Fungi are grouped into phyla (singular: phylum), or groupings, based on the features of their shape, size, function, biochemistry and more recently, their DNA and RNA sequences. The fungi in a phylum are more closely related to one another than fungi in two different phyla. At least, that’s the theory, but the success of the hyphal growth form means that convergent evolution – where two distantly related organisms tend to look / act the same – is quite common in the fungi, and as a result, confusion occurs when fungal biologists try to place each species into an ordered group. At present, however, there are six phyla, if we include the non-fungal Oomycota and Myxomycota. Classification within the fungi is based on the structures that produce the sexual spores:

1. Myxomycota

Members of this phylum are simple single-celled Protists and are more commonly known as the plasmodial slime moulds. During their life cycle, these organisms have a number of different phases, each resembling quite different organisms....

While these organisms may be bizarre, they are by no means uncommon. Agricultural soils may have as many as 1000 Myxoamoebae per gram!

The slime moulds include other groups of organisms, the cellular slime moulds (Acrasiomycota and the Dictyosteliomycota) and the plasmodiophorids (Plasmodiophoromycota). These groups are similar to the myxomycetes, but vary in key aspects of their life cycles and biology. The cellular slime moulds, for instance, live as single amoeba-like organisms, only aggregating when starved, and later forming Cellulose-containing fruiting bodies. The plasmodiophoromycota, however, are obligate intracellular parasites, living only inside plant cells. This group contains the important plant pathogen Plasmodiophora brassicae, which causes clubroot disease of cabbage and related plants.

The slime moulds exhibit a bizarre tendency to "mix and match" features from several kingdoms – they sporulate like fungi, have only a plasma membrane (i.e. no cell wall), like animals, when in the amoeba form, and some have plant-like cellulose-containing fruiting bodies. Such features suggest that slime moulds are very ancient, primitive organisms.

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2. Oomycota

The members of the Oomycota are called Oomycetes and are known commonly as the Pseudofungi, as they closely resemble the real fungi. Studies of their DNA, however, tell us that the oomycetes are the product of Convergent Evolution and actually are more closely related to brown algae. The key features which allow us to distinguish the oomycetes from the real fungi are their cell walls and their spores. Real fungal cell walls contain Chitin, but the oomycete cell walls contain Cellulose (as do plant cell walls). The hyphae of pseudofungi are not separated by septae, and the mycelial nucleus is diploid, with two sets of chromosomes.

Zoospores produced by asexually reproducing oomycetes are motile, with two hairlike flagella propelling the zoospore through liquid. Sexually reproducing oomycetes, however, form non-motile oospores.

Saprolegnia zoospore. Gordon Beakes © University of Newcastle upon Tyne. Image courtesy LTSN Bioscience ImageBank

The life cycle of a typical oomycete is summarised in the diagram below. Note that oomycetes have diploid (2n) nuclei throughout their life cycle, except for the haploid (n) nuclei formed in the oogonia and antheridia prior to fertilisation of the oosphere.

The Oomycota contains two main orders, the Saprolegniales and the Peronosporales.

The Saprolegniales (water moulds) include about 200 different species, and live in fresh water and on roots. The most important water mould is Saprolegnia ferax, a dangerous pathogen of fish which causes major economic damage to salmon farming.

The Peronosporales include many serious plant pathogens, including Pythium species, which cause diseases of seedlings. Some Pythium fungi even parasitize other pathogenic fungi, and can be used as biocontrol agents.

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3. Chytridomycota:

The chytridomycetes are mainly aquatic and rumen fungi. Some grow as branched chains of cells called a thallus, while others have the form of a single large cell. In each case the cell, or thallus, has rhizoids, root-like structures which attach it to a substrate. Like the pseudofungi, the chytrids have flagellated, motile zoospores. However, the chytrids are "true" fungi!

© Emin Ozkose et al. A new fungus! This a fluorescence microscopy image of Cyllamyces aberensis, a new chytrid fungus discovered at the University of Wales, Aberystwyth. This is one of a small number of chytrid species that produce a bulbous "holdfast" rather than filamentous rhizoids. You can see three sporangiophores growing out of the holdfast, bearing developing sporangia. The brightly stained blobs are the nuclei. For further details: Ozkose, E., Thomas, B.J., Davies, D.R., Griffith, G.W. and Theodorou, M.K. (2001). Cyllamyces aberensis gen. nov., sp. nov., an anaerobic gut fungus from cattle with bulbous holdfast, branched sporangiophores and polycentric development. Canadian Journal of Botany, 79, pp. 666-673. Download the pdf

The presence of motile zoospores can be explained by convergent evolution, with similar solutions to the difficulties of life in water having arisen in both chytridomycetes and pseudofungi.

The important roles of chytridomycetes include the decomposition of organic matter in both soil and water, and the symbiotic association between anaerobic chytrids (such as Neocallimastix frontalis and Cyllamyces aberensis) and cows. These chytrids grow within the rumen of the cow, and help with the initial digestion of cellulose-rich materials eaten by the cow.

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4. Zygomycota

The Zygomycetes include a number of both familiar and important fungi, and may be characterized by usually having aseptate mycelia. The life cycle of a typical zygomycete is summarised below. Like all true fungi, zygomycetes have haploid nuclei (except in the sexual spores):

Asexual reproduction occurs by means of non-motile spores, called sporangiospores as they are formed in a sporangium. Sexual reproduction occurs by fusion of cells from different “sexes” (mating types) called gametangia. The mating type of a zygomycete is controlled by alleles of a single gene. While fungal biologists can’t tell the difference between cells of different mating type by looking at them, the fungi themselves can recognise the opposite mating type by means of prohormones produced by each type. Such a system of reproduction is called heterothallism.

The Zygomycota are most commonly known to us as pin moulds and vesicular arbuscular mycorrhizal fungi (root associated fungi). Some species exhibit dimorphism. This is a phenomenon where the fungus shows different growth forms every alternate generation, forming mycelium in one generation, and yeast in the next.

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5. Ascomycota

The ascomycetes are the largest phylum, with over 40,000 species identified to date – and it has 46 orders. About half of these species exist as symbionts with photosynthetic microorganisms in lichen. The ascomycetes include perhaps the most economically and culturally important fungus (especially for students!), Saccharomyces, which is used to ferment a variety of substrates to give alcohol. Saccharomyces cerevisiae also gives us our daily bread.

As with the zygomycetes and insects, the structure of the ascomycetes depends heavily on chitin (but the zygomycete cell wall also contains glucose and protein). Yeasts also have mannan in their cell walls.

Ascomycetes reproduce both asexually and sexually:

In asexual reproduction, spores are formed as the result of mitosis (nuclear division in which the number of chromosomes in the daughter nuclei is the same as it was in the parent nucleus). The resulting mitospores (aso called conidia) are released in large numbers, and allow the ascomycete to disperse over a wide area.

The structure of the ascus varies within the group. Yeasts tend to have single asci (naked asci), which bud from the parent yeast. Most other orders, however, have their asci formed within a fruiting body called an ascocarp. These occur in several different forms:

Apothecium

Perithecium

Cleistothecium

Given that we know how the cells have divided to form the ascospores and that they are all conveniently held in one place, we can investigate how different genes segregate in species such as the bread mould Neurospora and the coprophile Sordaria.

As ever with fungi, there is something that breaks the rules, or can’t be filed nicely away with other similar fungi. Consider the two species Aspergillus niger and Aspergillus nidulans. Their names suggest that they are both in the same genus, as does their appearance.

However, since ascomycetes are classified on the structure of their ascospores, and Aspergillus niger only produces asexual mitospores it is classed as a mitosporic fungus and is in a different order from Aspergillus nidulans.

Such confusion has lead to a number of arguments about the ascomycete family tree, and if one were to look in even relatively recent fungal biology textbooks one would see little mention of the ascomycetes. One would however, find the terms Deuteromycetes and Fungi Imperfecti used frequently to describe what we now know to be ascomycetes. These groupings acted essentially as a convenient way of forgetting about the mitosporic fungi.

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6. Basidiomycota

These are the most structurally complex fungi, and include what we commonly call mushrooms, toadstools and bracket fungi. Basidiomycetes are characterized by a septate mycelium. The septa are highly complex and are pierced by a particular kind of pore termed a dolipore. The dolipore does not allow nuclei to pass through the septum. Consequently, hooked outgrowths called clamp connections are formed to ensure the proper distribution of nuclei as the hyphae grow:

Point to activate clamp connection

Like other fungi, the Basidiomycetes are haploid. But unlike most fungi, when two hyphae of different mating types fuse, the resulting mycelium has a strict organisation where each cell (defined by the septa) contains a pair of nuclei (one from each parent). The mycelium is said to be dihaploid or dikaryotic. As a result, the basidiomycetes are functionally diploid.

The key identifying feature, however, is that sexual spores in the Basidiomycota are produced by basidia.Two haploid nuclei in the basidium fuse, and this is followed by meiosis to form four haploid daughter nuclei. These migrate into the developing basidiospores, which are formed externally.

Asexual reproduction is uncommon in the basidiomycetes, but, where it does occur, the fungi reproduce by the means of conidia.

The Basidiomycota have three sub-phyla, which are:

a) Hymenomycetes

These are the classic mushrooms and toadstools, composed of highly complex fruiting bodies and networks of dikaryotic mycelia. The fruiting bodies or basidiocarps have pores or gills, which are lined with basidia. Often they are raised on a stalk or stipe to aid wind dispersal, while bracket fungi are formed from solid substrates such as tree trunks.

Hygrocybe conica © Gareth W. Griffith

Ganoderma applanatum © Gareth W. Griffith

The cultivated mushroom Agaricus bisporus, is a member of this group. But as its name suggests, it is unusual in that it produces only two basidiospores per basidium (pictured on the right), with each basidiospore containing two haploid nuclei. Gordon Beakes © University of Newcastle upon Tyne. Image courtesy LTSN Bioscience ImageBank

© Gareth W. Griffith

Basidiomycetes are also key decomposers and include the white rot fungi which can degrade lignin, the highly resistant polysaccharide found in brown wood.

b) Uredinomycetes

These are highly specialized plant pathogens which can only grow and reproduce on their host species or closely related species. Over 6000 members of the uredinomycetes (commonly known as rusts) have found this a suitable lifestyle. Important members of this sub-phyla include Puccinia graminis var. tritici and Uromyces appendiculatus. These are restricted to wheat and bean plants respectively. Puccinia graminis var. tritici causes take-all disease, and is a major wheat crop pathogen, despite having a highly complex and restrictive life cycle.

A field bean plant infected with rust Agriculture, University of Reading © University of Reading Image courtesy LTSN Bioscience ImageBank

c) Ustilagomycetes

The Ustilagomycetes are commonly known as smuts, and over 1000 members of this sub-phylum live in a similar manner to the rusts, as obligate biotrophic fungi – they can only grow on living plants. Maize Smut, caused by Ustilago maydis is an economically important disease.

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