Fungi classification and types

• ALSO KNOWN AS: Fungal systematics

Definition

The term fungi refers to eukaryotic, heterotrophic organisms that digest organic matter by secreting enzymes into the extracellular environment, assimilating nutrients, including fixed carbon, by osmosis. True fungi are classified into seven major phyla

General Characteristics

Except in unicellular forms, the basic growth pattern of fungi consists of filamentous hyphae (slender tubes that are the basic building blocks of fungi), with little cellular differentiation in vegetative tissues. Reproduction, both sexual and asexual, is by means of spores, usually microscopic.

Biologists formerly included fungus as the phylum Mycota within the plant kingdom, but beginning in the 1960s, they adopted a five kingdom classification; one of the kingdoms was reserved for fungi. With increasing knowledge of ultrastructure and physiological processes at the molecular level, it became evident that the fungi were not monophyletic. Sequencing of ribosomal deoxyribonucleic acid (DNA) confirmed this. It also helped clarify the probable taxonomic position of fungal species (including some important human pathogens) without diagnostic morphological features. Sequencing also aided taxonomists in constructing a more natural system reflecting phylogeny and actual biological affinity. From a practical point of view, the better a taxonomic system, the more useful it is for making identifications critical to diagnosis and for predicting what therapies are most promising.

Ribonucleic acid (RNA) sequencing and a form of mathematical analysis known as cladistics have identified dozens of distinct evolutionary lines among the eukaryotes, most of them consisting of obscure groups of protozoa. The Myxomycetes (slime molds), included with fungi in older classifications, are now considered to be animals closely related to one group of amoeboid protozoa. An important group of aquatic fungi organisms, the Oomycetes or Oomycota, are now placed in the kingdom Straminipila with several phyla of algae, including kelp and diatoms, that have the same flagellar structure and cell wall chemistry. The remaining fungi fall on that portion of the tree of life that also includes Metazoa (multicellular animals), vascular plants and green algae, and some protozoa.

The clade (group consisting of an organism and all its descendants) including the Zygomycota, Ascomycota, and Basidiomycota, sometimes termed Eumycota, consists of overwhelmingly terrestrial organisms that lack motile spores or any vestige of a flagellar base. Most are haploid except for the zygote, which immediately undergoes meiosis before the formation of spores. Several orders formerly included in the Zygomycetes may be distinct enough to warrant recognition at a higher taxonomic level. The Microsporidia, a group of obligate animal parasites formerly regarded as primitive or degenerate protozoa, groups with the Eumycota. The Chytridiomycota encompasses aquatic forms with zoospores equipped with a whiplash 9+2 flagellum, cell walls containing chitin, and, in a number of species, regular alternation between haploid and diploid generations. Many species are parasitic on algae.

Oomycota (Kingdom Stramenopiles)

The diagnostic feature of this small but economically important phylum of organisms is a motile zoospore bearing two flagella, one of the “tinsel” type, with numerous lateral fibrils (mastigonemes). Other ultrastructural and biochemical features distinguishing them from the Eumycota include cellulose rather than chitin as the principal cell wall component, tubular rather than flattened cristae in the mitochondria, and a starch-like cellular storage product, mycolaminarin.

The name “Oomycete” comes from the sexual phase of the life cycle, which involves production of specialized hyphal outgrowths of markedly unequal sizes, the oogonium and antheridium, in which meiosis takes place. These fuse, leading to karyogamy (fusion of nuclei) within the oogonium (female sexual organ in fungi); one or more diploid resting oospores then develop. Upon germination, a mass of diploid nonseptate hyphae are produced. Most species also produce spores asexually in sporangia (mother cells).

There are two well-marked classes within the Oomycota, the Peronosporomycetidae and the Saprolegniamycetidae. The first, including the Peronosporales, Rhypdiales, and Lagenidiales, consists mainly of biotrophic parasites of terrestrial plants. There is one oospore per oogonium. In many genera, the sporangia are wind-disseminated as a unit and may germinate on the host without production of zoospores. Phytophthora infestans, the cause of potato blight, belongs to the Peronosporales. The Saprolegniamycetidae, including the Saprolegniales and Leptomitales, consists of aquatic fungi with sporangia releasing zoospores directly into the environment. Oogonia produce multiple oospores.

Some Saprolegniales are important pathogens of fish and other aquatic animals. Pythium insidiosum attacks domestic animals in tropical regions and has been confirmed as a rare agent of human disease. It may be more common, as the clinical symptoms and morphology of the fungus suggest zygomycosis, and a firm diagnosis requires DNA sequencing of the pathogen.

Eumycota: Phylum Chytridiomycota

In older classifications, Chytridiomycetes were grouped with the Oomycetes in a general category, Phycomycetes, or algal-like fungi. The diagnostic feature is a zoospore with a single 9+2 flagellum, the same type found in plants and multicellular animals. Sexual reproduction is through fusion of zoospores to form a zygote. Some chytrids form extensive mycelium (mass of hyphae), while in others the vegetative body consists of a single cell anchored to the host by rhizoids that converts to a zoosporangium. Growth and asexual reproduction can take place in both the haploid and diploid phases.

Based on DNA sequencing, there are three distinct phyletic groups of fungi with uniflagellate zoospores: the Chytridiomycota, including the Chytridiales, Spizellomycetales, and Rhizophydiales; the Blastocladiomycota, which are mainly parasites on soil and freshwater invertebrates; and the Neocallimastigomycota, a small group of anaerobes inhabiting the stomachs of ruminants. There have been no known reports of human disease caused by Chytridiomycota, but Batrachochytrium dendrobalis causes a devastating disease of frogs and other amphibians.

Eumycota: Phylum Zygomycota

The Zygomycota are characterized by the absence of motile stages in the life cycle and by nonseptate hyphae, cell walls containing chitin, production of nonmotile sexual spores in sporangia, and fusion of hyphal outgrowths of equal size to form a diploid zygospore, often thick-walled and ornamented, that serves as a resting spore. About nine hundred species are known, amounting to approximately 1 percent of the total number of described fungi.

Based on DNA sequencing and morphology and host relationships, the Zygomycota have been divided into four classes, the Mucormycotina, Kickxellomycotina, Entomophthoramycotina, and Zoopagomycotina. Additionally, the Glomeromycetes, an ancient group of obligately mycorrhizal fungi symbiotic on the roots of higher plants, and the Microsporidia, specialized animal pathogens formerly classified as protozoa, appear to be more closely related to the Zygomycetes than to other Eumycota.

The subphylum Mucoromycotina, primarily comprising the main orders Mucorales, Endogonales, and Mortierellales, includes fast-growing saprophytes (organisms that live on dead or decaying matter) with abundant asexual reproduction, including the familiar black bread mold Rhizopus stolonifera. Species of Mucor and several other genera cause rare but extremely dangerous fulminating infections in immunocompromised persons.

Most members of the Kickxellomycotina and Zoopagomycotina are specialized parasites or commensals on invertebrate animals and other fungi. They have not been implicated in human disease. The Entomophthoromycota, which includes a number of insect pathogens used as agents of biological control, is characterized by conidia (a type of asexually produced spores) that are actively discharged. Several species of Conidiobolus and Basidiobolus ranarum infect humans, usually immunocompromised persons, producing chronic skin ulcers and polyps. The classification of Basidiobolus in the Entomophthorales has been questioned; its DNA sequence suggests affinity with the Chytridiomycetes.

Microsporidia, which cause chronic infections in many vertebrate animals, including humans, were originally thought to be protozoa and to be near the base of the eukaryotic family tree based on small cell size, small genomes, and a lack of mitochondria. A unique feature of the cell is a triggered filament that aids in penetration of host cells. DNA analysis suggests the simple structure is not primitive but instead evolved in the parasitic habitat.

Eumycota: Subkingdom Dikarya

The subkingdom Dikarya is a well-defined clade composed of the phyla Ascomycota and Basidiomycota and includes more than 90 percent of the species described as fungi. These predominantly terrestrial fungi lack motile spores and have chitinous cell walls. An extensive mycelium composed of regularly septate hyphae is usually present. The distinctive feature defining this clade is a life-cycle stage between plasmogamy (fusion of cells) and karyogamy (fusion of nuclei), during which the cells are binucleate, with a complete set of chromosomes from each parent. In Ascomycota, the binucleate stage is confined to the actual sexual fruit body, but in Basidiomycota it constitutes the main vegetative thallus—persisting, in some genera of wood-destroying fungi, for decades or even centuries.

Older classifications sometimes formally recognized a third class, the Deuteromycetes or Fungi Imperfecti, for fungi with septate hyphae and no known sexual cycle. Manuals for identifying these fungi still group them in a form-class for convenience. Some morphologically defined form-genera of asexually reproducing fungi, such as Penicillium and Alternaria, represent distinct biological entities connecting to genera defined by the sexual stage, while others do not. The trend in recent years has been to use biochemistry of metabolites to classify yeasts, which are very simple morphologically and represent a growth phase of many human pathogens. With the advent of DNA sequencing, it has become possible to correctly classify any organism of interest.

Phylum Ascomycota. These organisms have a vegetative thallus, except in yeasts, that comprises haploid septate hyphae, cells that are generally uninucleate. Asexual reproduction is by means of conidia unicellular to multicellular spores, typically airborne and often produced abundantly. Sexual reproduction in most families is initiated by fertilization of a specialized enlarged cell, the ascogonium, with small airborne conidia known as spermatia, followed by limited proliferation of binucleate cells. Karyogamy and meiosis take place inside a saclike cell called an ascus, within which ascospores (usually eight) are delimited.

The Ascomycota is the largest and most diverse natural phylum of Eumycota and includes the majority of species of medically important fungi and the majority of plant pathogens. Between one-quarter and one-third of the known species form symbiotic lichen associations with algae and cyanobacteria.

For the most part, the division of the Ascomycota into classes and orders, proposed in the mid-twentieth century and based on the structure and development of ascocarps (mature fruiting bodies) and asci (spore sacs), agrees with the division based on DNA sequencing. However, the old subclass Hemiascomycetes defined by the absence of fruit bodies and including the Taphrinales, mainly obligate biotrophic parasites of higher plants, and the Saccharomycetales (ascomycetous yeasts with no or limited mycelial growth) becomes the subphyla Taphrinomycota and Saccharomycota.

Molecular studies have shown that the important human pathogen Pneumocystis carinii, which occurs as undifferentiated yeastlike cells in host tissue and has not been successfully cultured, is a member of the Taphrinomycota. This pathogen causes diffuse pneumonia in patients who are immunocompromised. Another important pathogen, Candida albicans, is a representative member of the Saccharomycotina, which also includes brewer’s yeast. The yeast growth form is characterized by single cells that bud off multiple daughter cells from undifferentiated loci on the cell surface. Some yeasts, including C. albicans, have a diploid vegetative state.

The old class Euascomycetes, renamed subphylum Pezizomycotina, includes several recognized orders of Ascomycetes producing asci in distinct fruiting bodies. The most important divisions are Pezizomycetes, Eurotiomycetes, Laboulbeniomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes.

Pezizomycetes are fungi with disc-shaped fruit bodies (apothecia) and operculate asci, related hypogeous gastroid forms, the true truffles, Dothideomycetes, fungi with enclosed fruit bodies (perithecia), ascostromatic development, and bitunicate asci. This group includes many plant pathogens. Abundantly sporulating asexual stages are common allergens, and a few species are opportunistic human pathogens.

Eurotiomycetes are fungi with enclosed, aporate, often reduced fruit bodies, and simple thin-walled asci. Asexual stages of Eurotiales include the genera Penicillium and Aspergillus. This class includes the majority of true human pathogens and agents of food spoilage that produce toxins and carcinogens. The dermatophyte genera Trichophyton, Microsporum, and Epidermophyton and the serious pathogens Histoplasma (causes histoplasmosis) and Paracoccidioides (causes Paracoccidioidomycosis) belong to the order Onygenales.

Laboulbeniomycetes are specialized ectoparasites of arthropods, with very reduced thalli. Lecanoromycetes are Lichen mycobionts and saprophytes with apothecia and complex (but not functionally bitunicate) asci. Leotiomycetes are plant parasites that have unitunicate asci, apothecia, and ascohymenial development. Sordariomycetes have a perithecium fruit body, ascohymenial development, and unitunicate asci. This diverse group includes many important plant pathogens. Fusarium and Sporothrix are conidial stages of Sordariomycetes.

Phylum Basidiomycota. These organisms have a vegetative thallus, except in yeasts, comprised of haploid dikaryotic septate hyphae. Production of asexual spores is infrequent in Hymenomycetes but a regular part of the life cycles of Uredinomycetes (rusts) and Ustilagomycetes (smuts). Sexual reproduction is initiated by fusion of undifferentiated haploid mycelial cells (Hymenomycetes) or pycniospores functioning as spermatia (Uredinomycetes). Karyogamy and meiosis take place inside a club-like structure called a basidium, Basidiospores, produced externally, are forcibly discharged. Basidiomycetes are most important in nature as decomposers of wood, plant pathogens (rusts and smuts), and mycorrhizal symbionts of forest trees. Subphyla are Puccinomycotina, Ustilagomycotina, and Agaricomycotina.

From a human perspective, the most important groups in the subphylum Puccinomycotina are the Pucciniales (rusts), obligate biotrophic plant parasites with complex life cycles, and the Sporidiobolales, the main group of basidiomycetous yeasts. Of particular interest to medical mycologists is Cryptococcus (Filobasidiella) neoformans, in which multiple mitotic divisions follow meiosis in the basidium and basidiospores are budded off in chains.

The subphylum Ustilaginomycotina consists of mainly obligate plant parasites with complex life cycles, divided into two classes, the Ustilagomycetes (smuts) and Exobasidiomycetes (leaf curl diseases and some smuts). There is one human parasite, the dermatophyte yeast Melasseza.

As the name implies, the subphylum Agaricomycotina includes the familiar edible mushroom Agaricus campestris. Members of this group have a life cycle including a limited undifferentiated mycelial haploid phase followed by hyphal fusion establishing a dikaryon. Dikaryotic hyphae have characteristic clamp connections and complex dolipore septa. Basidia are typically borne in a layer (the hymenium) on complex fruit bodies. Basidia are septate in the Tremellomycetes (jelly fungi) and unicellular in the Agaricales (mushrooms), Polyporales (woody pore fungi), and Phallales (stinkhorns). The orders of the subphylum Agaricomycotina (Cystofilobasidiales, Filobasidiales, and Tremellales) have long been defined by microanatomy and chemistry rather than gross fruit-body form, and present classifications based on DNA analysis closely approximate older treatments. This subphylum contains no important human pathogens.

Impact

Having an accurate system of classification for fungi or any other group of organisms that have a significant impact on humans is critical to identifying species and devising methods of control that are tailored to the particular organism. In a clinical setting, healthcare providers need to identify the agent causing the disease to initiate appropriate therapies. In research laboratories, the development of effective therapies depends on understanding the biochemistry and life cycle of the target pathogen, a process greatly aided by being able to classify it with a biologically related species.

Human pathogenic fungi have always presented a challenge to medicine because fungi are more closely related to humans than are bacteria and most protozoa. Drugs that inhibit fungal growth are, therefore, likely to be toxic to humans. Most common fungal infections are superficial or localized and can be treated topically. However, growing populations of immunocompromised persons, including those with human immunodeficiency virus (HIV) infection, transplant recipients, and persons undergoing chemotherapy, have led to the emergence of a number of systemic, life-threatening mycoses.

DNA sequencing is a great aid in identifying and treating fungal diseases. It has established the taxonomic position and, therefore, the most promising avenues for therapy for morphologically ambiguous pathogens such as Microsporidia and Pneumocystis. DNA sequencing is becoming available as a clinical diagnostic tool for establishing the identity of a pathogen in tested persons.

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