossil fungus that breaks all the rules. Prototaxites is a Devonian fossil genus originally described by Canadian geologist J W Dawson in the mid-1800s. The fossil contained what appeared to be growth rings and was so large and that he interpreted it as an ancient conifer tree (Fig. 9).

Fig. 9. Prototaxites logani – a giant, lichen-like fossil from from the Devonian of Overath, Germany: (Left) portion of the ‘trunk’ (scale bar = 10cm); (Centre) thin-section showing ‘growth rings’ (scale bar = 10mm); and (Right) enlargement of the ‘trunk’ surface (scale bar = 10mm).

More recent anatomical studies have shown it to be composed of fungus-like filaments rather than plant cells. Although its affinities remain hotly debated, it may have been a giant, lichen-like structure or have had a mycorrhizal association with surrounding plants. Regardless of its affinities, these giant fungi (reaching diameters of 1m and heights of over 8m) ruled the landscape during the late Silurian and Early Devonian, at a time when green plants grew no more than half a metre tall.

Another group that may be encountered when searching for fossil fungi with the microscope is a member of the group Oomycetes (also called Peronosporomycetes or water moulds). These organisms are not true fungi, although they have some features in common. Both have hyphae and can be decomposers or parasites, but Oomycetes have reproductive structures that differ from true fungi. Today, Oomycetes includes the genus Phytophthora (the “plant destroyer”), which includes major parasites of crop plants the world over. Fossils of Palaeozoic and Mesozoic Oomycetes are reasonably common in silicified peats and coal balls, and they have very distinct, globe-shaped oogonia, commonly covered by branched spikes (Fig. 10).

Fig. 10. Selection of four oogonia (female reproductive organs) of oomycetes (water moulds) in a middle Permian permineralized peat, Antarctica. Scale bar = 10µm.

In the search for fossil fungi, it is important to remember that not everything in the rock that looks like a mushroom is a fungus. Many natural concretions can take on the shape of a mushroom (Fig. 11), but these are simply formed by precipitation of minerals into peculiar shapes within sedimentary rocks and have nothing to do with fungi at all.

Fig. 11. Pseudofossils – mushroom-like concretions in glacial clay, Sörmland, Sweden. Scale bar = 10mm.

In conclusion, fungi were everywhere in the ancient past and are still thriving beside us today. They have a fossil record that is much more complete than once thought and extends back as early as that of plants and animals. Fungi dominated the landscape during the rise of land plants, and they also proliferated in the aftermath of major extinction events. Fungi are key players in biotic interactions that involve symbiosis, parasitism, pathogenicity and decomposition. It is by studying fossil fungi that we gain insights into how the complexity of terrestrial ecosystems evolved through time. Fossil fungi are out there and waiting to be discovered.

About the authors

Violeta de Anca Prado is a student at Stockholm University and has been undertaking an internship investigating microbial fossils at the Swedish Museum of Natural History. Stephen McLoughlin is a Professor and Senior Curator of palaeobotany at the Swedish Museum of Natural History, Stockholm. He is presently investigating insect-plant-fungal interactions in the fossil record, especially in relation to ecosystem change through mass extinction events.

Further reading

Blackburn, C. de, 2006. Food Spoilage Microorganisms. Woodhead Publishing, Cambridge, 736 pp.

Loron, C.C., 2019. Early fungi from the Proterozoic era in Arctic Canada. Nature 570, 232–235.

Dighton, J., 2003 Fungal Ecology: Fungi in Ecosystem Processes. Dekker, New York, 432 pp.

Taylor, T.N., Krings, M. & Taylor, E.L., 2015. Fossil Fungi.Academic Press, London, 382 pp.

Vajda, V. & McLoughlin, S. 2004. Fungal Proliferation at the Cretaceous-Tertiary boundary. Science 303, 1489.

Webster, J. & Weber, R., 2007. Introduction to Fungi. Cambridge University Press, Cambridge, 841 pp.

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