Fungi and their Kingdoms

Classification

The scientific classification of living organisms started in the 18th century and at that time there were only two Kingdoms of living organisms—the Plant Kingdom and the Animal Kingdom. Anything that didn't move was put in the Plant Kingdom, so that's where fungi were classified. However, fungi are very strange 'plants' since they don't make their own food, as 'ordinary' plants do via photosynthesis. Despite that, the two-kingdom system was retained into the second half of the 20th century. By then, the electron microscope's ability to show fine microscopic structural detail was making it obvious that the two-Kingdom classification was inadequate.

While everyone now agrees that fungi do not belong in the Plant Kingdom, there is still some debate over the number of Kingdoms needed to accommodate the living world. This means that you are very likely to see a number of different classification schemes as you look in different books or web sites.

In the classification followed in the Fungi of Australia, the fungi are spread across three Kingdoms-Protoctista, Chromista and Eumycota. These Kingdoms are defined largely on the basis of certain microscopic features revealed by the electron microscope. In addition, studies of fungal biochemistry and, more recently, DNA studies have also helped determine relationships between different groups of organisms and show that fungi are more closely related to animals than plants. However, there is still a great difference between animals and fungi, with the two groups having diverged evolutionarily a billion or more years ago.

Even when the fungi were classified in the Plant Kingdom, people recognized that many of the microscopic fungi were not 'proper' fungi, since they differed significantly from the other organisms called fungi. Even today, the Eumycota are often referred to as the 'true fungi'. However, the word 'fungi' is still commonly used as a collective term for various Divisions from all three Kingdoms. All fungi release microscopic spores. These come in many forms, but in all cases the spores are either sexual or asexual reproductive units. Fungi in some Divisions produce mobile spores (zoospores) with filamentous asexual appendages called flagella. There are two types of flagellum: a smooth flagellum is called a whiplash flagellum; and, a flagellum where the main stem has fine, hair-like projections is a tinsel flagellum.

In some books or web sites you will see the term undulipodium, rather than flagellum.

The organisms in all of the Kingdoms mentioned here are eukaryotes. In a eukaryote there is a nucleus differentiated from the rest of the cell, and the genetic material (or chromosomes) are held in the nucleus.

This distinguishes them from the bacterial organisms, which have no such nucleus.

All the fungi are capable of producing asexually and many, but not all, also reproduce sexually—that is, by combining the genetic heritage of two parents. In many cases, the feeding stages looks quite different to the reproductive stages.

Examples of hierarchical classification

Many people use hierarchical information every day without necessarily realizing it. For example, if you're getting a parcel delivered from overseas you might write out your address much like this example,

12 Smith Street
Box Hill
Melbourne
Victoria
Australia

This uniquely identifies your geographic location and if you read the address in reverse you'll see that each line narrows things down a bit more. Going from the broadest geographic category to the finest you have:

Country Australia
State Victoria
City Melbourne
Suburb Box Hill
Street Smith
House number 12

Example of fungal hierarchy

In a similar way, any fungus can be similarly classified, through a sequence of categories, from broadest to finest. For example, here's the hierarchical classification of Aseroë rubra, one of the stinkhorn fungi:

Kingdom Eumycota
Division Basidiomycota
Class Euholobasidiomycetes
Order Phallales
Family Clathraceae
Genus Aseroë
Species rubra

In the classification hierarchy, Division is the first step below Kingdom. In this web site there are brief descriptions of the major characteristics of the Divisions in which the fungi are placed. To go any lower than Division would need more technical terminology and won't be done here. The first chapter in Fungi of Australia, Volume 1A gives considerable detail about classification down to order.

Kingdom Protoctista

The shortest way of defining the Protoctista is to say that they are what's left of the eukaryotes once you've defined the Chromista, Eumycota, Animals and Plants. Sometimes the term 'Protozoa' is used instead of Protoctista.

This is a diverse Kingdom, containing numerous micro-organisms (but also the giant kelps) and the only fungal representatives are the slime moulds, constituting the Division Myxomycota.

Given that this is an ill-defined Kingdom of 'left-overs', it is inevitable that as research continues there will be changes to the limits of this Kingdom. Already, some people think that this diverse Kingdom should be divided into several Kingdoms. Conversely, if you look at some older books you will find that many people previously included the Divisions Oomycota, Chytridiomycota and Hyphochytriomycota in the Protoctista.

Division Myxomycota

Within the Myxomycota the most commonly seen slime moulds are members of the Class Myxomycetes, often called the 'true slime moulds'. While there is much variation between the species of the true slime moulds, they all have a two-stage life cycle: a mobile feeding stage and a stationary sporing stage.

The mobile, feeding form (called a plasmodium) is typically of sloppy consistency and without cell walls. The plasmodium moves across the ground or through cavities in dead wood, engulfing bacteria, spores and organic debris. The most common plasmodial colours are yellow and white.

The plasmodium moves by pushing out one or more sloppy 'feelers' and the rest of the plasmodium then flows into the 'feelers'. Sometimes you get cross-connections between the advancing feelers, giving the plasmodium a net-like look.

Kingdom Chromista

Most members of this very diverse Kingdom are not fungi!

All the species in the Kingdom Chromista produce zoospores, and each zoospore has at least a tinsel flagellum. All species in this Kingdom have tubular hair-like projections on the tinsel flagellum.

In the Chromista there are both organisms that contain chlorophyll and organisms without chlorophyll. Those organisms with chlorophyll can, like plants, make their own food via photosynthesis. The fungal members lack chlorophyll, are unicellular or filamentous, and have cellulose in the cell walls. There are two Divisions of fungi in the Kingdom Chromista, all members of which have cellulose cell walls and are unicellular, or multicellular and filamentous. The separation of the two fungal Divisions in this Kingdom is based on the structure of the flagella on the zoospores.

The members of the Division Oomycota have biflagellate zoospores, with one posterior whiplash and one anterior tinsel flagellum while the members of the Division Hyphochytriomycota have zoospores with one anterior tinsel flagellum.

Members of the Division Oomycota (commonly called oomycetes) are found in many habitats. Some species are the 'water moulds' that are saprotrophs on plant and animal remains in wet soils and freshwater, or parasites of various aquatic organisms. The 'downy mildews' are in this Division and they are plant parasites known to many gardeners. Various species can also be found in sewerage-polluted waters. The saprotrophs in this Division are important as de-composers and re-cyclers of dead organic matter. There are under a thousand species of oomycetes in the world. One oomycete genus, Phytophthora, has caused considerable economic, social and ecological damage. The Irish Potato Famine of 1845 -1850 was caused by Phytophthora infestans. Unusually wet conditions allowed this fungus to grow well and destroy much of the Irish potato crop. A combination of death and emigration saw the population of Ireland drop by about 25%. Another species, Phytophthora cinnamomi, or Cinnamon Fungus, is a significant contributor to dieback in many Australian forests.

The Hyphochytriomycota (or hyphochytrids) are found in soil, freshwater and seawater (the seawater species being parasites of marine algae). Only a small number of genera and 25 species are known and, while they are of evolutionary interest, they are of little practical importance to people. The proper classification of the hyphochytrids is still uncertain and the group needs more study. So the placement of the group in the Chromista is tentative and future research may well move them elsewhere. Some hyphochytrids are parasitic on spores of Oomyctes.

Kingdom Eumycota (the 'true fungi')

In some of the simpler chytrids, the whole vegetative cell transforms into a spore—producing cell, while in others there is differentiation-with only a part of the vegetative phase transforming into a reproductive, spore-producing sporangium.

The chytrids show a wide variety of behaviour. Many are saprotrophs in soil or freshwater and include species capable of decomposing cellulose and others that degrade chitin (the constituent of insect exoskeletons).

There are also parasitic chytrids, with different species parasitizing plants, algae, fungi, invertebrates. Some cause few, if any, symptoms in their hosts while others are serious pathogens. At least one chytrid species parasitizes pollen grains! For some years many areas of the world (Australia included) have been seeing a decline in frog numbers. Research has shown that a chytrid, Batrachochytrium dendrobatidis, is a major culprit. However, the ecologies of these chytrid species are still not understood.

This site deals with chytrids in frogs, and has a strong Australian perspective and is well-written for a general audience -
http://www.jcu.edu.au/school/phtm/PHTM/frogs/adms/scope.htm

A number of anaerobic chytrids are found in the guts of plant-eating animals. Native Australian animals known to have gut chytrids include: red kangaroos, eastern grey kangaroos, swamp wallabies, red-neck wallabies, wallaroos and tamar wallabies. Chytrids are also found in the guts of non-Australian animals such as sheep, cattle, impala, llama, goats, reindeer, camels, horses, elephants, rhinoceroses. There are under a thousand species in this Division.

All species of fungi in the other four divisions are made up of hyphae (which are microscopically thin filaments) and none produce zoospores.

The hyphae of the Division Zygomycota do not have cross-walls (or septa).

This Division is divided into two classes—Trichomycetes and Zygomycetes.

The Trichomycetes are always associated with invertebrates, either as parasites or mutualists. Some are attached to invertebrate exoskeletons but, more commonly, they are attached to the lining of the digestive tracts of their hosts. Given their nature, most Trichomycetes are found only after dissection of their hosts.

The Zygomycetes are widespread in many habitats and there are saprotrophic, parasitic and mutualistic species. Most people will be very familiar with one widespread Zygomycete, the common bread mould Rhizopus stolonifer. A number of Zygomycetes, in particular the genus Pilobolus, are early colonisers of fresh dung. This picture of a Pilobolus on rabbit dung shows a small black disk on a swollen, colourless bladder. The black disk contains a mass of spores and is shot off when the bladder ruptures.

This picture of a species of Phycomyces growing on water agar shows numerous, branching hyphae.

Many of the Zygomycota are parasites of invertebrates such as amoebae, nematodes and insects. Many people will have seen dead houseflies, covered or surrounded by a white 'powder'. In fact, the fly will have been killed by a member of the Zygomycota and the powdery granules are asexual spores of the fungus, ready to infect any other fly that walks across that powdery layer. The infected flies often crawl to exposed areas, such as window panes, before dying.

The Zygomycota have traditionally included an Order of fungi called the Glomales, which includes the genus Glomus. These fungi are both ecologically and economically important, for they form mutualistic associations (called mycorrhizae) with numerous plant families. Recent research shows that they are a tight-knit, well-defined group with an evolutionary history separate from those of the other fungi in the Zygomycota. For these reasons a new Division, the Glomeromycota, has been proposed to accommodate them. The Glomeromycota were the first mycorrhizal fungi to evolve.

The hyphae of the remaining three divisions have septa.

The Fungi Anamorphici is an artificial division. It is defined in a negative way as all those Eumycota where production of sexual spores is unknown. In various books or web sites you will also come across names such as imperfect fungi, anamorphic fungi, deuteromycetes and mitosporic fungi for the members of this Division. The Fungi Anamorphici is the second-largest group of fungi after the Division Ascomycota. The picture clearly shows the filamentous hyphae of a species of Rhizoctonia and you can readily see the numerous septa across the hyphae.

It is very important to note that the word 'unknown', rather than 'impossible' was used in the definition. Many ascomycetes will at times produce asexual spores. While the sexual spores of ascomycetes are often produced in firm structures such as 'cup fungi' the asexual spores of the same species are often produced by quite different structures that, if looked at in isolation, would be classed in the Fungi Anamorphici. A small number of basidiomycetes are also known to produce asexual spores by such anamorphic forms.

In cases where such sexual-asexual pairs are known, there are two associated species names—one for the sexual form (or teleomorph) and the other for the asexual form (the anamorph)—seemingly contrary to the 'one organism, one name' principle. Many anamorphs were known before the corresponding teleomorph was found. Anamorphs are often economically important—as plant pathogens, as causes of animal diseases or of use in chemical manufacture. Many non-mycologists work with anamorphs and there is extensive literature about them. It is therefore useful to keep the anamorph name, so as to reduce the confusion for non-mycologists and keep the links with the existing literature.

Alternaria alternata produces its asexual spores in chains.

Many of the anamorphic forms have a powdery appearance—the powder being the asexual spores, which are typically produced in great abundance. For example, the greenish mould on a lemon may well be Penicillium digitatum, the anamorphic form of a species of Eupenicillium. If you rub your finger across a mouldy lemon you will pick up many thousands of those powdery, asexual spores.

It is possible that many species currently included in the Fungi Anamorphici may, at some future time, be found to be capable of producing sexual spores. If a connection between some member of the Fungi Anamorphici and, say, an ascomycete species is discovered—then the fungus would no longer be classed with the Fungi Anamorphici but would simply be the anamorphic form of an ascomycete species.

On the other hand there may be many Fungi Anamorphici which have lost the ability to produce sexual spores, so that no connection between such a fungus and any ascomycete or basidiomycete will ever be found by using only visible characteristics. However, DNA investigations can be helpful in suggesting links.

Amongst the Fungi Anamorphici there are many saprotrophs and many parasites. Many of the Fungi Anamorphici are economically or medically important, as some are used industrially to produce various chemicals and others cause diseases.

The fungi in the final two Divisions produce sexual spores, using genetic material from two parents, and are distinguished by the method of production of those spores.

The species in these two Divisions are the fungi that people are most familiar with, for they produce the easily seen fruiting bodies such as mushrooms, cup fungi, morels, puffballs, bracket fungi and so on. It is important to realize that the mushrooms, cup fungi morels and so on are each only a part of the fungus, with the bulk of the fungus being an out-of-sight network of hyphae, called a mycelium. While the fruiting bodies, especially the fleshy ones, are often short-lived, the mycelium is there throughout the year. The mycelium is the feeding part of the fungus, while the roles of the visible structures are simply to produce and disperse the sexual spores.

The Division Ascomycota is the Division with the greatest number of fungal species. In this Division the sexual spores are produced within microscopic sacs called asci. A spore-filled ascus is commonly (but not always) cylindrical in shape. Commonly, each ascus holds eight spores—but there are species with just one spore per ascus and others with over a hundred spores per ascus.

Various features of the ascus are used for classificatory purposes. Asci may be single-walled or double-walled. They may open to release spores or they may remain closed and not release the spores. In ascomycetes where the asci release the spores, each ascus may either rupture at the apex or have an apical lid that opens to allow the spores out. There is in fact considerable variation in the structure of the apex, best seen with an electron microscope. This information is used in high level ascomycete classification.

The most commonly seen ascomycetes are the simple cup fungi, such as this Aleuria aurantia. If you cross-section one of these cup- or disk-shaped fruiting bodies (called an apothecium) you'd find that the internal structure was of the following form:

The spore-filled asci would be present in the area marked in black. If you took a small section of the black area and magnified it you'd see something like the second diagram. There are numerous asci, shown in yellow and containing blue-grey spores.

Just as there are 'complex' apothecial fruiting bodies (like Morchella), so there are also complex perithecial fruiting bodies, where a number of perithecia are combined within a larger structure. An example is Cordyceps gunnii.

You can see that the Morchella is largely empty inside, whereas the Cordyceps is a solid structure.

These are all stylised drawings. For one thing, the asci are mostly much smaller (in relation to fruiting body size) than shown here and there is some variety in the internal structure between genera. However, these drawings illustrate the general nature of the internal structure found in a large number of ascomycetes.

While many species of the Division Ascomycota produce easily visible fruiting bodies, there are also many microscopic ascomycetes, many of which are economically important. For example, many yeasts are ascomycetes and many of these are economically important, for example those used in the manufacture of bread and wine. This picture shows spore-filled asci of the yeast Schizosaccaromyces octosporus.

In the Division Basidiomycota the sexual spores are produced on microscopic organs called basidia. A basidium is often somewhat club-shaped, generally with several terminal prongs, one spore being produced at the end of each prong (or sterigma). Commonly, each basidium has four projections and four spores—but some species may have just one projection and one spore per basidium and others up to eight. In most basidiomycetes the basidia have no dividing walls (or septa), but in a small number of genera the basidia are septate. All of these features are used in basidiomycete classification.

These drawings show a basidium of Anthracophyllum archeri, with no dividing walls, and a basidium of Tremella fuciformis, with dividing walls.

All mushrooms are basidiomycetes and the gills of a mushroom are lined with basidia.

The gills of a mushroom are lined with basidia. If you take a thin slice, across several gills and magnify it about a hundred times you'd see the basidia sticking out from the gills, as shown in the second diagram. The basidia are drawn in green, the spores in brown.

If you took a small section from a gill (such as the area contained in the blue rectangle in the above figure) and looked at it under the microscope at a magnification of several hundred times, you'd see something resembling the third figure. You can now see the basidia much more clearly and also see the hyphae that make up the gill tissue. In this diagram the hyphae are marked by the parallel pairs of greyish blue lines and you can also see the septa that divide the filamentous hyphae into separate compartments.

These are stylised diagrams and there is variation in structure between species, but the diagrams illustrate the general nature of gill structure.

Other commonly seen basidiomycetes are the boletes, polypores, coral fungi, jelly fungi, stinkhorns, birds-nest fungi and puffballs.

The boletes (Phlebopus marginatus) and polypores (Piptoporus australiensis, Aurantioporus pulcherrimus) are similarly structured. You can imagine each pore to be the mouth of a short tube that extends back into the body of the fruiting body. The walls of those tubes are lined with basidia.

In coral fungi (Clararia miniata, Ramaria ochraceosalmonicolor) and jelly fungi (Tremella fuciformis) the basidia line the coralloid or convoluted surfaces. In the basidiomycete truffle-like fungi the basidia are contained within the fruiting body.

In all of these basidiomycetes the basidia are persistent. Even by the time a mushroom has half-decayed, you can still find basidia on the gills. In puffballs and similar fungi (Calvatia sp., Pisolithus sp.) the basidia are present (within the fruiting body) while the puffball flesh is still fairly solid. Once a puffball has become powdery the basidia have broken down and disappeared. Similarly, by the time the stinkhorns (Aseroë rubra, Mutinus borneensis) and Birds Nest Fungi (Crucibulum laeve, Nidula emodensis) have mature spores, the basidia have long since disappeared. In the Birds Nest Fungi the spores are produced within the miniature 'eggs' that you can see within the cup-like structures.