2.5 The Kingdom Fungi
As we have seen, around the middle of the 20th century the three major kingdoms of eukaryotes were finally recognised. One of the crucial character differences was the mode of nutrition:
- Animals engulf.
- Plants photosynthesise.
- Fungi absorb externally-digested nutrients.
To these can be added many other differences. For example: in their cell membranes animals use cholesterol, fungi use ergosterol; in their cell walls, plants use cellulose (a glucose polymer), fungi use chitin (a glucosamine polymer); recent genomic surveys show that plant genomes lack gene sequences that are crucial in animal development, and vice-versa, and fungal genomes have none of the sequences that are important in controlling multicellular development in animals or plants. This latter point implies that animals, plants and fungi separated at a unicellular grade of organisation.
The fungal kingdom is now recognised as one of the oldest and largest clades of living organisms on Earth. Kingdom Fungi is a monophyletic group which diverged from a common ancestor with the animals about 800 to 900 million years ago. We continue to follow the phylogenetic classification scheme suggested by Hibbett et al. (2007), as this appears to be a well-corroborated phylogenetic framework but modified in accordance with McLaughlin et al. (2009), Jones et al. (2011), Powell & Letcher (2014), Spatafora et al. (2016) and McCarthy & Fitzpatrick (2017). In this summarised arrangement, the Eumycota (or true fungi), that make up the monophyletic clade called Kingdom Fungi, is comprised of the ten phyla (the taxon ‘phylum’ has been borrowed from animal taxonomy) listed immediately below:
- Zoopagomycota (comprises subphyla Entomophthoromycotina, Kickxellomycotina and Zoopagomycotina);
- Mucoromycota (comprises subphyla Glomeromycotina, Mortierellomycotina and Mucoromycotina);
- Ascomycota, (about 65,000 species in 6400 genera);
- Basidiomycota, (about 32,000 species in 1600 genera).
The last two phyla being combined in the subkingdom Dikarya (Hibbett et al. 2007) and there are four subphyla that were traditionally placed in the phylum Zygomycota (1065 species in 168 genera). These taxa will be described in more detail in Chapter 3 and we say something about Zygomycota below.
The last two phyla are combined in the subkingdom Dikarya by Hibbett et al. (2007). These taxa will be described in more detail in Chapter 3 and we say something about ‘Zygomycota’ and Microsporidia below. The Mycota (2nd edition), Vol. VII (in two parts A & B) (McLaughlin & Spatafora, 2014, 2015), includes treatments of the systematics and related topics for fungi and fungus-like organisms in four eukaryotic supergroups (the informal rank above kingdom), three of fungus-like organisms: Amoebozoa, Excavata, and SAR (Straminipila, Alveolata, and Rhizaria); and the true fungi in supergroup Opisthokonta that comprises the phyla mentioned immediately above; as well as specialised chapters on nomenclature, techniques, and evolution. Interestingly, the proteomic fungal tree of life is similar to, but not identical to, the outline shown above (Choi & Kim, 2017). The Classification of Kingdom Fungi and fungus-like organisms is outlined (and fully referenced) at the end of this book and this includes an explanation of ‘supergroups’ (and see Fig. 6 and its legend).
For the moment remember that when fungi were still classified in the Plant Kingdom (subkingdom Cryptogamia, Division Fungi, subdivision Eumycotina) they were separated into four classes:
- Deuteromycetes (the latter also known as Fungi Imperfecti because they lacked a sexual cycle).
You may still encounter these traditional names for groups of fungi, but if they are used today, you must appreciate that they can only be used informally. Many organisms included in these groups (particularly among the phycomycetes and the slime moulds) are no longer considered to the true fungi, even though mycologists might study them. This applies to many of the water moulds, like the Oomycota (which include the plant pathogen Phytophthora), and Hyphochytriomycota, all of which have been removed from the fungi, and are now classified with brown algae and diatoms in the Kingdom Chromista or Kingdom Straminipila (see Section 3.10). Similarly, the Amoebidales, which are parasites or commensals of living arthropods and previously considered to be trichomycete fungi within the ‘Zygomycota’ are now considered to be protozoan animals. None of the slime moulds are now considered to belong to Kingdom Fungi and their relationship to other organisms, especially animals, is still in dispute.
Molecular analyses have led to dramatic changes in our understanding of relationships of fungi placed in the traditional phyla Chytridiomycota and ‘Zygomycota’. The Chytridiomycota is retained in the 2007 scheme, but in a much more restricted sense. For one thing, one of its traditional orders, the Blastocladiales, has been raised to phylum status as the Blastocladiomycota. Similarly, the group of anaerobic rumen chytrids previously known as order Neocallimastigales has also been recognised as a distinct phylum, the Neocallimastigomycota.
In contrast, the phylum ‘Zygomycota’ is not accepted in the most recent classification because of remaining doubts about relationships between the groups that have traditionally been placed in this phylum (Benny et al., 2014). Benny et al. (2014) recognised the phylum ‘Glomeromycota’ and left four subphyla (Entomophthoromycotina, Kickxellomycotina, Mucoromycotina, and Zoopagomycotina) as ‘incertae sedis’, which means ‘of uncertain placement’. Spatafora et al. (2016) clarified the situation by proposing the two phyla Zoopagomycota (comprises subphyla Entomophthoromycotina, Kickxellomycotina and Zoopagomycotina) and Mucoromycota (comprises subphyla Glomeromycotina, Mortierellomycotina and Mucoromycotina). The name ‘Zygomycota’ may be reinstated at some time in the future, but at the time of writing, ‘Zygomycota’ has not been given a proper diagnosis and can only be used informally. We continue to use the old term ‘zygomycetes’ in Chapter 3 and elsewhere as a convenient ‘container’ for the subphyla mentioned above and, more importantly, because you are bound to encounter it in other, older, books.
Kingdom Fungi has also gained a few recruits on the basis of recent molecular phylogenetic analysis, notably Pneumocystis, the Microsporidia, and Hyaloraphidium. Pneumocystis carinii is a pathogen causing pneumonia in mammals, including humans (the human pathogen is called P. jirovecii), with weakened immune systems. Pneumocystis pneumonia (or PCP) is the most common opportunistic infection in people with HIV and has been a major cause of death of people infected with HIV. Pneumocystis was initially described as a trypanosome, but evidence from sequence analyses of several genes places it in the Taphrinomycotina in the Ascomycota.
The Microsporidia (Didier et al., 2014) are obligate intracellular parasites of animals. They are extremely reduced organisms, without mitochondria. Most infect insects, but they are also responsible for common diseases of crustaceans and fish, and have been found in most other animal groups, including humans (probably transmitted through contaminated food and/or water). They were thought to be a unique phylum of protozoa for many years. Molecular studies show that these organisms are related to the zygomycetes indicating that they should be classified in Kingdom Fungi or at least as a sister kingdom to Fungi.
Hyaloraphidium curvatum, an organism previously classified as a colourless green alga is now recognised as a fungus based on molecular sequence data, which show it is a member of the Monoblepharidales in the Chytridiomycota.
Updated July, 2018