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A fungus (
plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The plural of a noun typically denotes a quantity greater than the default qua ...
: fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as
yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species In biology, a species is the basic unit of biolo ...
s and molds, as well as the more familiar s. These organisms are classified as a kingdom, which is separate from the other eukaryotic life kingdoms of
plant Plants are mainly multicellular organisms, predominantly photosynthetic Photosynthesis is a process used by plants and other organisms to Energy transformation, convert light energy into chemical energy that, through cellular respiratio ...
s and
animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, ...
s. A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved molecules, typically by secreting digestive enzymes into their environment. Fungi do not . Growth is their means of mobility, except for
spores )'', growing on a thinning, thinned hybrid black poplar ''(populus, Populus x canadensis)''. The last stage of the moss#Life cycle, moss lifecycle is shown, where the sporophytes are visible before dispersion of their spores: the calyptra (1) is ...
(a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the ''Eumycota'' (''true fungi'' or ''Eumycetes''), which share a common ancestor (from a '' monophyletic group''), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar Mycetozoa, myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek language, Greek μύκης ', mushroom). In the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the small size of their structures, and their Crypsis, cryptic lifestyles in soil or on dead matter. Fungi include Symbiosis, symbionts of plants, animals, or other fungi and also parasites. They may become noticeable when Sporocarp (fungi), fruiting, either as mushrooms or as molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient Biogeochemical cycle, cycling and exchange in the environment. They have long been used as a direct source of human food, in the form of mushrooms and Tuber (genus), truffles; as a Bread#Leavening, leavening agent for bread; and in the Fermentation (food), 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 Enzyme#Industrial applications, industrially and in protease#Occurrence, detergents. Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce Bioactive compound, 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 Recreational drug use, recreationally or in traditional Entheogen, spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant Pathogenic fungi, pathogens of humans and other animals. Losses of crops due to fungal diseases (e.g., rice blast disease) or food Food spoilage, spoilage can have a large impact on human Food security, food supplies and local economies. The fungus kingdom encompasses an enormous diversity of taxon, taxa with varied ecologies, biological life cycle, life cycle strategies, and morphology (biology), morphologies ranging from unicellular aquatic chytrids to large mushrooms. However, little is known of the true biodiversity of Kingdom Fungi, which has been estimated at 2.2 million to 3.8 million species. Of these, only about 148,000 have been described, with over 8,000 species known to be detrimental to plants and at least 300 that can be pathogenic to humans. Ever since the pioneering 18th and 19th century Taxonomy (biology), taxonomical works of Carl Linnaeus, Christian Hendrik Persoon, and Elias Magnus Fries, fungi have been biological classification, 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 sequencing, 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 first decade of the 21st century have helped reshape the classification within Kingdom Fungi, which is divided into one Kingdom (biology)#Definition and associated terms, subkingdom, seven phylum, phyla, and ten subphyla.


Etymology

The English word ''fungus'' is directly adopted from the Latin ''fungus'' (mushroom), used in the writings of Horace and Pliny the Elder, Pliny. This in turn is derived from the Ancient Greek, Greek word ''sphongos'' (σφόγγος "sponge"), which refers to the macroscopic structures and morphology of mushrooms and molds;Ainsworth, p. 2. the root is also used in other languages, such as the German
Schwamm
' ("sponge") and
Schimmel
' ("mold"). The word ''mycology'' is derived from the Greek (μύκης "mushroom") and ''logos'' (λόγος "discourse"). It denotes the scientific study of fungi. The Latin adjectival form of "mycology" (''mycologicæ'') appeared as early as 1796 in a book on the subject by Christiaan Hendrik Persoon. The word appeared in English as early as 1824 in a book by Robert Kaye Greville. In 1836 the English naturalist Miles Joseph Berkeley's publication ''The English Flora of Sir James Edward Smith, Vol. 5.'' also refers to mycology as the study of fungi. A group of all the fungi present in a particular area or geographic region is known as mycobiota (plural noun, no singular), e.g., "the mycobiota of Ireland".


Characteristics

Before the introduction of Molecular phylogenetics, molecular methods for phylogenetic analysis, Taxonomy (biology), taxonomists considered fungi to be members of the Plant, plant kingdom because of similarities in lifestyle: both fungi and plants are mainly Sessility (zoology), immobile, and have similarities in general morphology and growth habitat. Like plants, fungi often grow in soil and, in the case of s, form conspicuous fruit bodies, which sometimes resemble plants such as mosses. The fungi are now considered a separate kingdom, distinct from both plants and animals, from which they appear to have genetic divergence, diverged around one billion years ago (around the start of the Neoproterozoic Era). 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: Fungal cells contain membrane-bound cell nucleus, nuclei with chromosomes that contain DNA with Noncoding DNA, noncoding regions called introns and coding regions called exons. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes, and ribosomes of the 80S type. 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 animalsDeacon, pp. 128–129.). * With animals: Fungi lack chloroplasts and are heterotrophic organisms and so require preformed organic compounds as energy sources. * With plants: Fungi have a cell wall and vacuoles. They reproduce by both sexual and asexual means, and like Primitive (phylogenetics), basal plant groups (such as ferns and mosses) produce spores. Similar to mosses and algae, fungi typically have haploid nuclei.Deacon, p. 58. * 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. * The cells of most fungi grow as tubular, elongated, and thread-like (filamentous) structures called hyphae, which may contain multiple nuclei and extend by growing at their tips. Each tip contains a set of aggregated vesicle (biology), vesicles—cellular structures consisting of proteins, lipids, and other organic molecules—called the Spitzenkörper. Both fungi and oomycetes grow as filamentous hyphal cells. In contrast, similar-looking organisms, such as filamentous green algae, grow by repeated cell division within a chain of cells. There are also single-celled fungi (
yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species In biology, a species is the basic unit of biolo ...
s) that do not form hyphae, and some fungi have both hyphal and yeast forms.Alexopoulos ''et al''., p. 30. * In common with some plant and animal species, List of bioluminescent fungi, more than 70 fungal species display bioluminescence. Unique features: * Some species grow as unicellular yeasts that reproduce by budding or binary fission, fission. Dimorphic fungi can switch between a yeast phase and a hyphal phase in response to environmental conditions. * The fungal cell wall is composed of glucans and ; while glucans are also found in plants and chitin in the exoskeleton of arthropods, fungi are the only organisms that combine these two structural molecules in their cell wall. Unlike those of plants and oomycetes, fungal cell walls do not contain cellulose. Most fungi lack an efficient system for the long-distance transport of water and nutrients, such as the xylem and phloem in many plants. To overcome this limitation, some fungi, such as ''Armillaria'', form Mycelial cord, rhizomorphs, which resemble and perform functions similar to the roots of plants. As eukaryotes, fungi possess a Biochemical pathway, biosynthetic pathway for producing terpenes that uses mevalonic acid and pyrophosphate as Precursor (chemistry), chemical building blocks. Plants and some other organisms have an additional terpene biosynthesis pathway in their chloroplasts, a structure that fungi and animals do not have. Fungi produce several secondary metabolites that are similar or identical in structure to those made by plants. Many of the plant and fungal enzymes that make these compounds differ from each other in peptide sequence, sequence and other characteristics, which indicates separate origins and convergent evolution of these enzymes in the fungi and plants.


Diversity

Fungi have a worldwide distribution, and grow in a wide range of habitats, including extreme environments such as desert fungi, deserts or areas with high salt concentrations or ionizing radiation, as well as in deep sea sediments. Some can survive the intense ultraviolet radiation, UV and cosmic radiation encountered during space travel. Most grow in terrestrial environments, though several species live partly or solely in aquatic habitats, such as the chytrid fungi ''Batrachochytrium dendrobatidis'' and ''Batrachochytrium salamandrivorans, B. salamandrivorans'', parasites that has been responsible for a worldwide decline in amphibian populations. These organisms spend part of their life cycle as a motile zoospore, enabling them to propel itself through water and enter their amphibian host. Other examples of aquatic fungi include those living in hydrothermal areas of the ocean. As of 2020, around 148,000 species of fungi have been species description, described by Taxonomy (biology), taxonomists, but the global biodiversity of the fungus kingdom is not fully understood. A 2017 estimate suggests there may be between 2.2 and 3.8 million species. The number of new fungi species discovered yearly has increased from 1,000 to 1,500 per year about 10 years ago, to about 2000 with a peak of more than 2,500 species in 2016. In the year 2019, 1882 new species of fungi were described, and it was estimated that more than 90% of fungi remain unknown. In mycology, species have historically been distinguished by a variety of methods and concepts. Classification based on morphology (biology), morphological characteristics, such as the size and shape of spores or fruiting structures, has traditionally dominated fungal taxonomy.Kirk ''et al''., p. 489. Species may also be distinguished by their Biochemistry, biochemical and physiology, physiological characteristics, such as their ability to metabolize certain biochemicals, or their reaction to Chemical tests in mushroom identification, chemical tests. The Species#The isolation species concept in more detail, biological species concept discriminates species based on their ability to mating in fungi, mate. The application of Molecular biology, 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.


Mycology

Mycology is the branch of biology concerned with the systematic study of fungi, including their genetic and biochemical properties, their taxonomy, and their use to humans as a source of medicine, food, and entheogen, psychotropic substances consumed for religious purposes, as well as their dangers, such as poisoning or infection. The field of phytopathology, the study of plant diseases, is closely related because many plant pathogens are fungi. The use of fungi by humans dates back to prehistory; Ötzi the Iceman, a well-preserved mummy of a 5,300-year-old Neolithic man found frozen in the Austrian Alps, carried two species of polypore mushrooms that may have been used as tinder (''Fomes fomentarius''), or for medicinal purposes (''Piptoporus betulinus''). Ancient peoples have used fungi as food sources–often unknowingly–for millennia, in the preparation of leavened bread and fermented juices. Some of the oldest written records contain references to the destruction of crops that were probably caused by pathogenic fungi.


History

Mycology is a relatively new science that became systematic after the development of the microscope in the 17th century. Although fungal spores were first observed by Giambattista della Porta in 1588, the seminal work in the development of mycology is considered to be the publication of Pier Antonio Micheli's 1729 work ''Nova plantarum genera''. Micheli not only observed spores but also showed that, under the proper conditions, they could be induced into growing into the same species of fungi from which they originated. Extending the use of the binomial nomenclature, binomial system of nomenclature introduced by Carl Linnaeus in his ''Species plantarum'' (1753), the Dutch Christian Hendrik Persoon (1761–1836) established the first classification of mushrooms with such skill as to be considered a founder of modern mycology. Later, Elias Magnus Fries (1794–1878) further elaborated the Biological classification, classification of fungi, using spore color and microscopic characteristics, methods still used by taxonomists today. Other notable early contributors to mycology in the 17th–19th and early 20th centuries include Miles Joseph Berkeley, August Carl Joseph Corda, Anton de Bary, the brothers Louis René Tulasne, Louis René and Charles Tulasne, Arthur Henry Reginald Buller, Arthur H. R. Buller, Curtis Gates Lloyd, Curtis G. Lloyd, and Pier Andrea Saccardo. In the 20th and 21st centuries, advances in biochemistry, genetics, molecular biology, biotechnology, DNA sequencing and phylogenetic analysis has provided new insights into fungal relationships and biodiversity, and has challenged traditional morphology-based groupings in fungal Taxonomy (biology), taxonomy.


Morphology


Microscopic structures

Most fungi grow as hyphae, which are cylindrical, thread-like structures 2–10micrometres, 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 fork, giving rise to two parallel-growing hyphae. Hyphae also sometimes fuse when they come into contact, a process called hyphal fusion (or anastomosis). These growth processes lead to the development of a mycelium, an interconnected network of hyphae. Hyphae can be either septum, 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. Septa have Pit connection#Characteristics, pores that allow cytoplasm, organelles, and sometimes nuclei to pass through; an example is the dolipore septum in fungi of the phylum Basidiomycota. Coenocytic hyphae are in essence multinucleate supercells. 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 arbuscular mycorrhiza, arbuscules of several mycorrhizal fungi, which penetrate into the host cells to consume nutrients. 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. 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.


Macroscopic structures

Fungal mycelia can become visible to the naked eye, for example, on various surfaces and substrate (biology), substrates, such as damp walls and spoiled food, where they are commonly called molds. Mycelia grown on solid agar media in laboratory petri dishes are usually referred to as colony (biology), colonies. These colonies can exhibit growth shapes and colors (due to spores or biological pigment, pigmentation) that can be used as diagnostic features in the identification of species or groups. Some individual fungal colonies can reach extraordinary dimensions and ages as in the case of a Clone (cell biology), clonal colony of ''Armillaria solidipes'', which extends over an area of more than 900hectare, ha (3.5 square miles), with an estimated age of nearly 9,000years. The apothecium—a specialized structure important in sexual reproduction in the ascomycetes—is a cup-shaped fruit body that is often macroscopic and holds the hymenium, a layer of tissue containing the spore-bearing cells. The fruit bodies of the basidiomycetes (basidiocarps) and some ascomycetes can sometimes grow very large, and many are well known as s.


Growth and physiology

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. Hyphae are specifically adapted for growth on solid surfaces, and to invade substrate (biology), substrates and tissues. They can exert large penetrative mechanical forces; for example, many plant pathogens, including ''Magnaporthe grisea'', form a structure called an appressorium that evolved to puncture plant tissues. The pressure generated by the appressorium, directed against the plant Epidermis (botany), epidermis, can exceed . The filamentous fungus ''Paecilomyces lilacinus'' uses a similar structure to penetrate the eggs of nematodes. The mechanical pressure exerted by the appressorium is generated from physiological processes that increase intracellular turgor by producing osmolytes such as glycerol. Adaptations such as these are complemented by cellulase, hydrolytic enzymes secreted into the environment to digest large organic molecules—such as polysaccharides, proteins, and lipids—into smaller molecules that may then be absorbed as nutrients. The vast majority of filamentous fungi grow in a polar fashion (extending in one direction) by elongation at the tip (apex) of the hypha. Other forms of fungal growth include intercalary extension (longitudinal expansion of hyphal compartments that are below the apex) as in the case of some Endophyte, endophytic fungi, or growth by volume expansion during the development of mushroom stipe (mycology), stipes and other large organs. Growth of fungi as Multicellularity, multicellular structures consisting of Somatic (biology), somatic and reproductive cells—a feature independently evolved in animals and plants—has several functions, including the development of fruit bodies for dissemination of sexual spores (see above) and biofilms for substrate colonization and intercellular communication. The fungi are traditionally considered heterotrophs, organisms that rely solely on carbon fixation, carbon fixed by other organisms for metabolism. Fungi have evolution, 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. In some species the pigment melanin may play a role in extracting energy from ionizing radiation, such as gamma rays, gamma radiation. This form of radiotrophic fungus, "radiotrophic" growth has been described for only a few species, the effects on growth rates are small, and the underlying Biophysics, biophysical and biochemical processes are not well known. This process might bear similarity to carbon fixation, CO2 fixation via Visible spectrum, visible light, but instead uses ionizing radiation as a source of energy.


Reproduction

Fungal reproduction is complex, reflecting the differences in lifestyles and genetic makeup within this diverse kingdom of organisms. 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 Biological life cycle, life cycle of a species, the teleomorph and the anamorph. 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

Asexual reproduction occurs via vegetative spores (conidium, conidia) or through Fragmentation (reproduction), mycelial fragmentation. Mycelial fragmentation occurs when a fungal mycelium separates into pieces, and each component grows into a separate mycelium. Mycelial fragmentation and vegetative spores maintain clone (genetics), clonal populations adapted to a specific Ecological niche, niche, and allow more rapid dispersal than sexual reproduction. The "Fungi imperfecti" (fungi lacking the perfect or sexual stage) or Deuteromycota comprise all the species that lack an observable sexual cycle. Deuteromycota is not an accepted taxonomic clade and is now taken to mean simply fungi that lack a known sexual stage.


Sexual reproduction

Sexual reproduction with meiosis has been directly observed in all fungal phyla except Glomeromycota (genetic analysis suggests meiosis in Glomeromycota as well). 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. Mating experiments between fungal isolates may identify species on the basis of biological species concepts. The major fungal groupings have initially been delineated based on the morphology of their sexual structures and spores; for example, the spore-containing structures, ascus, asci and basidium, basidia, can be used in the identification of ascomycetes and basidiomycetes, respectively. Fungi employ two mating systems: heterothallic species allow mating only between individuals of the opposite mating type, whereas homothallic species can mate, and sexually reproduce, with any other individual or itself. Most fungi have both a haploid and a 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. Many 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). In ascomycetes, dikaryotic hyphae of the hymenium (the spore-bearing tissue layer) form a characteristic ''hook'' at the hyphal septum. During cell division, the 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. 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. A basidiocarp is formed in which club-like structures known as basidia generate haploid basidiospores after karyogamy and meiosis. The most commonly known basidiocarps are mushrooms, but they may also take other forms (see Fungus#Morphology, Morphology section). In fungi formerly classified as Zygomycota, 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.


Spore dispersal

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. Specialized mechanical and physiological mechanisms, as well as spore surface structures (such as hydrophobins), enable efficient spore ejection. For example, the structure of the ascus, spore-bearing cells in some ascomycete species is such that the buildup of osmolyte, substances affecting cell volume and fluid balance enables the explosive discharge of spores into the air. 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 10,000G-force, g; the net result is that the spore is ejected 0.01–0.02cm, sufficient distance for it to fall through the Agaricales, gills or polypore, pores into the air below. Other fungi, like the puffballs, rely on alternative mechanisms for spore release, such as external mechanical forces. The hydnoid fungi (tooth fungi) produce spores on pendant, tooth-like or spine-like projections. The Nidulariaceae, bird's nest fungi use the force of falling water drops to liberate the spores from cup-shaped fruiting bodies. Another strategy is seen in the stinkhorns, a group of fungi with lively colors and putrid odor that attract insects to disperse their spores. Most of the researched species of fungus are transported by wind. Such species often produce dry or hydrophobic spores which do not absorb water and are readily scattered by raindrops, for example.


Homothallism

In homothallism, homothallic sexual reproduction, two ploidy, haploid nuclei derived from the same individual fuse to form a zygote that can then undergo meiosis. Homothallic fungi include species with an aspergillus-like asexual stage (anamorphs) occurring in numerous different genera, several species of the Ascomycota, ascomycete genus ''Cochliobolus'', and the ascomycete ''Pneumocystis jiroveccii''. The earliest mode of sexual reproduction among eukaryotes was likely homothallism, that is, selfing, self-fertile unisexual reproduction.


Other sexual processes

Besides regular sexual reproduction with meiosis, certain fungi, such as those in the genera ''Penicillium'' and ''Aspergillus'', may exchange genetic material via parasexuality, parasexual processes, initiated by anastomosis between hyphae and plasmogamy of fungal cells. 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 and is likely required for hybridization between species, which has been associated with major events in fungal evolution.


Evolution

Image:Prototaxites milwaukeensis.jpg, ''Prototaxites milwaukeensis'' (Penhallow, 1908)---a Middle Devonian fungus from Wisconsin. In contrast to Evolutionary history of plants, plants and Evolutionary history of life, 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 sporocarp (fungi), 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 taxon, extant fungi. Often recovered from a Permineralization, permineralized plant or animal host, these samples are typically studied by making thin-section preparations that can be examined with optical microscope, light microscopy or transmission electron microscopy. Researchers study compression fossils by dissolving the surrounding matrix with acid and then using light or scanning electron microscopy to examine surface details. The earliest fossils possessing features typical of fungi date to the Paleoproterozoic era, some (annum, Ma); these multicellular benthic organisms had filamentous structures capable of anastomosis. Other studies (2009) estimate the arrival of fungal organisms at about 760–1060Ma on the basis of comparisons of the rate of evolution in closely related groups. For much of the Paleozoic Era (542–251Ma), the fungi appear to have been aquatic and consisted of organisms similar to the extant chytrids in having flagellum-bearing spores. The evolutionary adaptation from an aquatic to a terrestrial lifestyle necessitated a diversification of ecological strategies for obtaining nutrients, including parasitism, Saphrotrophic nutrition, saprobism, and the development of Mutualism (biology), mutualistic relationships such as mycorrhiza and lichenization. Recent (2009) studies suggest that the ancestral ecological state of the Ascomycota was saprobism, and that independent lichenization events have occurred multiple times. In May 2019, scientists reported the discovery of a fossilized fungus, named ''Ourasphaira giraldae'', in the Northern Canada, Canadian Arctic, that may have grown on land a billion years ago, well before
plant Plants are mainly multicellular organisms, predominantly photosynthetic Photosynthesis is a process used by plants and other organisms to Energy transformation, convert light energy into chemical energy that, through cellular respiratio ...
s were living on land. Pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) have been reported in South China. Earlier, it had been presumed that the fungi colonized the land during the Cambrian (542–488.3Ma), also long before land plants. Fossilized hyphae and spores recovered from the Ordovician of Wisconsin (460Ma) resemble modern-day Glomerales, and existed at a time when the land flora likely consisted of only non-vascular bryophyte-like plants. Prototaxites, which was probably a fungus or lichen, would have been the tallest organism of the late Silurian and early Devonian. Fungal fossils do not become common and uncontroversial until the early Devonian (416–359.2Ma), when they occur abundantly in the Rhynie chert, mostly as Zygomycota and Chytridiomycota. At about this same time, approximately 400Ma, the Ascomycota and Basidiomycota diverged, and all modern Class (biology), classes of fungi were present by the Late Carboniferous (Pennsylvanian (geology), Pennsylvanian, 318.1–299Ma). Lichens formed a component of the early terrestrial ecosystems, and the estimated age of the oldest terrestrial lichen fossil is 415Ma; this date roughly corresponds to the age of the oldest known sporocarp (fungi), sporocarp fossil, a ''Paleopyrenomycites'' species found in the Rhynie Chert. The oldest fossil with microscopic features resembling modern-day basidiomycetes is ''Palaeoancistrus'', found permineralized with a fern from the Pennsylvanian. 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 late Cretaceous, 90Ma. Some time after the Permian–Triassic extinction event (251.4Ma), 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. However, the relative proportion of fungal spores relative to spores formed by algae, algal species is difficult to assess, the spike did not appear worldwide, and in many places it did not fall on the Permian–Triassic boundary. 65 million years ago, immediately after the Cretaceous–Paleogene extinction event that famously killed off most dinosaurs, there is a dramatic increase in evidence of fungi, apparently the death of most plant and animal species leading to a huge fungal bloom like "a massive compost heap".


Taxonomy

Although commonly included in botany curricula and textbooks, fungi are more closely related to
animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, ...
s than to plants and are placed with the animals in the monophyletic group of opisthokonts. Analyses using molecular phylogenetics support a monophyletic group, monophyletic origin of fungi. The Taxonomy (biology), taxonomy of fungi is in a state of constant flux, especially due to recent research based on DNA comparisons. These current phylogenetic analyses often overturn classifications based on older and sometimes less discriminative methods based on morphological features and biological species concepts obtained from experimental matings. There is no unique generally accepted system at the higher taxonomic levels and there are frequent name changes at every level, from species upwards. Efforts among researchers are now underway to establish and encourage usage of a unified and more consistent Botanical nomenclature, nomenclature. Fungal species can also have multiple scientific names depending on their life cycle and mode (sexual or asexual) of reproduction. Web sites such as Index Fungorum and Integrated Taxonomic Information System, ITIS list current names of fungal species (with cross-references to older synonyms). The 2007 classification of Kingdom Fungi is the result of a large-scale collaborative research effort involving dozens of mycologists and other scientists working on fungal taxonomy. It recognizes seven phylum, phyla, two of which—the Ascomycota and the Basidiomycota—are contained within a branch representing subkingdom Dikarya, the most species rich and familiar group, including all the mushrooms, most food-spoilage molds, most plant pathogenic fungi, and the beer, wine, and bread yeasts. The accompanying cladogram depicts the major fungal Taxon, taxa and their relationship to opisthokont and unikont organisms, based on the work of Philippe Silar, "The Mycota: A Comprehensive Treatise on Fungi as Experimental Systems for Basic and Applied Research" and Tedersoo et al. 2018. The lengths of the branches are not proportional to evolutionary distances.


Taxonomic groups

The major phylum, phyla (sometimes called divisions) of fungi have been classified mainly on the basis of characteristics of their sexual reproduction, reproductive structures. Currently, nine major Lineage (evolution), lineages have been identified: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Ascomycota and Basidiomycota. Phylogenetic analysis has demonstrated that the Microsporidia, unicellular parasites of animals and protists, are fairly recent and highly derived endobiotic fungi (living within the tissue of another species). One 2006 study concludes that the Microsporidia are a sister group to the true fungi; that is, they are each other's closest evolutionary relative. Hibbett and colleagues suggest that this analysis does not clash with their classification of the Fungi, and although the Microsporidia are elevated to phylum status, it is acknowledged that further analysis is required to clarify evolutionary relationships within this group. The Chytridiomycota are commonly known as chytrids. These fungi are distributed worldwide. Chytrids and their close relatives Neocallimastigomycota and Blastocladiomycota (below) are the only fungi with active motility, producing zoospores that are capable of active movement through aqueous phases with a single flagellum, leading early taxonomists to classify them as protists. Molecular phylogenetics, Molecular phylogenies, inferred from rRNA sequences in ribosomes, suggest that the Chytrids are a Basal (phylogenetics), basal group divergent from the other fungal phyla, consisting of four major clades with suggestive evidence for paraphyly or possibly polyphyly. The Blastocladiomycota were previously considered a taxonomic clade within the Chytridiomycota. Recent molecular data and ultrastructure, ultrastructural characteristics, however, place the Blastocladiomycota as a sister clade to the Zygomycota, Glomeromycota, and Dikarya (Ascomycota and Basidiomycota). The blastocladiomycetes are Saprotrophic nutrition, saprotrophs, feeding on decomposing organic matter, and they are parasites of all eukaryotic groups. Unlike their close relatives, the chytrids, most of which exhibit Biological life cycle#Haplontic life cycle, zygotic meiosis, the blastocladiomycetes undergo Biological life cycle#Haplodiplontic life cycle, sporic meiosis. The Neocallimastigomycota were earlier placed in the phylum Chytridomycota. Members of this small phylum are anaerobic organisms, living in the digestive system of larger herbivorous mammals and in other terrestrial and aquatic environments enriched in cellulose (e.g., domestic waste landfill sites). They lack mitochondria but contain hydrogenosomes of mitochondrial origin. As in the related chrytrids, neocallimastigomycetes form zoospores that are posteriorly uniflagellate or polyflagellate. File:Ascocarp2.png, alt=Cross-section of a cup-shaped structure showing locations of developing meiotic asci (upper edge of cup, left side, arrows pointing to two gray cells containing four and two small circles), sterile hyphae (upper edge of cup, right side, arrows pointing to white cells with a single small circle in them), and mature asci (upper edge of cup, pointing to two gray cells with eight small circles in them), Diagram of an apothecium (the typical cup-like reproductive structure of Ascomycetes) showing sterile tissues as well as developing and mature asci. Members of the Glomeromycota form arbuscular mycorrhizae, a form of mutualist symbiosis wherein fungal hyphae invade plant root cells and both species benefit from the resulting increased supply of nutrients. All known Glomeromycota species reproduce asexually. The symbiotic association between the Glomeromycota and plants is ancient, with evidence dating to 400 million years ago. Formerly part of the Zygomycota (commonly known as 'sugar' and 'pin' molds), the Glomeromycota were elevated to phylum status in 2001 and now replace the older phylum Zygomycota. Fungi that were placed in the Zygomycota are now being reassigned to the Glomeromycota, or the subphyla incertae sedis Mucoromycotina, Kickxellomycotina, the Zoopagomycotina and the Entomophthoromycotina. Some well-known examples of fungi formerly in the Zygomycota include black bread mold (''Rhizopus stolonifer''), and ''Pilobolus'' species, capable of ejecting spores several meters through the air. Medically relevant genera include ''Mucor'', ''Rhizomucor'', and ''Rhizopus''. The Ascomycota, commonly known as sac fungi or ascomycetes, constitute the largest taxonomic group within the Eumycota. These fungi form meiotic spores called ascospores, which are enclosed in a special sac-like structure called an ascus. This phylum includes morels, a few s and Tuber (genus), truffles, unicellular
yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species In biology, a species is the basic unit of biolo ...
s (e.g., of the genera ''Saccharomyces'', ''Kluyveromyces'', ''Pichia'', and ''Candida (genus), Candida''), and many filamentous fungi living as saprotrophs, parasites, and mutualistic symbionts (e.g. lichens). Prominent and important genera of filamentous ascomycetes include ''Aspergillus'', ''Penicillium'', ''Fusarium'', and ''Claviceps''. Many ascomycete species have only been observed undergoing asexual reproduction (called anamorphic species), but analysis of molecular data has often been able to identify their closest teleomorphs in the Ascomycota. Because the products of meiosis are retained within the sac-like ascus, ascomycetes have been used for elucidating principles of genetics and heredity (e.g., ''Neurospora crassa''). Members of the Basidiomycota, commonly known as the club fungi or basidiomycetes, produce meiospores called basidiospores on club-like stalks called basidium, basidia. Most common mushrooms belong to this group, as well as rust (fungus), rust and smut (fungus), smut fungi, which are major pathogens of grains. Other important basidiomycetes include the maize pathogen ''Ustilago maydis'', human commensalism, commensal species of the genus ''Malassezia'', and the opportunistic infection, opportunistic human pathogen, ''Cryptococcus neoformans''.


Fungus-like organisms

Because of similarities in morphology and lifestyle, the slime molds (mycetozoans, plasmodiophorids, acrasids, ''Fonticula'' and labyrinthulids, now in Amoebozoa, Rhizaria, Excavata, Opisthokonta and Stramenopiles, respectively), water molds (oomycetes) and hyphochytrids (both Stramenopiles) were formerly classified in the kingdom Fungi, in groups like Mastigomycotina, Gymnomycota and Phycomycetes. The slime molds were studied also as protozoans, leading to an ambiregnal, duplicated taxonomy. Unlike true fungi, the cell walls of oomycetes contain cellulose and lack . Hyphochytrids have both chitin and cellulose. Slime molds lack a cell wall during the assimilative phase (except labyrinthulids, which have a wall of scales), and ingest nutrients by ingestion (phagocytosis, except labyrinthulids) rather than absorption (osmotrophy, as fungi, labyrinthulids, oomycetes and hyphochytrids). Neither water molds nor slime molds are closely related to the true fungi, and, therefore, taxonomists no longer group them in the kingdom Fungi. Nonetheless, studies of the oomycetes and myxomycetes are still often included in mycology textbooks and primary research literature. The Eccrinales and Amoebidiales are opisthokont protists, previously thought to be zygomycete fungi. Other groups now in Opisthokonta (e.g., ''Corallochytrium'', Ichthyosporea) were also at given time classified as fungi. The genus ''Blastocystis'', now in Stramenopiles, was originally classified as a yeast. ''Ellobiopsis'', now in Alveolata, was considered a chytrid. The bacteria were also included in fungi in some classifications, as the group Schizomycetes. The Rozellida clade, including the "ex-chytrid" ''Rozella'', is a genetically disparate group known mostly from environmental DNA sequences that is a sister group to fungi. Members of the group that have been isolated lack the chitinous cell wall that is characteristic of fungi. The nucleariids may be the next sister group to the eumycete clade, and as such could be included in an expanded fungal kingdom. Many Actinomycetales (Actinobacteria), a group with many filamentous bacteria, were also long believed to be fungi.


Ecology

Although often inconspicuous, fungi occur in every environment on Earth and play very important roles in most ecosystems. Along with bacteria, fungi are the major decomposers in most terrestrial (and some aquatic) ecosystems, and therefore play a critical role in biogeochemical cycles and in many food webs. As decomposers, they play an essential role in nutrient cycling, especially as saprotrophs and symbionts, degrading organic matter to inorganic molecules, which can then re-enter anabolic metabolic pathways in plants or other organisms.


Symbiosis

Many fungi have important symbiotic relationships with organisms from most if not all Kingdom (biology), kingdoms. These interactions can be Mutualism (biology), mutualistic or antagonistic in nature, or in the case of commensal fungi are of no apparent benefit or detriment to the host.


With plants

Mycorrhizal symbiosis between plants and fungi is one of the most well-known plant–fungus associations and is of significant importance for plant growth and persistence in many ecosystems; over 90% of all plant species engage in mycorrhizal relationships with fungi and are dependent upon this relationship for survival. The mycorrhizal symbiosis is ancient, dating back to at least 400 million years. It often increases the plant's uptake of inorganic compounds, such as nitrate and phosphate from soils having low concentrations of these key plant nutrients. The fungal partners may also mediate plant-to-plant transfer of carbohydrates and other nutrients. Such mycorrhizal communities are called "common mycorrhizal networks". A special case of mycorrhiza is myco-heterotrophy, whereby the plant parasitizes the fungus, obtaining all of its nutrients from its fungal symbiont. Some fungal species inhabit the tissues inside roots, stems, and leaves, in which case they are called endophytes. Similar to mycorrhiza, endophytic colonization by fungi may benefit both symbionts; for example, endophytes of grasses impart to their host increased resistance to herbivores and other environmental stresses and receive food and shelter from the plant in return.


With algae and cyanobacteria

Lichens are a symbiotic relationship between fungi and photosynthetic algae or cyanobacteria. The photosynthetic partner in the relationship is referred to in lichen terminology as a "photobiont". The fungal part of the relationship is composed mostly of various species of ascomycetes and a few basidiomycetes. Lichens occur in every ecosystem on all continents, play a key role in soil formation and the initiation of Ecological succession, biological succession, and are prominent in some extreme environments, including polar region, polar, Alpine climate, alpine, and semiarid climate, semiarid desert regions. They are able to grow on inhospitable surfaces, including bare soil, rocks, Bark (botany), tree bark, wood, shells, barnacles and leaves. As in mycorrhizas, the photobiont provides sugars and other carbohydrates via photosynthesis to the fungus, while the fungus provides minerals and water to the photobiont. The functions of both symbiotic organisms are so closely intertwined that they function almost as a single organism; in most cases the resulting organism differs greatly from the individual components. Lichenization is a common mode of nutrition for fungi; around 27% of known fungi—more than 19,400 species—are lichenized. Characteristics common to most lichens include obtaining organic carbon by photosynthesis, slow growth, small size, long life, long-lasting (seasonal) Vegetative reproduction, vegetative reproductive structures, mineral nutrition obtained largely from airborne sources, and greater tolerance of desiccation than most other photosynthetic organisms in the same habitat.


With insects

Many insects also engage in Ant-fungus mutualism, mutualistic relationships with fungi. Several groups of ants cultivate fungi in the order Agaricales as their primary food source, while ambrosia beetles cultivate various species of fungi in the bark of trees that they infest. Likewise, females of several wood wasp species (genus ''Sirex'') inject their eggs together with spores of the wood-rotting fungus ''Amylostereum areolatum'' into the Wood#Heartwood and sapwood, sapwood of pine trees; the growth of the fungus provides ideal nutritional conditions for the development of the wasp larvae. At least one species of stingless bee has a relationship with a fungus in the genus ''Monascus'', where the larvae consume and depend on fungus transferred from old to new nests. Termites on the African savannah are also known to cultivate fungi, and yeasts of the genera ''Candida (genus), Candida'' and ''Lachancea'' inhabit the Gastrointestinal tract, gut of a wide range of insects, including neuropterans, beetles, and cockroaches; it is not known whether these fungi benefit their hosts. Fungi ingrowing dead wood are essential for Xylophagy, xylophagous insects (e.g. woodboring beetles). They deliver nutrients needed by Xylophagy, xylophages to nutritionally scarce Coarse woody debris, dead wood. Thanks to this nutritional enrichment the larvae of woodboring insect is able to grow and develop to adulthood. The larvae of many families of fungicolous flies, particularly those within the superfamily Sciaroidea such as the Mycetophilidae and some Keroplatidae feed on fungal fruiting bodies and sterile mycorrhizae.


As pathogens and parasites

Many fungi are parasites on plants, animals (including humans), and other fungi. Serious pathogens of many cultivated plants causing extensive damage and losses to agriculture and forestry include the rice blast fungus ''Magnaporthe oryzae'', tree pathogens such as ''Ophiostoma ulmi'' and ''Ophiostoma novo-ulmi'' causing Dutch elm disease and ''Cryphonectria parasitica'' responsible for chestnut blight, and plant pathogens in the genera ''Fusarium'', ''Ustilago'', ''Alternaria'', and ''Cochliobolus''. Some carnivorous fungi, like ''Paecilomyces lilacinus'', are Nematophagous fungus, predators of nematodes, which they capture using an array of specialized structures such as constricting rings or adhesive nets. Many fungi that are plant pathogens, such as ''Magnaporthe oryzae'', can switch from being biotrophic (parasitic on living plants) to being necrotrophic (feeding on the dead tissues of plants they have killed). This same principle is applied to fungi-feeding parasites, including ''Asterotremella albida'', which feeds on the fruit bodies of other fungi both while they are living and after they are dead. Some fungi can cause serious diseases in humans, several of which may be fatal if untreated. These include aspergillosis, candidiasis, coccidioidomycosis, cryptococcosis, histoplasmosis, Eumycetoma, mycetomas, and paracoccidioidomycosis. Furthermore, persons with Immunodeficiency, immuno-deficiencies are particularly susceptible to disease by genera such as ''Aspergillus'', ''Candida (genus), Candida'', ''Cryptococcus neoformans, Cryptoccocus'', ''Histoplasma'', and ''Pneumocystis''. Other fungi can attack eyes, nails, hair, and especially skin, the so-called Dermatophyte, dermatophytic and keratinophilic fungi, and cause local infections such as ringworm and athlete's foot. Fungal spores are also a cause of allergies, and fungi from different taxonomic groups can evoke allergic reactions.


As targets of mycoparasites

The organisms which parasitize fungi are known as mycoparasitic organisms. Certain species of the genus ''Pythium'', which are oomycetes, have potential as biocontrol agents against certain fungi. Fungi can also act as mycoparasitism, mycoparasites or antagonists of other fungi, such as ''Hypomyces chrysospermus'', which grows on bolete mushrooms. Fungi can also become the target of infection by mycoviruses.


Mycotoxins

Many fungi produce biological activity, biologically active compounds, several of which are toxin, toxic to animals or plants and are therefore called mycotoxins. Of particular relevance to humans are mycotoxins produced by molds causing food spoilage, and poisonous mushrooms (see above). Particularly infamous are the lethal amatoxins in some ''Amanita'' mushrooms, and Ergotamine, ergot alkaloids, which have a long history of causing serious epidemics of ergotism (St Anthony's Fire) in people consuming rye or related cereals contaminated with sclerotia of the ergot fungus, ''Claviceps purpurea''. Other notable mycotoxins include the aflatoxins, which are insidious Hepatotoxicity, liver toxins and highly carcinogenic metabolites produced by certain ''Aspergillus'' species often growing in or on grains and nuts consumed by humans, ochratoxins, patulin, and trichothecenes (e.g., T-2 mycotoxin) and fumonisins, which have significant impact on human food supplies or animal livestock. Mycotoxins are secondary metabolites (or natural products), and research has established the existence of biochemical pathways solely for the purpose of producing mycotoxins and other natural products in fungi. Mycotoxins may provide Fitness (biology), fitness benefits in terms of physiological adaptation, competition with other microbes and fungi, and protection from consumption (fungivore, fungivory). Many fungal secondary metabolites (or derivatives) are used medically, as described under Human Use below.


Pathogenic mechanisms

''Ustilago maydis'' is a pathogenic plant fungus that causes smut disease in maize and teosinte. Plants have evolved efficient defense systems against pathogenic microbes such as ''U. maydis''. A rapid defense reaction after pathogen attack is the oxidative burst where the plant produces reactive oxygen species at the site of the attempted invasion. ''U. maydis'' can respond to the oxidative burst with an oxidative stress response, regulated by the gene ''YAP1''. The response protects ''U. maydis'' from the host defense, and is necessary for the pathogen's virulence. Furthermore, ''U. maydis'' has a well-established recombinational DNA repair system which acts during mitosis and meiosis. The system may assist the pathogen in surviving DNA damage arising from the host plant's oxidative defensive response to infection. ''Cryptococcus neoformans'' is an encapsulated yeast that can live in both plants and animals. ''C.neoformans'' usually infects the lungs, where it is phagocytosed by alveolar macrophages. Some ''C.neoformans'' can survive intracellular, inside macrophages, which appears to be the basis for latency period, latency, disseminated disease, and resistance to antifungal agents. One mechanism by which ''C.neoformans'' survives the hostile macrophage environment is by up-regulating the expression of genes involved in the oxidative stress response. Another mechanism involves meiosis. The majority of ''C.neoformans'' are mating "type a". Filaments of mating "type a" ordinarily have haploid nuclei, but they can become diploid (perhaps by endoduplication or by stimulated nuclear fusion) to form blastospores. The diploid nuclei of blastospores can undergo meiosis, including recombination, to form haploid basidiospores that can be dispersed. This process is referred to as monokaryotic fruiting. This process requires a gene called ''DMC1'', which is a conserved homologue of genes ''recA'' in bacteria and ''RAD51'' in eukaryotes, that mediates homologous chromosome pairing during meiosis and repair of DNA double-strand breaks. Thus, ''C.neoformans'' can undergo a meiosis, monokaryotic fruiting, that promotes recombinational repair in the oxidative, DNA damaging environment of the host macrophage, and the repair capability may contribute to its virulence.


Human use

The human use of fungi for food preparation or preservation and other purposes is extensive and has a long history. Mushroom farming and mushroom gathering are large industries in many countries. The study of the historical uses and sociological impact of fungi is known as ethnomycology. Because of the capacity of this group to produce an enormous range of natural products with antimicrobial or other biological activities, many species have long been used or are being developed for industrial production of antibiotics, vitamins, and Taxol#Production, anti-cancer and Lovastatin, cholesterol-lowering drugs. More recently, methods have been developed for genetic engineering of fungi, enabling metabolic engineering of fungal species. For example, genetic modification of yeast species—which are easy to grow at fast rates in large fermentation vessels—has opened up ways of pharmaceutical production that are potentially more efficient than production by the original source organisms.


Therapeutic uses


Modern chemotherapeutics

Many species produce metabolites that are major sources of pharmacology, pharmacologically active drugs. Particularly important are the antibiotics, including the penicillins, a structurally related group of β-lactam antibiotics that are synthesized from small peptides. Although naturally occurring penicillins such as penicillin G (produced by ''Penicillium chrysogenum'') have a relatively narrow spectrum of biological activity, a wide range of other penicillins can be produced by Chemical synthesis, chemical modification of the natural penicillins. Modern penicillins are semisynthesis, semisynthetic compounds, obtained initially from fermentation (biochemistry), fermentation cultures, but then structurally altered for specific desirable properties. Other antibiotics produced by fungi include: ciclosporin, commonly used as an immunosuppressant during organ transplant, transplant surgery; and fusidic acid, used to help control infection from Methicillin-resistant Staphylococcus aureus, methicillin-resistant ''Staphylococcus aureus'' bacteria. Widespread use of antibiotics for the treatment of bacterial diseases, such as tuberculosis, syphilis, leprosy, and others began in the early 20th century and continues to date. In nature, antibiotics of fungal or bacterial origin appear to play a dual role: at high concentrations they act as chemical defense against competition with other microorganisms in species-rich environments, such as the rhizosphere (ecology), rhizosphere, and at low concentrations as quorum sensing, quorum-sensing molecules for intra- or interspecies signaling. Other drugs produced by fungi include griseofulvin isolated from ''Penicillium griseofulvum'', used to treat fungal infections, and statins (HMG-CoA reductase inhibitors), used to inhibit cholesterol synthesis. Examples of statins found in fungi include mevastatin from ''Penicillium citrinum'' and lovastatin from ''Aspergillus terreus'' and the Pleurotus ostreatus, oyster mushroom. Fungi produce compounds that inhibit viruses and cancer cells. Specific metabolites, such as polysaccharide-K, ergotamine, and Beta-lactam antibiotic, β-lactam antibiotics, are routinely used in clinical medicine. The shiitake mushroom is a source of lentinan, a clinical drug approved for use in cancer treatments in several countries, including Japan. In Europe and Japan, polysaccharide-K (brand name Krestin), a chemical derived from ''Trametes versicolor'', is an approved adjuvant for cancer therapy.


Traditional and folk medicine

Certain mushrooms enjoy usage as therapeutics in folk medicines, such as Traditional Chinese medicine. Notable medicinal mushrooms with a well-documented history of use include ''Agaricus subrufescens'', ''Ganoderma lucidum'', and ''Ophiocordyceps sinensis''.


Cultured foods

Baker's yeast or ''Saccharomyces cerevisiae'', a unicellular fungus, is used to make bread and other wheat-based products, such as pizza dough and dumplings. Yeast species of the genus ''Saccharomyces'' are also used to produce alcoholic beverages through fermentation. Shoyu koji mold (''Aspergillus oryzae'') is an essential ingredient in brewing Shoyu (soy sauce) and sake, and the preparation of miso, while ''Rhizopus'' species are used for making tempeh. Several of these fungi are Domestication, domesticated species that were Breeding program, bred or selected according to their capacity to ferment food without producing harmful mycotoxins (see below), which are produced by very closely related ''Aspergillus flavus, Aspergilli''. Quorn (food product), Quorn, a Meat analogue, meat substitute, is made from ''Fusarium venenatum''.


In food

Edible mushrooms include commercially raised and wild-harvested fungi. ''Agaricus bisporus'', sold as button mushrooms when small or Portobello mushrooms when larger, is the most widely cultivated species in the West, used in salads, soups, and many other dishes. Many Asian fungi are commercially grown and have increased in popularity in the West. They are often available fresh in grocery stores and markets, including straw mushrooms (''Volvariella volvacea''), oyster mushrooms (''Pleurotus ostreatus''), shiitakes (''Lentinula edodes''), and enokitake (''Flammulina'' spp.). Many other mushroom species are Mushroom hunting, harvested from the wild for personal consumption or commercial sale. Lactarius deliciosus, Milk mushrooms, morels, chanterelles, truffles, Craterellus, black trumpets, and ''porcini'' mushrooms (''Boletus edulis'') (also known as king boletes) demand a high price on the market. They are often used in gourmet dishes. Certain types of cheeses require inoculation of milk curds with fungal species that impart a unique flavor and texture to the cheese. Examples include the blue cheese, blue color in cheeses such as Stilton cheese, Stilton or Roquefort, which are made by inoculation with ''Penicillium roqueforti''. Molds used in cheese production are non-toxic and are thus safe for human consumption; however, mycotoxins (e.g., aflatoxins, roquefortine C, patulin, or others) may accumulate because of growth of other fungi during cheese ripening or storage.


Poisonous fungi

Many mushroom species are Mushroom poisoning, poisonous to humans and cause a range of reactions including slight digestive problems, allergy, allergic reactions, hallucinations, severe organ failure, and death. Genera with mushrooms containing deadly toxins include ''Conocybe'', ''Galerina'', ''Lepiota'', and, the most infamous, ''Amanita''. The latter genus includes the destroying angel ''(Amanita virosa, A.virosa)'' and the death cap ''(Amanita phalloides, A.phalloides)'', the most common cause of deadly mushroom poisoning. The false morel (''Gyromitra esculenta'') is occasionally considered a delicacy when cooked, yet can be highly toxic when eaten raw. ''Tricholoma equestre'' was considered edible until it was implicated in serious poisonings causing rhabdomyolysis. Amanita muscaria, Fly agaric mushrooms (''Amanita muscaria'') also cause occasional non-fatal poisonings, mostly as a result of ingestion for its Psychedelics, dissociatives and deliriants, hallucinogenic properties. Historically, fly agaric was used by different peoples in Europe and Asia and its present usage for religious or shamanism, shamanic purposes is reported from some ethnic groups such as the Koryaks, Koryak people of northeastern Siberia. As it is difficult to accurately identify a safe mushroom without proper training and knowledge, it is often advised to assume that a wild mushroom is poisonous and not to consume it.Hall, p. 7.


Pest control

In agriculture, fungi may be useful if they actively compete for nutrients and space with pathogenic microorganisms such as bacteria or other fungi via the competitive exclusion principle, or if they are parasitism, parasites of these pathogens. For example, certain species may be used to eliminate or suppress the growth of harmful plant pathogens, such as insects, mites, weeds, nematodes, and other fungi that cause diseases of important crop plants. This has generated strong interest in practical applications that use these fungi in the biological control of these agricultural pests. Entomopathogenic fungi can be used as biopesticides, as they actively kill insects. Examples that have been used as biological insecticides are ''Beauveria bassiana'', ''Metarhizium'' spp., ''Hirsutella'' spp., ''Paecilomyces'' (''Isaria'') spp., and ''Lecanicillium lecanii''. Endophytic fungi of grasses of the genus ''Neotyphodium'', such as ''Neotyphodium coenophialum, N. coenophialum'', produce alkaloids that are toxic to a range of invertebrate and vertebrate herbivores. These alkaloids protect grass plants from herbivory, but several endophyte alkaloids can poison grazing animals, such as cattle and sheep. Infecting cultivars of pasture or forage grasses with ''Neotyphodium'' endophytes is one approach being used in plant breeding, grass breeding programs; the fungal strains are selected for producing only alkaloids that increase resistance to herbivores such as insects, while being non-toxic to livestock.


Bioremediation

Certain fungi, in particular white rot, white-rot fungi, can degrade insecticides, herbicides, pentachlorophenol, creosote, coal tars, and heavy fuels and turn them into carbon dioxide, water, and basic elements. Fungi have been shown to biomineralization, biomineralize uranium oxides, suggesting they may have application in the bioremediation of radioactively polluted sites.


Model organisms

Several pivotal discoveries in biology were made by researchers using fungi as model organisms, that is, fungi that grow and sexually reproduce rapidly in the laboratory. For example, the one gene-one enzyme hypothesis was formulated by scientists using the bread mold ''Neurospora crassa'' to test their biochemical theories. Other important model fungi are ''Aspergillus nidulans'' and the yeasts ''Saccharomyces cerevisiae'' and ''Schizosaccharomyces pombe'', each of which with a long history of use to investigate issues in eukaryotic cell biology and genetics, such as cell cycle regulation, chromatin structure, and gene regulation. Other fungal models have more recently emerged that address specific biological questions relevant to medicine, plant pathology, and industrial uses; examples include ''Candida albicans'', a dimorphic, opportunistic human pathogen, ''Magnaporthe grisea'', a plant pathogen, and ''Pichia pastoris'', a yeast widely used for eukaryotic protein production.


Others

Fungi are used extensively to produce industrial chemicals like citric acid, citric, gluconic acid, gluconic, lactic acid, lactic, and malic acid, malic acids, and industrial enzymes, such as lipases used in biological detergents, cellulases used in making cellulosic ethanol and stonewashed jeans, and amylases, invertases, proteases and xylanases.


See also

* Conservation of fungi * Fantastic Fungi * Marine fungi * MycoBank * Mycosis * Outline of fungi


References


Cited literature

* * * * * * * * *


External links


Tree of Life web project: Fungi
* Mushroom Observer
mushroomobserver.org
, a collaborative fungus recording and identification project

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