Fungi Temporal range: Early Devonian–Recent (but see text) PreЄ Є O S D C P T J K Pg N
Clockwise from top left: Amanita muscaria, a basidiomycete; Sarcoscypha coccinea, an ascomycete; bread covered in mold; a chytrid; an Aspergillus conidiophore.
Scientific classification
Domain:	Eukaryota
(unranked):	Opisthokonta
Kingdom:	Fungi (L., 1753) R.T. Moore, 1980[1]
Subkingdoms/Phyla/Subphyla[2]
Blastocladiomycota Chytridiomycota Glomeromycota Microsporidia Neocallimastigomycota Dikarya (inc. Deuteromycota) Ascomycota Pezizomycotina Saccharomycotina Taphrinomycotina Basidiomycota Agaricomycotina Pucciniomycotina Ustilaginomycotina Subphyla incertae sedis Entomophthoromycotina Kickxellomycotina Mucoromycotina Zoopagomycotina

A fungus ( /ˈfʌŋɡəs/; plural: fungi^[3] or funguses^[4]) is a member of a large group of eukaryotic organisms that includes microorganisms such as yeasts and molds (British English: moulds), as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from plants, animals, and bacteria. One major difference is that fungal cells have cell walls that contain chitin, unlike the cell walls of plants, which contain cellulose. These and other differences show that the fungi form a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (a monophyletic group). This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology, which is often regarded as a branch of botany, even though genetic studies have shown that fungi are more closely related to animals than to plants.

Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their cryptic lifestyles in soil, on dead matter, and as symbionts of plants, animals, or other fungi. They may become noticeable when fruiting, either as mushrooms or molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange. They have long been used as a direct source of food, such as mushrooms and truffles, as a leavening agent for bread, and in fermentation of various food products, such as wine, beer, and soy sauce. Since the 1940s, fungi have been used for the production of antibiotics, and, more recently, various enzymes produced by fungi are used industrially and in detergents. Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, that are toxic to animals including humans. The fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g. rice blast disease) or food spoilage can have a large impact on human food supplies and local economies.

The fungus kingdom encompasses an enormous diversity of taxa with varied ecologies, life cycle strategies, and morphologies ranging from single-celled aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at around 1.5 million species, with about 5% of these having been formally classified.^{[citation needed]} Ever since the pioneering 18th and 19th century taxonomical works of Carl Linnaeus, Christian Hendrik Persoon, and Elias Magnus Fries, fungi have been classified according to their morphology (e.g., characteristics such as spore color or microscopic features) or physiology. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, which has sometimes challenged the historical groupings based on morphology and other traits. Phylogenetic studies published in the last decade have helped reshape the classification of Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla.

Etymology[link]

The English word fungus is directly adopted from the Latin fungus (mushroom), used in the writings of Horace and Pliny.^[5] This in turn is derived from the Greek word sphongos/σφογγος ("sponge"), which refers to the macroscopic structures and morphology of mushrooms and molds;^[6] the root is also used in other languages, such as the German Schwamm ("sponge") and Schimmel ("mold").^[7] The use of the word mycology, which is derived from the Greek mykes/μύκης (mushroom) and logos/λόγος (discourse),^[8] to denote the scientific study of fungi is thought to have originated in 1836 with English naturalist Miles Joseph Berkeley's publication The English Flora of Sir James Edward Smith, Vol. 5.^[6]

Characteristics[link]

Before the introduction of molecular methods for phylogenetic analysis, taxonomists considered fungi to be members of the Plant Kingdom because of similarities in lifestyle: both fungi and plants are mainly immobile, and have similarities in general morphology and growth habitat. Like plants, fungi often grow in soil, and in the case of mushrooms form conspicuous fruiting bodies, which sometimes bear resemblance to plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago.^[9][10] Some morphological, biochemical, and genetic features are shared with other organisms, while others are unique to the fungi, clearly separating them from the other kingdoms:

Shared features:

• With other eukaryotes: As other eukaryotes, fungal cells contain membrane-bound nuclei with chromosomes that contain DNA with noncoding regions called introns and coding regions called exons. In addition, fungi possess membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes, and ribosomes of the 80S type.^[11] They have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols (e.g., mannitol), disaccharides, (e.g., trehalose), and polysaccharides (e.g., glycogen, which is also found in animals^[12]).
• With animals: Fungi lack chloroplasts and are heterotrophic organisms, requiring preformed organic compounds as energy sources.^[13]
• With plants: Fungi possess a cell wall^[14] and vacuoles.^[15] They reproduce by both sexual and asexual means, and like basal plant groups (such as ferns and mosses) produce spores. Similar to mosses and algae, fungi typically have haploid nuclei.^[16]
• With euglenoids and bacteria: Higher fungi, euglenoids, and some bacteria produce the amino acid L-lysine in specific biosynthesis steps, called the α-aminoadipate pathway.^[17][18]
• The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures and are called hyphae, which may contain multiple nuclei and extend at their tips. Each tip contains a set of aggregated vesicles—cellular structures consisting of proteins, lipids, and other organic molecules—called Spitzenkörper.^[19] Both fungi and oomycetes grow as filamentous hyphal cells.^[20] In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells.^[12]
• In common with some plant and animal species, more than 60 fungal species display the phenomenon of bioluminescence.^[21]

Unique features:

• Some species grow as single-celled yeasts that reproduce by budding or binary fission. Dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions.^[22]
• The fungal cell wall is composed of glucans and chitin; while the former compounds are also found in plants and the latter in the exoskeleton of arthropods,^[23][24] fungi are the only organisms that combine these two structural molecules in their cell wall. In contrast to plants and the oomycetes, fungal cell walls do not contain cellulose.^[25]

Omphalotus nidiformis, a bioluminescent mushroom

Most fungi lack an efficient system for long-distance transport of water and nutrients, such as the xylem and phloem in many plants. To overcome these limitations, some fungi, such as Armillaria, form rhizomorphs,^[26] that resemble and perform functions similar to the roots of plants. Another characteristic shared with plants includes a biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as chemical building blocks.^[27] However, plants have an additional terpene pathway in their chloroplasts, a structure fungi do not possess.^[28] Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants.^[27] Many of the plant and fungal enzymes that make these compounds differ from each other in sequence and other characteristics, which indicates separate origins and evolution of these enzymes in the fungi and plants.^[27][29]

Diversity[link]

Fungi have a worldwide distribution, and grow in a wide range of habitats, including extreme environments such as deserts or areas with high salt concentrations^[30] or ionizing radiation,^[31] as well as in deep sea sediments.^[32] Some can survive the intense UV and cosmic radiation encountered during space travel.^[33] Most grow in terrestrial environments, though several species live partly or solely in aquatic habitats, such as the chytrid fungus Batrachochytrium dendrobatidis, a parasite that has been responsible for a worldwide decline in amphibian populations. This organism spends part of its life cycle as a motile zoospore, enabling it to propel itself through water and enter its amphibian host.^[34] Other examples of aquatic fungi include those living in hydrothermal areas of the ocean.^[35]

Around 100,000 species of fungi have been formally described by taxonomists,^[36] but the global biodiversity of the fungus kingdom is not fully understood.^[37] On the basis of observations of the ratio of the number of fungal species to the number of plant species in selected environments, the fungal kingdom has been estimated to contain about 1.5 million species;^[38] a recent (2011) estimate suggests there may be over 5 million species.^[39] In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.^[40] Species may also be distinguished by their biochemical and physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to chemical tests. The biological species concept discriminates species based on their ability to mate. The application of molecular tools, such as DNA sequencing and phylogenetic analysis, to study diversity has greatly enhanced the resolution and added robustness to estimates of genetic diversity within various taxonomic groups.^[41]

Morphology[link]

Microscopic structures[link]

An environmental isolate of Penicillium
1. hypha 2. conidiophore 3. phialide 4. conidia 5. septa

Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10 µm in diameter and up to several centimeters in length. Hyphae grow at their tips (apices); new hyphae are typically formed by emergence of new tips along existing hyphae by a process called branching, or occasionally growing hyphal tips bifurcate (fork) giving rise to two parallel-growing hyphae.^[42] The combination of apical growth and branching/forking leads to the development of a mycelium, an interconnected network of hyphae.^[22] Hyphae can be either septate or coenocytic: septate hyphae are divided into compartments separated by cross walls (internal cell walls, called septa, that are formed at right angles to the cell wall giving the hypha its shape), with each compartment containing one or more nuclei; coenocytic hyphae are not compartmentalized.^[43] Septa have pores that allow cytoplasm, organelles, and sometimes nuclei to pass through; an example is the dolipore septum in the fungi of the phylum Basidiomycota.^[44] Coenocytic hyphae are essentially multinucleate supercells.^[45]

Many species have developed specialized hyphal structures for nutrient uptake from living hosts; examples include haustoria in plant-parasitic species of most fungal phyla, and arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients.^[46]

Although fungi are opisthokonts—a grouping of evolutionarily related organisms broadly characterized by a single posterior flagellum—all phyla except for the chytrids have lost their posterior flagella.^[47] Fungi are unusual among the eukaryotes in having a cell wall that, in addition to glucans (e.g., β-1,3-glucan) and other typical components, also contains the biopolymer chitin.^[48]

Macroscopic structures[link]

Armillaria solidipes

Fungal mycelia can become visible to the naked eye, for example, on various surfaces and substrates, such as damp walls and on spoiled food, where they are commonly called molds. Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colonies. These colonies can exhibit growth shapes and colors (due to spores or pigmentation) that can be used as diagnostic features in the identification of species or groups.^[49] Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of a clonal colony of Armillaria solidipes, which extends over an area of more than 900 ha (3.5 square miles), with an estimated age of nearly 9,000 years.^[50]

The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped fruiting body that holds the hymenium, a layer of tissue containing the spore-bearing cells.^[51] The fruiting bodies of the basidiomycetes (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well-known as mushrooms.

Growth and physiology[link]

Mold growth covering a decaying peach. The frames were taken approximately 12 hours apart over a period of six days.

The growth of fungi as hyphae on or in solid substrates or as single cells in aquatic environments is adapted for the efficient extraction of nutrients, because these growth forms have high surface area to volume ratios.^[52] Hyphae are specifically adapted for growth on solid surfaces, and to invade substrates and tissues.^[53] They can exert large penetrative mechanical forces; for example, the plant pathogen Magnaporthe grisea forms a structure called an appressorium that evolved to puncture plant tissues.^[54] The pressure generated by the appressorium, directed against the plant epidermis, can exceed 8 megapascals (1,200 psi).^[54] The filamentous fungus Paecilomyces lilacinus uses a similar structure to penetrate the eggs of nematodes.^[55]

The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol.^[56] Morphological adaptations such as these are complemented by hydrolytic enzymes secreted into the environment to digest large organic molecules—such as polysaccharides, proteins, lipids, and other organic substrates—into smaller molecules that may then be absorbed as nutrients.^[57][58][59] The vast majority of filamentous fungi grow in a polar fashion—i.e., by extension into one direction—by elongation at the tip (apex) of the hypha.^[60] Alternative forms of fungal growth include intercalary extension (i.e., by longitudinal expansion of hyphal compartments that are below the apex) as in the case of some endophytic fungi,^[61] or growth by volume expansion during the development of mushroom stipes and other large organs.^[62] Growth of fungi as multicellular structures consisting of somatic and reproductive cells—a feature independently evolved in animals and plants^[63]—has several functions, including the development of fruiting bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication.^[64]

The fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixed by other organisms for metabolism. Fungi have evolved a high degree of metabolic versatility that allows them to use a diverse range of organic substrates for growth, including simple compounds such as nitrate, ammonia, acetate, or ethanol.^[65][66] For some species it has been shown that the pigment melanin may play a role in extracting energy from ionizing radiation, such as gamma radiation; however, this form of "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlying biophysical and biochemical processes are not known.^[31] The authors speculate that this process might bear similarity to CO₂ fixation via visible light, but instead utilizing ionizing radiation as a source of energy.^[67]

Reproduction[link]

Polyporus squamosus

Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms.^[68] It is estimated that a third of all fungi reproduce using more than one method of propagation; for example, reproduction may occur in two well-differentiated stages within the life cycle of a species, the teleomorph and the anamorph.^[69] Environmental conditions trigger genetically determined developmental states that lead to the creation of specialized structures for sexual or asexual reproduction. These structures aid reproduction by efficiently dispersing spores or spore-containing propagules.

Asexual reproduction[link]

Asexual reproduction via vegetative spores (conidia) or through mycelial fragmentation is common; it maintains clonal populations adapted to a specific niche, and allows more rapid dispersal than sexual reproduction.^[70] The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species which lack an observable sexual cycle.^[71]

Sexual reproduction[link]

Sexual reproduction with meiosis exists in all fungal phyla (with the exception of the Glomeromycota).^[72] It differs in many aspects from sexual reproduction in animals or plants. Differences also exist between fungal groups and can be used to discriminate species by morphological differences in sexual structures and reproductive strategies.^[73][74] Mating experiments between fungal isolates may identify species on the basis of biological species concepts.^[74] The major fungal groupings have initially been delineated based on the morphology of their sexual structures and spores; for example, the spore-containing structures, asci and basidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Some species may allow mating only between individuals of opposite mating type, while others can mate and sexually reproduce with any other individual or itself. Species of the former mating system are called heterothallic, and of the latter homothallic.^[75]

Most fungi have both an haploid and diploid stage in their life cycles. In sexually reproducing fungi, compatible individuals may combine by fusing their hyphae together into an interconnected network; this process, anastomosis, is required for the initiation of the sexual cycle. Ascomycetes and basidiomycetes go through a dikaryotic stage, in which the nuclei inherited from the two parents do not combine immediately after cell fusion, but remain separate in the hyphal cells (see heterokaryosis).^[76]

The 8-spored asci of Morchella elata, viewed with phase contrast microscopy

In ascomycetes, dikaryotic hyphae of the hymenium (the spore-bearing tissue layer) form a characteristic hook at the hyphal septum. During cell division, formation of the hook ensures proper distribution of the newly divided nuclei into the apical and basal hyphal compartments. An ascus (plural asci) is then formed, in which karyogamy (nuclear fusion) occurs. Asci are embedded in an ascocarp, or fruiting body. Karyogamy in the asci is followed immediately by meiosis and the production of ascospores. After dispersal, the ascospores may germinate and form a new haploid mycelium.^[77]

Sexual reproduction in basidiomycetes is similar to that of the ascomycetes. Compatible haploid hyphae fuse to produce a dikaryotic mycelium. However, the dikaryotic phase is more extensive in the basidiomycetes, often also present in the vegetatively growing mycelium. A specialized anatomical structure, called a clamp connection, is formed at each hyphal septum. As with the structurally similar hook in the ascomycetes, the clamp connection in the basidiomycetes is required for controlled transfer of nuclei during cell division, to maintain the dikaryotic stage with two genetically different nuclei in each hyphal compartment.^[78] A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis.^[79] The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Morphology section).

In glomeromycetes (formerly zygomycetes), haploid hyphae of two individuals fuse, forming a gametangium, a specialized cell structure that becomes a fertile gamete-producing cell. The gametangium develops into a zygospore, a thick-walled spore formed by the union of gametes. When the zygospore germinates, it undergoes meiosis, generating new haploid hyphae, which may then form asexual sporangiospores. These sporangiospores allow the fungus to rapidly disperse and germinate into new genetically identical haploid fungal mycelia.^[80]

Spore dispersal[link]

Both asexual and sexual spores or sporangiospores are often actively dispersed by forcible ejection from their reproductive structures. This ejection ensures exit of the spores from the reproductive structures as well as traveling through the air over long distances.

The bird's nest fungus Cyathus stercoreus

Specialized mechanical and physiological mechanisms, as well as spore surface structures (such as hydrophobins), enable efficient spore ejection.^[81] For example, the structure of the spore-bearing cells in some ascomycete species is such that the buildup of substances affecting cell volume and fluid balance enables the explosive discharge of spores into the air.^[82] The forcible discharge of single spores termed ballistospores involves formation of a small drop of water (Buller's drop), which upon contact with the spore leads to its projectile release with an initial acceleration of more than 10,000 g;^[83] the net result is that the spore is ejected 0.01–0.02 cm, sufficient distance for it to fall through the gills or pores into the air below.^[84] Other fungi, like the puffballs, rely on alternative mechanisms for spore release, such as external mechanical forces. The bird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies.^[85] Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores.^[86]

Other sexual processes[link]

Besides regular sexual reproduction with meiosis, certain fungi, such as those in the genera Penicillium and Aspergillus, may exchange genetic material via parasexual processes, initiated by anastomosis between hyphae and plasmogamy of fungal cells.^[87] The frequency and relative importance of parasexual events is unclear and may be lower than other sexual processes. It is known to play a role in intraspecific hybridization^[88] and is likely required for hybridization between species, which has been associated with major events in fungal evolution.^[89]

Evolution[link]

In contrast to plants and animals, the early fossil record of the fungi is meager. Factors that likely contribute to the under-representation of fungal species among fossils include the nature of fungal fruiting bodies, which are soft, fleshy, and easily degradable tissues and the microscopic dimensions of most fungal structures, which therefore are not readily evident. Fungal fossils are difficult to distinguish from those of other microbes, and are most easily identified when they resemble extant fungi.^[90] Often recovered from a permineralized plant or animal host, these samples are typically studied by making thin-section preparations that can be examined with light microscopy or transmission electron microscopy.^[91] Compression fossils are studied by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details.^[92]

The earliest fossils possessing features typical of fungi date to the Proterozoic eon, some 1,430 million years ago (Ma); these multicellular benthic organisms had filamentous structures with septa, and were capable of anastomosis.^[93] More recent studies (2009) estimate the arrival of fungal organisms at about 760–1060 Ma on the basis of comparisons of the rate of evolution in closely related groups.^[94] For much of the Paleozoic Era (542–251 Ma), the fungi appear to have been aquatic and consisted of organisms similar to the extant chytrids in having flagellum-bearing spores.^[95] The evolutionary adaptation from an aquatic to a terrestrial lifestyle necessitated a diversification of ecological strategies for obtaining nutrients, including parasitism, saprobism, and the development of mutualistic relationships such as mycorrhiza and lichenization.^[96] Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times.^[97]

The fungi probably colonized the land during the Cambrian (542–488.3 Ma), long before land plants.^[98] Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460 Ma) resemble modern-day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like plants.^[99] Prototaxites, which was probably a fungus or lichen, would have been the tallest organism of the late Silurian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–359.2 Ma), when they are abundant in the Rhynie chert, mostly as Zygomycota and Chytridiomycota.^{[98][100][101]} At about this same time, approximately 400 Ma, the Ascomycota and Basidiomycota diverged,^[102] and all modern classes of fungi were present by the Late Carboniferous (Pennsylvanian, 318.1–299 Ma).^[103]

Lichen-like fossils have been found in the Doushantuo Formation in southern China dating back to 635–551 Ma.^[104] Lichens were a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 400 Ma;^[105] this date corresponds to the age of the oldest known sporocarp fossil, a Paleopyrenomycites species found in the Rhynie Chert.^[106] The oldest fossil with microscopic features resembling modern-day basidiomycetes is Palaeoancistrus, found permineralized with a fern from the Pennsylvanian.^[107] Rare in the fossil record are the Homobasidiomycetes (a taxon roughly equivalent to the mushroom-producing species of the Agaricomycetes). Two amber-preserved specimens provide evidence that the earliest known mushroom-forming fungi (the extinct species Archaeomarasmius leggetti) appeared during the mid-Cretaceous, 90 Ma.^[108][109]

Some time after the Permian–Triassic extinction event (251.4 Ma), a fungal spike (originally thought to be an extraordinary abundance of fungal spores in sediments) formed, suggesting that fungi were the dominant life form at this time, representing nearly 100% of the available fossil record for this period.^[110] However, the relative proportion of fungal spores relative to spores formed by algal species is difficult to assess,^[111] the spike did not appear worldwide,^[112][113] and in many places it did not fall on the Permian–Triassic boundary.^[114]

Taxonomy[link]