David Moore's World of Fungi: where mycology starts

Table of Contents

1. Fungal evolution
2. Kingdom fungi
3. Diversification
4. Origins of fungi
5. Bibliography
6. Links
7. Glossar

Kingdom Fungi

Around the middle of the twentieth century the three major kingdoms of eukaryotes were finally recognised (discussed in the Diversification section). 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, most 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.

Approximately 98,000 fungal species have been described to date, the majority being members of the Ascomycota (about 64,000 known species) and the Basidiomycota (about 32,000 known species). These numbers will always be approximate because about 1000 new species are described each year (an average of 1229 species per year during 1980-9, 1097 species per year in 1990-9, though only 850 species were described in 2007), and because not all ‘new’ descriptions are genuinely new; some have been described before under different names. In these cases the names are described as synonyms and one of them is chosen as the true name for the species (the earliest, most accurate description that follows the international rules of nomenclature) and the rest are reduced to synonymy, but they stay on the list and can never be used for any other species.

Because there are so many species of fungi for which no sexual stage is known, at least at the time when they are first described, a particular peculiarity of fungal taxonomy is the practice of assigning different generic and specific names to the asexual (called the anamorph) and sexual stages (called the teleomorph). When subsequent work establishes the connection between the two stages, two names will apply to the one organism and in this case the name that was defined first will take precedence. A particular example is that the well-known Aspergillus nidulans is an anamorph that has a teleomorph which was named Emericella. Strictly speaking, the generic name Emericella should take precedence, but it’s taken a long time for the geneticists and molecular biologists who have spent their lives working with Aspergillus nidulans to call their strains Emericella nidulans. This sort of thing can be a confusing complication to students of mycology, so you have to be aware of this peculiarity and take it in your stride because it is likely to happen more frequently as more molecular taxonomy is performed and reveals more synonyms. One thing this peculiarity of giving different names to sexual and asexual stages does do, of course, is increase the number of taxonomic names recorded for fungi.

In fact, around 300,000 species names exist, and this provides another opportunity for estimating how many real species we know about because major ‘monographs’ (the research studies in which taxonomists critically review all the species in a genus or family) suggest an average rate of synonymy of about 2.5 invalid names for each valid name. So if this ratio is applied to all 300,000 names we can estimate the upper limit of accepted known species to be about 120,000. This compares with an estimate of 1.5 million species currently present on Earth (Hawksworth, 2001; Hibbett et al., 2011).

The fungal kingdom is now recognised as one of the oldest and largest clades of living organisms. Kingdom Fungi is a monophyletic group which diverged from a common ancestor with the animals about 800 to 900 million years ago. In the most recent phylogenetic classification scheme, the true fungi (or Eumycota), which make up this monophyletic clade called Kingdom Fungi, comprise the seven phyla (the taxon ‘phylum’ has been borrowed from animal taxonomy):

• Chytridiomycota (706 species in 105 genera);
• Blastocladiomycota (179 species in 14 genera);
• Neocallimastigomycota (20 species in 6 genera);
• Microsporidia (1,300+ species in 170 genera);
• Glomeromycota (169 species in 12 genera);
• Ascomycota (64,163 species in 6355 genera);
• Basidiomycota (31,515 species in 1589 genera).

The last two phyla are combined in the Subkingdom Dikarya (Hibbett et al. 2007) and there are four subphyla that were traditionally placed in the phylum Zygomycota (1,065 species in 168 genera), though this traditional phylum is polyphyletic and is currently in an uncertain state (see below).

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:

• Phycomycetes;
• Ascomycetes;
• Basidiomycetes;
• Deuteromycetes (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 be 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. 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 traditionally 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. The consequences of this decision are the recognition of the phylum Glomeromycota and of four subphyla incertae sedis (meaning 'of uncertain position'): Mucoromycotina, Kickxellomycotina, Zoopagomycotina and Entomophthoromycotina. As more work is done and the position clarifies, the name Zygomycota may be reinstated to encompass some of the taxa once represented in the traditional group. At the time of writing Zygomycota has not been given a proper diagnosis and can only be used informally as a convenient ‘container’ for the four 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 with weakened immune systems (pneumocystis pneumonia or PCP) is the most common opportunistic infection in people with HIV and has been a major killer 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 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. Recent molecular studies show that these organisms are related to the Zygomycota.

Hyaloraphidium curvatum, an organism previously classified as a colourless green alga, is now recognised as a fungus on the basis of molecular sequence data, which show it is a member of the Monoblepharidales in the Chytridiomycota.

Updated December 15, 2016