3.5 The traditional zygomycetes

The thousand or so species in this group generally have a multinucleate mycelium with little or no septation (i.e. coenocytic) that produces asexual spores in a mitosporangium (a sporangium in which spores are produced by mitosis). But the characteristic feature of the informal ‘phylum’ zygomycetes is that they form sexual spores in a zygosporangium.

The name is derived from the way in which they reproduce sexually. Zygos is Greek for ‘joining’ or ‘a yoke’ (the wooden crosspiece bound to the necks of a pair of oxen or horses that is then connected to the load they are pulling). So zygomycetes reproduce through the fusion or conjugation of two hyphal branches (= gametangia) to form a zygote which eventually gives rise to the zygosporangium when it produces spores.

The gametangia arise from hyphae of a single mycelium in homothallic species, or from different but sexually compatible mycelia in heterothallic species. Zygosporangia usually have thickened walls and act as resting spores; they are notoriously difficult to germinate in the laboratory. The zygospore wall contains sporopollenin, which is a complex, highly cross-linked polymer also found in the exine (outer wall layer) of pollen grains. Its presence, together with melanin, helps to explain the long-lived nature of zygospores. Long-lived resistant spores spread the organism in time, to survive periodic adverse environmental conditions; while non-dormant spores (dispersal spores) spread the organism in space, to colonise new territory.

These fungi are ecologically very diverse, very widely distributed and very common, though frequently overlooked. CLICK HERE to see a page of illustrations.

Clearly, this group of zygomycetes is a primitive and early diverging lineage of Kingdom Fungi; primitive features being that they have coenocytic aseptate hyphae for all or part of their life cycle and they are unable to make tissues or complex fruiting structures. They may be primitive, but they are certainly successful, and you are never far away from a member of this group. In the traditional classification some organisms were included that are more properly placed with the slime moulds (e.g. Amoebidiales and Eccrinales) protists that separated from the true fungi when animals and fungi diverged from the opisthokont lineage. The problem with the traditional ‘phylum Zygomycota’ is that it is polyphyletic and cannot retain rank as a natural phylum. In the 2007 classification (Hibbett et al., 2007) the name remains undefined leaving the following subphyla in an uncertain position (Benny et al., 2014):

  • Mucoromycotina (containing the Orders Mucorales, Endogonales and Mortierellales);
  • Entomophthoromycotina (Order Entomophthorales);
  • Zoopagomycotina (Order Zoopagales);
  • Kickxellomycotina (Orders Kickxellales, Dimargaritales, Harpellales, and Asellariales).

Spatafora et al. (2016) have formally redefined the group using phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes, and 192 proteins. They abandon use of the name ‘Zygomycota’ to avoid any further confusion and instead recognise that zygomycetes comprise two major clades, leading them to propose a formal phylogenetic classification comprising the two phyla Zoopagomycota and Mucoromycota, six subphyla, four classes and 16 orders.

Zoopagomycota comprises the subphyla Entomophthoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, that is, mycoparasites).

Mucoromycota comprises subphyla Glomeromycotina (see Section 3.6), Mortierellomycotina, and Mucoromycotina and is a sister phylum to the Dikarya (Ascomycota and Basidiomycota). It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material.

What follows are edited and summarised notes from the phylogenetic commentaries given by Spatafora et al. (2016); you should refer to the original for the formal referencing of synonyms, authorities and typifications.

In phylum Zoopagomycota, sexual reproduction, where known, involves the production of zygospores by gametangial conjugation. Morphologies associated with asexual reproductive states include sporangia, merosporangia, conidia, and chlamydospores. Zoopagomycota is the earliest diverging clade of zygomycetous fungi. It comprises three subphyla in which associations with animals (e.g. pathogens, commensals, mutualists) form a common ecological theme, although species from several lineages are mycoparasites (e.g. Syncephalis, Piptocephalis, and Dimargaritales which are obligate mycoparasites). Although some of the fungi in Zoopagomycota can be maintained in axenic culture, most species of Zoopagomycota are most frequently observed growing in association with a host organism and are more difficult to maintain in pure culture than species of Mucoromycota. Haustoria are produced by some of the animal pathogens and mycoparasites. Zoopagomycota hyphae may be compartmentalised by septa that may be complete or uniperforate with electron opaque lenticular plugs in the latter. Zygospore formation typically involves modified hyphal tips, thallus cells, or hyphal bodies (yeast-like cells) that function as gametangia.

  • Subphylum: Entomophthoromycotina includes three classes and three orders of saprobic and insect pathogenic fungi. The thallus may consist of coenocytic or septate hyphae, which may fragment to form hyphal bodies, or it may comprise only hyphal bodies. Asexual reproduction is by conidiogenesis from branched or unbranched conidiophores; primary conidia are forcibly discharged, and secondary conidia are either forcibly or passively released. Sexual reproduction involves the formation of either zygospores by gametangial copulation, involving hyphal compartments or hyphal bodies. Classes: Basidiobolomycetes; Entomophthoromycetes; Neozygitomycetes; and Orders: Basidiobolales; Entomophthorales (parasites of small animals, including arthropods, rotifers and even amoebae); Neozygitales.
  • Subphylum: Kickxellomycotina species may be saprobes, mycoparasites, and symbionts of insects; the latter includes Harpellales that are typically found within the hindguts of aquatic life history stages. Mycelium is regularly divided into compartments by bifurcate septa that often have lenticular occlusions. Sexual reproduction involves the formation of variously shaped zygospores by gametangial conjugation of relatively undifferentiated sexual hyphal compartments. Sporophores may be produced from septate, simple, or branched somatic hyphae. Asexual reproduction involves the production of single- or multispored merosporangia arising from a specialised vesicle (sporocladium), sporiferous branchlets, or an undifferentiated sporophore apex. Orders: Asellariales; Dimargaritales; Harpellales; Kickxellales. The Harpellales and Asellariales are specialised for attachment to the gut wall of arthropods and are obligate endosymbionts. They are so widespread that just about every arthropod that crawls past you will carry these fungi within. CLICK HERE to see a page of illustrations.
  • Subphylum: Zoopagomycotina include mycoparasites and predators or parasites of small invertebrates and amoebae. The hyphal diameter is characteristically narrow in thalli that are branched or unbranched; sometimes specialised haustoria are produced in association with hosts. Only a handful of species have been successfully maintained in axenic culture. Sexual reproduction, where known, is by gametangial conjugation, forming globose zygospores on suspensor cells. Asexual reproduction is by arthrospores, chlamydospores, conidia, or multispored merosporangia that may be simple or branched.

Phylum Mucoromycota of Spatafora et al. (2016) contains Mucoromycotina, Mortierellomycotina, and Glomeromycotina. Characters associated with sexual reproductive states, where known, include zygospore production by gametangial conjugation. Asexual reproductive states can involve chlamydospores and spores produced in sporangia and sporangioles. Mucoromycota shares a most recent common ancestor with Dikarya and is characterised by plant symbionts, decomposers of plant debris, plant pathogens and only rare ecological interactions with animals (primarily opportunistic infections). Zygospores tend to be globose, smooth or ornamented, and produced on opposed or apposed suspensor cells with or without appendages. Asexual reproduction typically involves the production of sporangiospores in sporangia or sporangioles, or chlamydospores. Hyphae tend to be large diameter and coenocytic except for the delimitation of reproductive structures by adventitious septa.

  • Subphylum: Glomeromycotina contains Archaeosporales, Diversisporales, Glomerales, and Paraglomerales (Redecker & Schüßler 2014). Sexual reproduction is unknown and asexual reproduction is by specialised spores that resemble azygospores or chlamydospores. Class Glomeromycetes, Orders: Archaeosporales; Diversisporales; Glomerales; Paraglomerales (see Section 3.6 below).
  • Subphylum: Mortierellomycotina; Order: Mortierellales. Mortierellomycotina reproduce asexually by sporangia. Molecular phylogenetic analyses reveal considerable diversity within Mortierellomycotina and environmental sampling shows a diversity of taxa associated with soils, rhizosphere, and plant roots. Mortierella species are known as prolific producers of fatty acids, especially arachidonic acid and they frequently harbour bacterial endosymbionts. Most species of Mortierellomycotina only form microscopic colonies, but at least two species in the genus Modicella make multicellular sporocarps.
  • Subphylum: Mucoromycotina; Orders: Endogonales, Mucorales and Umbelopsidales. This subphylum features the largest number of described species of Mucoromycota and includes the well-known model species Mucor mucedo and Phycomyces blakesleeanus. It also includes industrially important species of Rhizopus and other genera. Where known, sexual reproduction within Mucoromycotina is by typical zygospore formation and asexual reproduction typically involves the copious production of sporangia and/or sporangioles. Species are frequently isolated from soil, dung, plant debris, and sugar-rich plant parts (like fruits). Fungi in the Mucoromycotina represent the majority of zygomycetous fungi in pure culture. Some Mucorales are extremely fast growing in culture and can often be found on mouldy bread or fruit. Endogonales are either ectomycorrhizal on plant roots (remember the Glomeromycotina are endomycorrhizal) or are saprotrophic. Sexual reproduction involves the production of zygospores by apposed gametangia within a simple sporocarp that may be hypogeous, embedded in heavily decayed wood, or produced among foliage of mosses or liverworts. Ectomycorrhizas have probably evolved twice within Endogonales. Endogonales represents an independent origin of mycorrhizae relative to the arbuscular mycorrhizas of Glomeromycotina and ectomycorrhizas of Dikarya and like many of Mucoromycota, they harbour endohyphal bacteria. Order: Umbelopsidales contains the genus Umbelopsis. Asexual reproduction is by sporangia and chlamydospores. Sporangiophores may be branched. Sporangia are typically pigmented red or ochre, multi- or single-spored and with or without conspicuous columella. Sporangiospores are globose, ellipsoidal, or polyhedral and pigmented like sporangia. Chlamydospores are filled with oil globules and often abundant in culture. Sexual reproduction is unknown. Species in the Umbelopsidales were previously classified in Mucorales or Mortierellales. Umbelopsidales is a distant sister group to Mucorales. Like Mortierellales, species of Umbelopsidales are frequently isolated from rhizosphere soils, with increasing evidence that these fungi occur as root endophytes.

Asexual spores in the traditional zygomycetes are single-celled and include mitosporic sporangiospores, made within the sporangium by internal cleavage of sporangial cytoplasm (as described above for Blastocladiella) and true conidia (which are borne on specialised hyphae called conidiophores). Sporangiospores are dispersed by wind or animals after rupture of the sporangium wall. Conidia are formed by the Entomophthorales and are forcibly discharged.

Names to look out for include Mucor, a typical filamentous mould that occurs as a saprotroph in soil, and on decaying fruits and vegetables. It is found everywhere in nature. Some Mucor spp. cause diseases (called zygomycosis) in man, frogs, other amphibians, cattle, and pigs. Strains isolated from human infections are unusually thermotolerant, most other strains being unable to grow at 37°C. Species names to look out for are Mucor hiemalis, M. amphibiorum, M. circinelloides, and M. racemosus.

The genus Rhizopus is characterised by very fast growing and coarse hyphae and colonies spread by means of creeping aerial hyphae known as stolons that branch into pigmented root-like rhizoids when they contact the substratum. Sporangiophores, singly or in groups, arise from nodes directly above the rhizoids. The fungus is common on decaying fruits, and in soil and house dust, and can be a pest in microbiology laboratories because their rapid growth and dry, easily air-distributed spores enable them to take over culture media in a few days.

Rhizopus oligosporous is used to transform soy bean paste into the fermented food called tempeh in some Asian countries. However, it also produces the alkaloid agroclavine which is toxic to humans. Rhizopus oryzae (also known as R. arrhizus) is the most common causative agent of zygomycosis, accounting for some 60% of cases; it is a serious (and often fatal) opportunistic infection in immunosuppressed patients (in an opportunistic infection a vigorous saprotrophic organism becomes a disease organism by taking advantage of a weakened host).

Rhizopus rot is a soft rot of harvested or over-ripe stone fruits, such as peaches, nectarines, sweet cherries, and plums; it can be caused by several species including  R. nigricans and R. stolonifer.

Phycomyces blakesleeanus is another filamentous fungus in the order Mucorales; this one gets its fame from the amount of basic research done with it over the years. Phycomyces produces numerous tall sporangiophores that are very sensitive to light. An enormous amount of research has been directed to investigate phototropism, and then other environmental sensitivities like gravitropism. Spore germination, carotene biosynthesis and sexual development have all been studied in depth and genetic analysis carried out. It may be worth mentioning that the non-septate, and therefore unicellular, sporangiophores of P. blakesleeanus are more than 100 μm wide (= 0.1 mm) and can grow to a height of 60 cm or more. Another remarkable fungus!

Basidiobolus is usually considered to be a member of the Entomophthorales (although some phylogenetic studies have grouped Basidiobolus with Chytridiomycota), but in the AFTOL study Basidiobolus spp. emerged in a novel position, separate from the majority of chytrids and Entomophthorales (White et al., 2006). Basidiobolus is isolated from the dung of amphibians, reptiles, and insectivorous bats, as well as wood lice, plant debris and soil. It is cosmopolitan, but human infections due to Basidiobolus are reported mostly from Africa, South America, and tropical Asia. Isolates pathogenic to humans belong to a unique species, Basidiobolus ranarum. The real claims to fame, though, come from the size of the mycelial cells, several hundred µm long (the apical compartment can be 300 to 400 µm long, and the fact that the cells have a single large nucleus which may be more than 25 µm in length (a yeast cell is only about 5 µm long). The nucleus undergoes a mitosis that is readily visible by conventional light microscopy and this feature has been exploited to study how inhibitors of mitosis work. This is a good example of using a very unusual fungus to study a particular biological problem. The huge nucleus contains an equally huge nucleolus (about 15 µm in length) (Jordan et al., 1980). In addition, Basidiobolus has remarkable conidia which are shot explosively from the mycelium using what’s been described as a rocket mechanism; the conidium remains intact and attached to the upper part of the conidiophore as the apex of the conidiophore bursts explosively. Basidiobolus appears ideal for studies of the cell cycle, mitosis, and explosive spore dispersal.

The genus Cunninghamella is also commonly found in soil and plant material, particularly in Mediterranean and subtropical zones. It has also been recovered from animal material, cheese, and Brazil nuts. Cunninghamella bertholletiae, C. elegans, and C. echinulata are the most common species, C. bertholletiae is the only known human and animal pathogen, another opportunistic fungus that may cause infections in immunocompromised hosts.

Mortierella species are also common soil fungi and the genus contains over 70 recognised species, however, M. wolfii is probably the only (again, opportunistic) pathogen of man and other animals in this genus.

A peculiarity of Mucoromycota is the occurrence of endosymbiotic bacteria (often with greatly reduced genomes) dwelling within the fungal cells. Like the endobacteria of insects, those of fungi show a range of behaviours from mutualism to antagonism. The data suggest that some of the benefits derived by mycorrhizal fungi from their endobacteria may be shared with the plant host, giving rise to a three-level inter-domain/inter-kingdom interaction (Bonfante & Desirò, 2017; Venice et al., 2019; Bonfante & Venice, 2020). Here we refer you to Section 13.10 for an account of the way the Rhizobium-legume symbioses form the bacterium-plant symbiotic interface by making use of molecular components derived from the arbuscular mycorrhizal fungal partner of the legume.

The words ‘entomo + phthora’ mean ‘insect destroyer’ and Entomophthora is the generic name for fungi that attack and kill flies and many other insects with two wings (= Diptera). Entomophthora muscae, attacks houseflies. The fungus grows inside the body of the insect. The mycelium of the fungus grows into the region of the fly’s brain that controls behaviour, inducing the fly to land on a nearby surface and crawl up as high as possible. Eventually the hyphae of the fungus grow throughout the body of the fly and it dies. The mycelium then proliferates to the point where it pushes the abdominal segments apart and bursts through to give the fly a banded appearance; the bands being tight columns of cells that produce and shoot off the spores that eventually form a white halo encircling the body of the dead fly. Waiting to infect the next victim.

Updated January, 2020