Fungal classification or taxonomy as shall be seen later in this section is usually based on the sexual spores produced by the organisms. This is because the asexual forms of most fungi especially those that are of medical importance are not well known; and those groups of fungi that are of medical importance are sexual spore producers. The kingdom fungi comprise four (4) or more distinct divisions (i.e., phylum) or groups of fungal organisms classified based on their sexual cycle, spore formation and/or mode of reproduction (i.e., sexual or asexual reproduction). Kingdom fungi contain diverse species of organisms (including yeasts, moulds and mushrooms) that have enormous medical, industrial and economic applications. The main fungal classes or divisions are zygomycetes, ascomycetes, basidiomycetes and deuteromycetes. Only deuteromycetes produce conidia (i.e., asexual spores) but sexual spores are produced by fungi in the phylum or division’s known as zygomycetes, ascomycetes and basidiomycetes.


Generally, the classification of fungi is based on:

  1. The sexual cycle of the fungi (sexual or asexual).
  2. The hyphal or hyphae morphology of the fungi (septate or non-septate).
  3. The type of spore formed by the fungi (conidia or sexual spores).


Zygomycetes are commonly known as the bread moulds. Fungi in this division or phylum include Rhizopus species (Figure 1), Mucor species (Figure 2), Absidia species and Pilobolus species. Zygomycetes are found in the fungi phylum or division known as Zygomycota. The zygomycetes are ubiquitously found in the environment where they colonize the soil and decaying materials. They are saprophytic and environmental fungi with little or no clinical significance. However, some zygomycetes cause zygomycosis in animals and humans since they are occasional parasites of animals, humans and even plants. Zygomycosis are fungal infections caused by zygomycetes. Examples of zygomycosis include mucormycosis (caused by Mucor species and other zygomycetes such as Rhizopus and Absidia species) and entomophthoramycosis (caused by Basidiobolus haptosporus, a mucormycete). Mucormycosis and entomophthoramycosis are caused by zygomycetes in the order Mucorales and Entomophthorales. Though members of the Entomophthorales are pathogens of insects and other vertebrates, they also parasitize humans and animals.

Figure 1. A sketch of Rhizopus species. Photo courtesy:
Figure 2. A sketch of Mucor species. Photo courtesy:

Both mucormycosis and entomophthoramycosis are commonly seen in immunocompromised individuals, heavy antibiotic users, transplant patients, severely malnourished patients and patients on chemotherapy. Mucormycosis is clinically characterized as fungal or hyphae growth in blood vessels, skin, gastrointestinal tract and other organs while entomophthoramycosis is clinically characterized by localized infection of the nasal mucosa and its surrounding tissues. The Mucorales and the Entomophthorales are the two orders of zygomycetes that cause human disease. However, the majority of human disease is caused by members in the order, Mucorales. Fungi infections caused by members of the Mucorales and Entomophthorales are generally known as opportunistic fungal infections because they only occur in people with a compromised immune system as aforementioned.

Fungi in the division Zygomycota undergo both sexual and asexual reproduction. They are usually characterized by the presence of sexual spores, asexual sporangiospores and the presence of septate or aseptate hyphae. Zygomycetes produce zygospores as their teleomorph during sexual reproduction. Zygomycetes are largely saprophytes, and they live on decaying plant and animal matter in the soil as aforementioned. The zygomycetes are often known for their fast growth and multiplication in any environment that they colonize. The hyphae of fungi in the division Zygomycota are mostly aseptate (i.e., without cross-walls) and they are said to be coenocytic or multinucleated in form. Fungi in this division form asexual spores or conidia through the formation of sporangia (singular: sporangium) which contain numerous sporangiospores. However, sexual spores known as zygospores (produced by fungi in the division, Zygomycota) are formed through the mating of two haploid nuclei or fusion of morphologically similar gametangia that divide by the process of meiosis and mitosis. Generally, the zygomycetes parasitize plants, animals and humans but fungi in this division are mainly known for their food spoilage activities. Zygomycetes such as Rhizopus species and Mucor species are important food spoilage fungi; and they are fast growing fungi with numerous economic importance.     


Ascomycetes are fungi that reproduce sexually through the formation of endogenous ascospores (i.e., sexual spores) normally enclosed in a sac known as the ascus sac. The asci (singular: ascus) are known to contain about four or eight ascospores that characterize the sexual spores of ascomycetes. Fungi in this division or phylum are commonly known as sac or cup fungi because of their asci which is characteristically known for its raised and elongated filamentous structure. The ascus of ascomycetes are usually formed inside a multicellular fruiting structure known as ascocarp; and the ascocarp of ascomycetes can assume different morphology and shape in their natural environment. Ascomycetes contain a large and diverse group of fungi with various economic and clinical importances. Ascomycetes also reproduce asexually to produce conidia or spores which aid in the propagation and dispersal of the organism in the environment.

Ascomycetes form well developed branching septate hyphae (i.e., hyphae with cross-walls). They are ubiquitously found in the soil as saprophytes. A handful of ascomycetes parasitize plants, humans and animals. Some ascomycetes are unicellular cells while others exhibit dimorphism, and thus can either exist as yeast or mould in their natural environment. The division Ascomycota includes moulds, mildews and yeasts. Representative fungi in this group are Microsporum, Trichophyton, Piedraia, Blastomyces, Aspergillus, Saccharomyces cerevisiae (baker’s yeast)and Histoplasma species. Majority of the ascomycetes are causative agents of dermatophytosis in humans (for example, ringworm). They also cause disease in plants and animals. For example,Claviceps purpurea is an ascomycete that parasitizes plants to cause ergot disease. C. purpurea causes ergotism (a psychotic and neurological disease) in humans and animals that eat crop plants infested by the fungus. Aspergillus species such as A. niger (Figure 3) is another important fungal organism of the division Ascomycota that causes black mould disease on fruits and vegetables. A. niger is ubiquitous in the soil, and it is also a common contaminant of indoor environments where it produces characteristic black colonies or hyphae on the contaminated material including furniture, clothes and food.

Figure 3. A sketch of Aspergillus niger. Photo courtesy:

A. flavus (Figure 4) and A. fumigatus (Figure 5) are other Aspergillus species that are important pathogenic fungus of humans. Some species of Aspergillus (A. flavus in particular) are also known to produce potent toxins known as aflatoxins. Aflatoxins are typical example of mycotoxins that are cancer-causing in nature.

Figure 4a. Aspergillus flavus. Photo courtesy:
Figure 4b. Aspergillus flavus. Photo courtesy:
Figure 5. A sketch of Aspergillus fumigatus. Photo courtesy:

Mycotoxins are toxins produced by fungi. A. flavus and other fungi that produce aflatoxins are common contaminants of food especially grains which they infest to produce the potent toxin. Human consumption of food contaminated by aflatoxins can cause carcinogenic effects in the individual who consumes such food or food products. Ascomycetes possess tremendous economic value. Many lichens are ascomycetes. Ascomycetes can therefore go into symbiotic association with other organisms such as algae. Lichens are a symbiotic relationship of two distinct organisms, in this case a fungus and an algae or cyanobacteria. The dominant partner in the lichen community is a fungus; and majority of these fungus are in the Ascomycota division. Lichens produce several secondary metabolites that are used industrially and for many pharmaceutical and medical purposes because some of the metabolites possess antimicrobial activity. As saprobes, ascomycetes are important decomposers in the environment. Ascomycetes are important starting material in the production of many industrial products including foods such as wine, bread and other beverages. Saprobes are organisms that carry out a saprophytic mode of nutrition and thus derive their nourishment (energy and carbon) from non-living or decaying organic matter that they degrade or breakdown.   


Basidiomycetes are fungi that form sexual spores known as basidiospores. The basidiospores which are usually four in number are generally carried on a club-shaped structure known as the basidium (plural: basidia). The spores of basidiomycetes (i.e., basidiospores) are usually developed on the basidia instead of being wrapped or enveloped within the fungal cell. Basidia are microscopic projections or cells from which basidiospores are developed from. Fungi in the basidiomycota division are commonly known as club fungi due to their characteristic morphology that resembles that of a club or baseball bats. Basidiomycetes have septate hyphae like the ascomycetes but their hyphae are more complex in nature. Their basidiospores are enclosed within fruiting bodies known as basidiocarps. The basidiomycetes or basidiomycota division contain a large array of fungi especially the mushroom-forming fungi; and fungi in this division or group possess diverse economic importance. Examples of fungi that are basidiomycetes include toadstools, shelf fungi, mushrooms, smut fungi, Cryptococcus neoformans, rust fungi and puffballs.

Fungi in the division basidiomycota possess tremendous economic importance. For example, the mushrooms in the Agaricus species such as A. campestris and A. bisporus are amongst the important mushrooms used as a source of human food. Mushroom cultivation either for domestic or commercial use is an important aspect of microbiology; and all over the world, mushroom is cultivated and sold because of their perceived medical and health importance. Basidiomycetes are ubiquitously found in the natural environment as saprophytes and parasites of animals and humans as well as plants. Though a handful of the basidiomycetes such as the Agaricus mushrooms are edible and can be eaten as food, some group of mushrooms especially the Amanita species are poisonous and can cause severe clinical condition when eaten ignorantly. On the other hand, basidiomycetes are important tools for biotechnological applications. For example, a plethora of basidiomycetes produce enzymes such as cellulases, xylanases, ligninases, peroxidases and luccases that are important for the degradation of many biomass in the industry. In their natural environment, basidiomycetes act as natural lignocellulose and cellulolytic microbes because of their innate ability to degrade recalcitrant molecules such as lignin and cellulose respectively.  


Deuteromycetes are generally known as “imperfect fungi” unlike the ascomycetes, zygomycetes and basidiomycetes which are “true fungi”. True fungi already have well established sexual and asexual means of reproduction which aid in their classification. However, deuteromycetes are known as imperfect fungi because they have a sexual cycle of reproduction which have not been confirmed or observed. The majority of fungi generally reproduce either by sexual means or asexual means of reproduction. And the reproduction stage or properties of fungi plays a key role in their classification. However, in some fungi, only the asexual method of reproduction has been observed; and such fungi are known as fungi imperfecti or deuteromycetes. Generally, imperfect fungi are fungi which do not fit into the commonly established taxonomic classifications of fungi that are based on the morphological characteristics of fungal sexual structures. And another name for fungi imperfecti is deuteromycetes or deuteromycota. This division (i.e., deuteromycota) contains fungi whose teleomorphs (i.e., sexual reproducing forms) discovery is still in the continuum, and have not been fully observed like fungi in the Zygomycota, Basidiomycota and Ascomycota division. Deuteromycetes contain a variety of heterogeneous fungal organisms with much economic importance. Deuteromycetes are characterized by an anamorphic stage in which asexual spores or conidia are produced. Fungi in the division deuteromycetes have no known sexual cycle of reproduction, and they mainly reproduce through the formation of conidia or asexual spores.

The division deuteromycota contain many important human pathogens including Candida, Histoplasma, Coccidioides and Paracoccidioides and other dematiaceous fungi. However, other imperfect fungi such as Penicillium speciesare important to humans and medicine. For example, the antibiotic penicillin is naturally soured from Penicillium species such as P. chrysogenum and P. notatum. It is noteworthy that the division deuteromycetes is only but an artificial classification of fungi (i.e., it is a non-phylogenetic class); and as the sexual stage of organisms in this group is being discovered, the imperfect fungi will be regrouped into the correct fungal division or phylum that they actually belong to. Generally, the deuteromycetes are ubiquitously found in the environment especially in the soil, and they are important pathogens of plants, animals and humans. Basidiomycetes also contain fungi that possess entomopathogenic properties, and thus could be used as microbial pest control agents as a way of ensuring food security around the globe. Some deuteromycetes also possess entomopathogenic properties, and thus can be used to control the infestation of crop plants by pest in the farmland. Top among the deuteromycetes that are entomopathogenic in nature is the causative agent of the white muscardine disease of silkworm, Beauveria bassiana. The discovery of B. bassiana as the causative agent of silkworm played a contributory role in the development of this field of mycology. As an entomopathogen, B. bassiana infects a wide variety of pests and/or insects including aphids, termites, moths, caterpillars, thrips, and whitefly that destroy economically-important crops or plants in the farmland.     


Other fungal divisions include the Chytridiomycetes and Glomeromycetes groups. Chytridiomycetes are simple true fungi commonly known as chytrids; and they include many free-living fungi and those that parasitize plants and animals and as well as protists in the natural environment. Chytrid fungi are ubiquitous in the environment, and they reproduce asexually to form motile zoospores. Sexual reproduction in chytridiomycetes results in the formation of zygote that eventually becomes a sporangium. Species of fungi in the division chytridiomycetes include Allomyces and Batrachochytrium which causes mycoses in amphibians especially frogs. Glomeromycetes on the other hand are known for their symbiotic associations with plant roots. They form endomycorrhizae (a fungal-plant root association) with herbaceous plants. The main role of glomeromycetes in this association is to help the plant roots to absorb nutrients and water from the soil. Glomeromycetes only form asexual spores. The penetration of the plant cell walls by the fungal hyphae lead to the formation of arbuscules or swollen structures around the plant roots, a phenomenon characteristic of the glomeromycetes fungi-plant relationship.      

Further reading

Anaissie E.J, McGinnis M.R, Pfaller M.A (2009). Clinical Mycology. 2nd ed. Philadelphia, PA: Churchill Livingstone Elsevier. London.

Baumgardner D.J (2012). Soil-related bacterial and fungal infections. J Am Board Fam Med, 25:734-744.

Calderone R.A and Cihlar R.L (eds). Fungal Pathogenesis: Principles and Clinical Applications. New York: Marcel Dekker; 2002.

Champoux J.J, Neidhardt F.C, Drew W.L and Plorde J.J (2004). Sherris Medical Microbiology: An Introduction to Infectious Diseases. 4th edition. McGraw Hill Companies Inc, USA.       

Gladwin M and Trattler B (2006). Clinical Microbiology Made Ridiculously Simple. 3rd edition. MedMaster, Inc., Miami, USA.

Larone D.H (2011). Medically Important Fungi: A Guide to Identification. Fifth edition. American Society of Microbiology Press, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA.

Stephenson S.L (2010). The Kingdom Fungi: The Biology of Mushrooms, Molds and Lichens. First edition. Timber Press.

Sullivan D.J and Moran G.P (2014). Human Pathogenic Fungi: Molecular Biology and Pathogenic Mechanisms. Second edition. American Society of Microbiology Press, USA.

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